Contacts of the helix formed by residues 25 - 52 (chain D) in PDB entry 5YWB
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 GLY 25 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ASN* 1.3 74.8 - - - +
26D CYS* 1.3 62.6 + - - +
28D VAL* 3.1 9.3 + - - +
29D ASP* 2.9 22.1 + - - +
106D LEU* 5.1 5.1 - - - +
153D LYS* 4.6 2.3 + - - -
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Residues in contact with CYS 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C TRP* 5.6 1.0 - - - -
95C PHE* 4.2 18.8 - - + -
24D ASN 3.4 0.2 - - - -
25D GLY* 1.3 75.0 - - - +
27D PHE* 1.3 56.5 + - - +
29D ASP* 3.3 8.9 + - - +
30D ALA* 2.9 29.8 + - - +
103D HIS* 5.7 3.6 - - - -
105D HIS* 5.1 13.0 - - + +
106D LEU* 3.6 25.6 - - - -
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Residues in contact with PHE 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU* 4.1 17.0 - - + +
95C PHE* 3.4 35.3 - + + -
96C ALA* 3.6 31.4 - - + -
24D ASN* 3.1 30.0 + - + +
26D CYS* 1.3 79.8 - - - +
28D VAL* 1.3 67.1 + - + +
30D ALA* 3.3 5.0 + - - +
31D LEU* 2.9 46.6 + - + +
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Residues in contact with VAL 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ASN* 3.2 19.1 - - + +
25D GLY* 3.1 7.9 + - - +
27D PHE* 1.3 81.8 - - + +
29D ASP* 1.3 66.1 + - - +
31D LEU* 3.3 8.9 + - + +
32D ASN* 2.9 31.5 + - - +
149D THR* 4.8 0.4 - - - +
152D ILE* 3.6 28.3 - - + -
153D LYS* 3.5 35.4 - - + +
156D LYS* 5.0 13.9 - - + -
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Residues in contact with ASP 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D GLY 2.9 13.1 + - - +
26D CYS* 3.3 12.5 + - - +
28D VAL* 1.3 75.9 - - - +
30D ALA* 1.3 57.2 + - - +
32D ASN* 3.1 5.2 + - - +
33D VAL* 2.9 32.0 + - - +
105D HIS* 3.2 26.5 - - + +
106D LEU* 4.8 8.3 - - + +
109D PRO* 3.7 10.8 - - + +
153D LYS* 3.5 13.5 - - - +
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Residues in contact with ALA 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C MET* 5.4 2.9 - - + +
91C TRP* 3.6 34.3 - - + -
92C LEU* 4.7 11.4 - - + -
95C PHE* 5.6 2.2 - - + -
26D CYS 2.9 15.6 + - - +
27D PHE* 3.7 6.3 - - - +
29D ASP* 1.3 76.9 - - - +
31D LEU* 1.3 63.4 + - - +
33D VAL* 2.9 20.5 + - - +
34D VAL* 3.0 19.0 + - + +
105D HIS* 6.2 1.5 - - + +
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Residues in contact with LEU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU* 4.9 19.4 - - + +
27D PHE* 2.9 38.9 + - + +
28D VAL* 3.6 8.5 - - + +
30D ALA* 1.3 76.8 - - - +
32D ASN* 1.3 60.6 + - - +
34D VAL* 3.7 8.7 + - + +
35D PRO* 3.2 17.9 - - + +
149D THR* 3.4 21.3 - - + +
152D ILE* 4.9 21.3 - - + -
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Residues in contact with ASN 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D VAL* 2.9 20.0 + - - +
29D ASP 3.5 8.3 - - - +
30D ALA 3.1 0.2 - - - -
31D LEU* 1.3 76.3 - - - +
33D VAL* 1.3 65.6 + - - +
34D VAL 3.1 0.2 - - - -
35D PRO* 3.1 12.1 - - - +
36D HIS* 3.1 23.3 + - - +
109D PRO* 4.4 10.9 - - + +
149D THR* 3.4 33.9 + - - +
150D LYS* 3.4 42.2 - - - +
153D LYS* 3.4 23.9 - - - +
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Residues in contact with VAL 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C MET* 4.2 21.8 - - + -
29D ASP 2.9 19.4 + - - +
30D ALA* 2.9 12.6 + - - +
32D ASN* 1.3 77.7 - - - +
34D VAL* 1.3 66.2 + - - +
35D PRO 3.5 0.3 - - - -
36D HIS* 3.5 11.3 + - - +
37D VAL* 3.3 20.6 + - + +
105D HIS* 5.5 1.3 - - - +
108D MET* 4.1 13.9 - - + -
109D PRO* 3.8 29.8 - - + -
112D MET* 4.1 15.7 - - + -
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Residues in contact with VAL 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C MET* 4.2 26.5 - - + -
89C VAL* 6.1 4.0 - - + -
92C LEU* 4.0 29.2 - - + -
30D ALA* 3.0 16.3 + - + +
