Contacts of the helix formed by residues 32 - 69 (chain T) in PDB entry 3H1I
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 32 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R TYR* 5.5 4.5 - - - -
73S ARG* 2.5 41.9 + - - -
27T PRO 4.6 3.5 - - - +
28T ASN* 3.3 31.2 + - + +
30T PHE 2.8 4.4 + - - -
31T SER* 1.3 76.8 + - - +
33T ALA* 1.3 72.2 + - - +
35T PRO* 3.1 11.4 - - - +
36T ASN* 2.9 21.2 + - - +
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Residues in contact with ALA 33 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3003Q CDL 3.8 26.9 + - - +
73S ARG* 4.1 11.7 - - - +
26T ILE* 6.0 1.6 - - + -
27T PRO 4.9 2.5 - - - +
28T ASN 2.8 11.7 + - - +
29T ILE* 2.8 29.2 - - + +
30T PHE 3.9 0.2 + - - -
32T ASP* 1.3 81.4 + - - +
34T LEU* 1.3 69.1 + - + +
36T ASN* 2.8 13.3 + - - +
37T VAL* 3.4 10.1 + - - +
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Residues in contact with LEU 34 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3003Q CDL 3.9 20.2 - - - +
29T ILE* 3.0 13.0 - - + +
30T PHE* 3.4 38.6 - - + -
33T ALA* 1.3 77.3 - - - +
35T PRO* 1.3 63.2 - - + +
37T VAL* 2.5 41.1 + - + +
38T TRP* 2.9 11.4 + - - +
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Residues in contact with PRO 35 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30T PHE 2.7 31.2 - - - +
31T SER* 3.6 12.8 - - - +
32T ASP 3.1 12.6 - - - +
34T LEU* 1.3 89.5 - - + +
36T ASN* 1.3 52.9 + - - +
38T TRP* 3.1 10.1 + - + +
39T ARG* 2.7 33.8 + - - +
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Residues in contact with ASN 36 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3003Q CDL 4.6 4.3 - - - +
72S HIS 4.6 1.8 - - - +
73S ARG* 3.1 44.5 - - - +
74S ILE 5.5 0.5 + - - -
32T ASP* 2.9 28.7 + - - +
33T ALA 2.8 10.0 + - - +
35T PRO* 1.3 75.4 - - - +
37T VAL* 1.3 57.6 + - - +
39T ARG* 2.8 36.2 + - - +
40T ARG* 2.7 41.9 + - - +
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Residues in contact with VAL 37 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3004P CDL 3.9 31.4 - - + +
3003Q CDL 4.3 28.5 - - - +
33T ALA 3.5 6.3 - - - +
34T LEU* 2.5 41.5 + - + +
36T ASN* 1.3 73.1 - - - +
38T TRP* 1.3 54.2 + - - +
40T ARG* 3.4 12.5 + - - +
41T PHE* 2.9 30.5 + - + +
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Residues in contact with TRP 38 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34T LEU 2.9 8.4 + - - +
35T PRO* 3.2 11.4 - - + +
37T VAL* 1.3 74.3 - - - +
39T ARG* 1.3 69.3 + - - +
41T PHE* 3.0 45.1 + + - +
42T SER* 2.7 44.9 + - - -
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Residues in contact with ARG 39 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3007P PEE 5.4 4.0 + - - -
29S TYR* 5.9 0.4 + - - -
72S HIS 3.9 13.2 + - - -
73S ARG* 4.6 1.8 - - - +
74S ILE* 3.6 40.2 - - - +
35T PRO 2.7 16.4 + - - +
36T ASN* 2.8 68.6 + - - +
38T TRP* 1.3 77.4 - - - +
40T ARG* 1.3 86.1 + - - +
42T SER* 3.4 5.9 - - - -
43T SER* 3.2 20.5 + - - -
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Residues in contact with ARG 40 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3004P CDL 2.9 71.8 + - - +
3007P PEE 4.3 7.0 - - - +
3003Q CDL 3.5 38.8 + - - -
72S HIS* 3.0 48.2 + - - +
36T ASN* 2.7 28.8 + - - +
37T VAL* 3.6 13.4 - - - +
39T ARG* 1.3 91.4 - - - +
41T PHE* 1.3 71.4 + - - +
43T SER* 2.7 23.3 + - - -
44T GLN* 3.2 8.4 + - - +
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Residues in contact with PHE 41 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3004P CDL 3.4 37.5 + - + +
37T VAL* 2.9 22.9 + - + +
38T TRP* 3.4 38.1 - + - +
40T ARG* 1.3 73.1 - - - +
42T SER* 1.3 70.6 + - - +
44T GLN* 3.2 1.6 + - - +