31D LEU* 3.8 9.9 - - + +
33D VAL* 1.3 76.3 - - - +
35D PRO* 1.3 73.5 - - + +
37D VAL* 3.0 20.0 + - + +
38D PHE* 3.0 13.9 + - + +
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Residues in contact with PRO 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D LEU* 3.2 14.6 - - + +
32D ASN* 3.1 24.7 - - - +
34D VAL* 1.3 83.1 - - + +
36D HIS* 1.3 64.5 + - + +
38D PHE* 3.1 10.5 + - + +
39D LEU 3.0 19.1 + - - -
142D TYR* 3.5 23.4 - - + -
145D LEU* 4.2 31.0 - - + +
146D ALA* 4.6 6.1 - - + +
149D THR* 4.1 17.3 - - + +
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Residues in contact with HIS 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ASN* 3.1 35.7 + - - -
33D VAL* 3.8 3.6 - - - +
34D VAL 3.3 0.6 - - - -
35D PRO* 1.3 76.5 - - + +
37D VAL* 1.3 58.3 + - - +
39D LEU* 3.3 2.3 + - - +
40D LEU* 2.9 35.9 + - + +
109D PRO* 3.9 8.6 + - - +
112D MET* 3.6 31.9 - - + +
113D ALA* 3.4 39.9 - - + +
116D ALA* 3.6 3.7 - - + +
142D TYR* 2.8 37.2 + + - -
146D ALA* 5.0 5.8 - - + -
150D LYS* 5.6 4.3 + - - -
179D TYR* 3.5 10.8 - + - -
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Residues in contact with VAL 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LEU* 4.9 7.0 - - + -
88C MET* 4.4 29.6 - - + -
33D VAL* 3.3 12.2 + - + +
34D VAL* 3.0 13.1 + - + +
36D HIS* 1.3 76.8 - - - +
38D PHE* 1.3 67.7 + - + +
40D LEU* 3.4 4.8 + - - -
41D PHE* 2.9 64.0 + - + -
112D MET* 3.9 20.6 - - + -
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Residues in contact with PHE 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LEU* 4.5 24.7 - - + -
34D VAL* 3.0 14.5 + - + +
35D PRO* 3.4 14.8 - - + +
37D VAL* 1.3 79.1 - - + +
39D LEU* 1.3 63.4 + - + +
41D PHE* 3.2 6.4 + - - +
42D ILE* 3.0 59.9 + - + +
138D ALA 5.7 3.4 - - - -
141D ILE* 5.2 15.0 - - + -
142D TYR* 5.4 8.1 - - + -
145D LEU* 5.3 14.4 - - + -
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Residues in contact with LEU 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D PRO 3.0 14.5 + - - +
36D HIS 3.9 3.4 - - - +
38D PHE* 1.3 78.1 - - + +
40D LEU* 1.3 60.7 + - - +
41D PHE 3.0 1.6 - - - -
42D ILE* 3.3 6.8 + - + +
43D THR* 2.9 29.1 + - - -
116D ALA* 3.9 21.1 - - + +
119D THR* 3.9 11.9 - - + -
120D SER* 4.7 1.6 - - - +
123D TYR* 4.5 15.0 - - + -
138D ALA* 4.3 13.7 - - + +
139D LEU* 4.3 18.4 - - + -
142D TYR* 3.5 50.7 - - + -
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Residues in contact with LEU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D HIS 2.9 17.6 + - - +
37D VAL* 3.9 4.0 - - - +
39D LEU* 1.3 76.9 - - - +
41D PHE* 1.3 67.4 + - + +
43D THR* 3.1 6.5 - - + +
44D PHE* 2.9 40.0 - - + -
112D MET* 3.7 29.2 - - + +
115D MET* 3.3 57.4 - - + +
116D ALA* 4.0 3.8 - - - +
119D THR* 3.6 19.5 - - + +
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Residues in contact with PHE 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C CYS* 3.6 44.4 - - + -
84C LEU* 3.7 29.4 - - + -
85C LEU* 3.4 42.4 - - + -
88C MET* 5.8 0.2 - - + -
37D VAL* 2.9 48.5 + - + +
38D PHE 3.7 4.0 - - - +
39D LEU 3.0 0.2 - - - -
40D LEU* 1.3 89.1 - - + +
42D ILE* 1.3 64.1 + - + +
43D THR 3.2 0.2 - - - -
44D PHE* 3.6 7.7 + + - +
45D PRO* 3.3 17.8 - - - +
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Residues in contact with ILE 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C CYS* 5.7 0.2 - - - -
85C LEU* 5.7 3.8 - - + -
38D PHE* 3.0 50.0 + - + +
39D LEU* 3.3 8.7 + - + +
41D PHE* 1.3 77.2 - - + +
43D THR* 1.3 65.0 + - - +
44D PHE 3.3 0.7 + - - -
45D PRO* 3.4 12.1 - - - +
46D ILE* 4.2 12.5 + - + +
123D TYR* 3.4 18.7 + - + +
138D ALA* 5.3 9.6 - - + -
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Residues in contact with THR 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LEU 2.9 14.5 + - - +