45T VAL* 2.8 48.3 + - + -
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Residues in contact with SER 42 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38T TRP* 2.7 42.0 + - - -
39T ARG* 3.4 12.1 - - - -
40T ARG 3.0 0.6 + - - -
41T PHE* 1.3 80.0 - - - +
43T SER* 1.3 56.2 + - - -
44T GLN 2.6 13.7 + - - -
45T VAL* 2.9 22.9 + - - +
46T PHE* 4.0 3.9 + - - -
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Residues in contact with SER 43 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39T ARG 3.2 10.1 + - - -
40T ARG* 2.7 24.4 + - - -
42T SER* 1.3 77.1 - - - +
44T GLN* 1.3 67.5 + - - +
46T PHE* 4.6 5.4 + - - +
47T LYS* 4.0 18.1 - - - +
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Residues in contact with GLN 44 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104P TYR* 4.2 1.0 + - - -
323P GLN* 3.5 17.5 + - - +
327P TRP* 5.0 2.2 - - - +
3004P CDL 3.5 37.9 - - - +
3007P PEE 3.1 40.2 + - - -
40T ARG 3.2 9.3 + - - +
41T PHE 3.2 5.8 + - - +
42T SER 2.6 6.1 + - - -
43T SER* 1.3 78.9 + - - +
45T VAL* 1.3 65.8 + - - +
46T PHE 3.1 3.1 - - - -
47T LYS* 2.8 43.8 + - - +
48T VAL* 3.1 19.0 + - + +
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Residues in contact with VAL 45 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3004P CDL 4.4 13.4 - - + +
41T PHE* 2.8 45.2 + - + +
42T SER* 2.9 22.9 + - - +
44T GLN* 1.3 70.4 - - - +
46T PHE* 1.3 83.0 + - + +
49T ALA* 3.0 49.8 + - + +
50T PRO* 3.2 0.7 - - - +
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Residues in contact with PHE 46 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324P THR* 4.9 2.1 + - - -
42T SER 4.0 4.4 + - - -
43T SER 5.0 5.6 - - - +
44T GLN 2.9 1.6 + - - -
45T VAL* 1.3 100.8 - - + +
47T LYS* 1.3 61.5 + - + +
50T PRO* 3.1 24.5 - - + +
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Residues in contact with LYS 47 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317P THR 5.3 1.0 + - - -
320P PRO* 4.2 21.8 - - + +
323P GLN* 3.4 39.4 - - + +
324P THR* 4.0 22.6 + - - +
327P TRP* 4.0 18.2 - - + +
23S ALA 4.9 7.7 + - - -
43T SER* 4.0 13.2 + - - +
44T GLN* 2.8 34.2 + - - +
46T PHE* 1.3 79.0 - - + +
48T VAL* 1.3 69.0 + - + +
50T PRO* 3.8 1.7 - - - +
51T PRO* 3.6 12.6 - - - +
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Residues in contact with VAL 48 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327P TRP* 3.5 45.6 - - + +
3004P CDL 4.4 20.2 - - + +
3007P PEE 3.8 22.0 - - + +
44T GLN* 3.1 18.5 + - - +
45T VAL 4.3 0.2 - - - +
47T LYS* 1.3 76.0 - - + +
49T ALA* 1.3 70.2 + - - +
51T PRO* 3.0 21.5 - - - +
52T PHE* 3.9 30.3 + - + -
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Residues in contact with ALA 49 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3004P CDL 5.5 1.3 - - + +
45T VAL* 3.0 31.7 + - + +
48T VAL* 1.3 79.9 - - - +
50T PRO* 1.3 68.1 - - + +
52T PHE* 3.1 8.7 + - - +
53T LEU* 2.8 27.9 + - + +
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Residues in contact with PRO 50 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324P THR* 5.9 1.3 - - - +
45T VAL 3.2 13.7 - - - +
46T PHE* 3.1 31.9 - - + +
47T LYS 3.8 2.0 - - - +
48T VAL 3.1 5.1 - - - -
49T ALA* 1.3 90.7 - - + +
51T PRO* 1.3 72.6 - - + +
53T LEU* 3.2 9.3 + - + +
54T GLY* 2.8 17.8 + - - -
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Residues in contact with PRO 51 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324P THR* 4.9 4.3 - - + +
327P TRP* 3.9 26.2 - - + +
328P LEU* 3.5 42.7 - - + +
331P ALA* 4.3 4.7 - - + +
47T LYS 3.6 8.1 - - - +
48T VAL 3.0 24.0 - - - +
50T PRO* 1.3 88.6 - - + +
52T PHE* 1.3 63.5 + - + +
54T GLY* 2.9 4.8 + - - +
55T ALA* 2.8 22.7 + - - +
----------------------------------------------------------
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Residues in contact with PHE 52 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327P TRP* 3.9 22.0 - + - -
330P VAL* 3.9 18.2 - - + -
331P ALA* 3.4 38.8 - - + -
334P LEU* 4.3 14.8 - - + -
3007P PEE 4.3 22.4 - - + -
48T VAL* 3.9 30.1 - - + -
49T ALA* 3.1 10.8 + - - +
51T PRO* 1.3 77.1 - - - +
53T LEU* 1.3 66.4 + - - +
55T ALA* 3.0 15.3 + - - +
56T TYR* 3.0 14.0 + - - +
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Residues in contact with LEU 53 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49T ALA* 2.8 18.9 + - + +
50T PRO* 3.4 11.2 - - + +
52T PHE* 1.3 74.2 - - - +
54T GLY* 1.3 64.2 - - - +
56T TYR* 3.3 14.1 - - + +
57T LEU* 3.2 43.8 + - + +
----------------------------------------------------------
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Residues in contact with GLY 54 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50T PRO 2.8 14.3 + - - -
51T PRO* 2.9 6.2 + - - -
53T LEU* 1.3 79.8 - - - +
55T ALA* 1.3 64.4 + - - +
57T LEU* 3.4 14.8 + - - +
58T LEU* 3.3 14.4 + - - +
----------------------------------------------------------
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Residues in contact with ALA 55 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331P ALA* 4.7 6.7 - - + +
334P LEU* 6.0 5.6 - - + -
335P ILE* 3.6 36.8 - - + -
51T PRO 2.8 13.0 + - - +
52T PHE* 3.4 11.2 - - - +
54T GLY* 1.3 69.8 - - - +
56T TYR* 1.3 57.3 + - - +
58T LEU* 2.4 36.1 + - - +
59T TYR* 2.7 11.2 + - - -
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Residues in contact with TYR 56 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52T PHE 3.0 8.4 + - - +
53T LEU* 3.3 20.0 - - + +
55T ALA* 1.3 76.4 - - - +
57T LEU* 1.3 69.3 + - + +
59T TYR* 2.9 26.3 + + - +
60T SER* 2.6 52.5 + - - -
----------------------------------------------------------
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Residues in contact with LEU 57 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53T LEU* 3.2 31.6 - - + +
54T GLY* 3.4 13.5 - - - +
55T ALA 2.7 3.0 + - - -
56T TYR* 1.3 86.7 - - + +
58T LEU* 1.3 52.3 + - - +
59T TYR 2.6 10.2 + - - -
60T SER* 2.7 6.9 + - - +
61T TRP* 2.6 37.9 + - + +
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Residues in contact with LEU 58 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335P ILE* 4.6 20.6 - - + -
338P TRP* 3.6 9.8 - - + -
351P ILE* 3.8 41.7 - - + -
54T GLY 3.3 8.1 + - - +
55T ALA* 2.4 20.6 + - - +
57T LEU* 1.3 73.8 - - - +
59T TYR* 1.3 57.1 + - - +
61T TRP* 4.1 17.5 - - + -
62T GLY 3.4 11.3 + - - -
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Residues in contact with TYR 59 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338P TRP* 2.9 57.4 - + + -
342P GLN* 5.1 2.0 - - - -
55T ALA 2.7 7.1 + - - +
56T TYR* 3.0 36.8 - + - +
57T LEU 2.6 3.6 + - - -
58T LEU* 1.3 73.4 - - - +
60T SER* 1.3 76.0 + - - -
61T TRP 3.2 0.2 + - - -
62T GLY 3.4 1.0 + - - -
63T THR* 2.9 46.4 + - + +
----------------------------------------------------------
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Residues in contact with SER 60 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56T TYR* 2.6 41.3 + - - -
57T LEU* 2.7 11.1 + - - -
59T TYR* 1.3 78.5 - - - +
61T TRP* 1.3 64.8 + - - -
63T THR* 3.0 7.7 + - - -
64T GLN* 2.9 42.0 + - - +
----------------------------------------------------------
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Residues in contact with TRP 61 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346P HIS* 5.1 6.5 - + - -