40D LEU* 3.1 25.1 - - + +
42D ILE* 1.3 78.2 - - - +
44D PHE* 1.3 67.5 + - + +
45D PRO 3.5 0.2 - - - -
46D ILE* 3.6 2.1 + - - +
47D LEU* 2.8 34.7 + - + +
119D THR* 3.2 31.3 + - + +
122D VAL* 5.1 4.7 - - - +
123D TYR* 3.3 35.3 + - - -
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Residues in contact with PHE 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C MET* 4.1 25.1 - - + -
81C CYS* 5.8 2.0 - - + -
40D LEU* 2.9 37.0 - - + +
41D PHE* 3.6 8.2 + + - +
42D ILE 3.2 0.2 - - - -
43D THR* 1.3 86.5 - - + +
45D PRO* 1.3 68.6 - - + +
47D LEU* 4.0 5.6 - - + +
48D PHE* 2.9 74.0 + + - -
115D MET* 6.3 3.6 - - + -
119D THR* 5.6 0.9 - - - -
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Residues in contact with PRO 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ILE* 4.2 11.6 - - + +
77C MET* 5.4 3.1 - - + -
78C SER* 4.4 20.0 - - - +
81C CYS* 5.3 9.0 - - + -
41D PHE 3.3 18.4 - - - +
42D ILE* 3.4 10.3 - - - +
44D PHE* 1.3 91.7 - - + +
46D ILE* 1.3 59.4 + - + +
48D PHE* 3.1 5.9 + - + +
49D ILE* 2.9 38.9 + - + +
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Residues in contact with ILE 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ILE* 4.3 10.5 - - + +
43D THR 3.6 5.5 + - - +
44D PHE 3.4 0.2 - - - -
45D PRO* 1.3 79.0 - - + +
47D LEU* 1.3 58.7 + - - +
49D ILE* 3.3 10.3 + - + +
50D GLY* 2.9 27.2 + - - -
123D TYR* 3.3 29.6 - - + +
126D ASN* 4.4 12.6 + - + +
135D LEU* 3.7 35.7 - - + -
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Residues in contact with LEU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D THR* 2.8 29.2 + - + +
44D PHE* 4.0 8.3 - - + +
46D ILE* 1.3 77.6 - - - +
48D PHE* 1.3 61.1 + - + +
50D GLY 3.8 0.2 - - - -
51D TRP* 2.9 31.4 + - - +
122D VAL* 4.6 18.2 - - + -
126D ASN* 4.2 12.0 + - - +
----------------------------------------------------------
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Residues in contact with PHE 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 4.8 3.6 - - - +
73C LEU* 4.8 22.9 - - + -
74C ILE* 4.4 20.6 - - + +
77C MET* 3.4 39.0 - - + -
44D PHE* 2.9 57.0 + + - +
45D PRO* 3.7 3.1 - - + +
47D LEU* 1.3 79.3 - - + +
49D ILE* 1.3 60.5 + - - +
51D TRP* 3.8 19.6 - + + +
52D GLY* 3.0 24.4 + - - -
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Residues in contact with ILE 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C VAL* 4.6 34.8 - - + +
62C THR* 5.1 16.7 - - + +
63C LEU* 4.9 12.8 - - + +
66C LEU* 4.9 12.7 - - + +
74C ILE* 3.6 21.1 - - + -
45D PRO* 2.9 26.1 + - + +
46D ILE* 3.8 8.5 - - + +
48D PHE* 1.3 77.1 - - - +
50D GLY* 1.3 63.3 + - - +
52D GLY* 3.4 15.2 + - - -
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Residues in contact with GLY 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ILE 2.9 15.4 + - - -
47D LEU* 3.8 1.8 - - - -
49D ILE* 1.3 79.5 - - - +
51D TRP* 1.3 59.1 + - - +
52D GLY 4.8 1.0 - - - -
126D ASN* 5.2 10.1 - - - -
----------------------------------------------------------
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Residues in contact with TRP 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C HIS* 4.0 32.8 - + - -
73C LEU* 5.3 9.6 - - + -
47D LEU 2.9 19.3 + - - +
48D PHE* 4.2 19.5 - + + +
50D GLY* 1.3 76.3 - - - +
52D GLY* 1.3 70.9 + - - +
----------------------------------------------------------
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Residues in contact with GLY 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 3.9 32.4 - - - +
67C LYS* 5.8 0.7 + - - -
70C HIS* 4.6 17.1 + - - -
48D PHE 3.0 18.5 + - - -
49D ILE 3.4 9.7 + - - -
50D GLY 4.8 1.1 - - - -
51D TRP* 1.3 89.6 - - - +
----------------------------------------------------------
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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