347P PRO* 3.4 33.4 - - + -
350P ILE* 6.1 1.3 - - + -
351P ILE* 3.8 14.1 - - + -
57T LEU* 2.6 22.3 + - + +
58T LEU* 4.1 15.7 - - + +
60T SER* 1.3 73.9 - - - +
62T GLY* 1.3 79.9 + - - +
64T GLN* 3.0 4.4 + - - +
65T GLU* 2.8 55.4 + - + +
----------------------------------------------------------
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Residues in contact with GLY 62 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338P TRP* 4.4 0.9 - - - -
347P PRO* 3.3 19.5 - - - +
348P PHE* 4.2 5.1 - - - -
351P ILE* 4.0 5.4 - - - -
58T LEU 3.4 7.0 + - - -
59T TYR 3.4 4.6 + - - -
61T TRP* 1.3 99.9 - - - +
63T THR* 1.3 61.4 - - - +
65T GLU* 4.4 0.4 - - - -
66T PHE* 3.0 26.3 + - - +
----------------------------------------------------------
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Residues in contact with THR 63 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338P TRP* 4.0 5.9 + - - -
342P GLN* 5.3 1.4 + - - -
348P PHE* 4.7 8.2 - - - -
59T TYR* 2.9 48.2 + - + +
60T SER* 3.2 7.9 - - - +
62T GLY* 1.3 76.4 - - - +
64T GLN* 1.3 66.3 + - + +
66T PHE* 3.3 9.1 - - - +
67T GLU* 3.1 32.0 + - + +
----------------------------------------------------------
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Residues in contact with GLN 64 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60T SER* 2.9 34.0 + - - +
61T TRP* 3.7 3.6 - - - +
63T THR* 1.3 81.1 - - + +
65T GLU* 1.3 56.6 + - - +
66T PHE 2.9 4.3 - - - -
67T GLU* 2.7 30.0 + - + +
68T ARG* 2.8 14.0 + - - +
----------------------------------------------------------
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Residues in contact with GLU 65 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346P HIS* 4.6 9.0 + - + -
347P PRO* 4.2 15.3 - - + -
61T TRP* 2.8 53.6 + - + +
62T GLY* 4.0 3.4 - - - +
64T GLN* 1.3 72.7 - - - +
66T PHE* 1.3 58.3 + - - +
68T ARG* 3.3 34.2 + - - +
69T LEU* 3.0 37.5 + - + +
----------------------------------------------------------
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Residues in contact with PHE 66 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342P GLN* 5.7 1.1 - - - -
343P PRO* 4.3 16.8 - - + -
345P GLU* 2.9 33.2 - - + -
346P HIS 3.3 22.0 - - - -
347P PRO* 3.9 9.6 - - + +
348P PHE* 4.2 23.8 - + + -
62T GLY 3.0 19.4 + - - +
63T THR* 3.3 7.6 - - - +
64T GLN 2.9 0.4 - - - -
65T GLU* 1.3 73.9 - - - +
67T GLU* 1.3 68.3 + - + +
69T LEU* 2.8 29.2 + - + +
70T LYS* 3.3 42.4 + - + +
----------------------------------------------------------
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Residues in contact with GLU 67 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63T THR* 3.1 18.5 + - + +
64T GLN* 2.7 17.1 + - + +
66T PHE* 1.3 85.5 - - - +
68T ARG* 1.3 59.7 + - - +
70T LYS* 3.3 42.3 + - - +
71T ARG* 3.4 16.4 - - - +
----------------------------------------------------------
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Residues in contact with ARG 68 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64T GLN 2.8 17.5 + - - +
65T GLU* 3.3 26.2 + - - +
67T GLU* 1.3 68.9 - - - +
69T LEU* 1.3 85.6 + - - +
70T LYS 3.0 9.3 + - - -
71T ARG* 3.2 29.7 + - + +
----------------------------------------------------------
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Residues in contact with LEU 69 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346P HIS* 4.2 39.7 - - + +
2Q GLU* 5.1 4.2 - - - +
65T GLU* 3.0 22.7 - - + +
66T PHE* 2.8 13.4 + - + +
68T ARG* 1.3 107.1 - - - +
70T LYS* 1.3 59.8 + - - +
71T ARG 4.1 3.8 - - - +
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il