Contacts of the helix formed by residues 20 - 53 (chain A) in PDB entry 3D0G
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 THR 20 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER* 1.3 79.1 - - - +
21A THR* 1.3 63.6 + - - +
22A GLU* 2.9 19.5 + - - +
23A GLU* 3.5 19.9 + - - +
24A LEU* 3.1 24.6 + - - +
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Residues in contact with THR 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A THR* 1.3 75.7 - - - +
22A GLU* 1.3 60.1 + - - +
24A LEU* 3.4 10.8 + - + +
25A ALA* 2.9 27.9 + - - +
83A TYR* 4.3 13.9 - - + -
84A PRO* 3.8 31.4 - - + +
87A GLU* 2.7 42.0 + - + +
88A ILE* 5.3 4.7 - - + -
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Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A THR* 2.9 9.4 + - - +
21A THR* 1.3 76.7 - - - +
23A GLU* 1.3 66.6 + - - +
25A ALA* 3.4 6.0 + - + +
26A LYS* 3.2 40.4 + - - +
87A GLU 4.3 3.9 + - - +
88A ILE* 3.4 31.1 - - + +
89A GLN* 2.8 44.7 + - - +
90A ASN* 3.3 24.1 - - - +
93A VAL* 4.3 8.3 - - + -
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER* 3.8 30.2 - - - +
20A THR* 3.5 22.0 + - - +
21A THR 3.3 0.4 - - - -
22A GLU* 1.3 81.1 - - - +
24A LEU* 1.3 59.8 + - - +
25A ALA 3.1 1.1 + - - -
26A LYS* 2.8 34.4 + - - +
27A THR* 3.4 26.2 + - - -
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER* 4.2 18.4 - - - +
20A THR 3.1 26.5 + - - +
21A THR* 3.4 9.2 + - + +
23A GLU* 1.3 77.3 - - - +
25A ALA* 1.3 60.6 + - - +
27A THR* 4.2 5.1 - - - -
28A PHE* 3.3 22.7 + - - +
83A TYR* 3.4 23.8 + - + +
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR 2.9 16.7 + - - +
22A GLU* 3.6 10.8 - - + +
23A GLU 3.1 0.4 - - - -
24A LEU* 1.3 76.5 - - - +
26A LYS* 1.3 55.9 + - + +
27A THR 3.3 0.2 - - - -
28A PHE* 3.2 4.1 + - - +
29A LEU* 2.7 44.8 + - + +
83A TYR* 4.3 11.0 - - + -
88A ILE* 4.7 7.4 - - + -
93A VAL* 5.7 4.7 - - + -
97A LEU* 4.2 24.2 - - + -
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Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLU* 3.2 33.0 + - + +
23A GLU* 2.8 37.5 + - - +
25A ALA* 1.3 76.4 - - - +
27A THR* 1.3 54.5 + - - +
29A LEU* 3.2 6.9 + - - +
30A GLU* 2.8 48.9 + - + +
90A ASN* 4.7 9.6 - - - -
93A VAL* 4.2 23.6 - - + -
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Residues in contact with THR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU 3.4 15.4 + - - -
24A LEU* 4.5 5.2 - - - -
25A ALA 3.3 0.4 - - - -
26A LYS* 1.3 75.3 - - - +
28A PHE* 1.3 65.2 + - - +
30A GLU* 3.9 12.9 + - + +
31A THR* 3.2 31.6 + - - +
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Residues in contact with PHE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU 3.3 18.6 + - - +
25A ALA 3.2 7.6 + - - +
27A THR* 1.3 81.2 - - - +
29A LEU* 1.3 74.5 + - + +
31A THR* 3.3 5.8 + - - -
32A PHE* 3.1 18.2 + - + +
76A GLN* 3.3 44.8 - - - +
79A LEU* 4.0 20.9 - - + -
80A ALA* 3.7 25.4 - - + -
83A TYR* 3.7 25.6 - + + +
97A LEU* 4.3 6.5 - - + -
100A LEU* 3.7 15.5 - - + -
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 2.7 34.9 + - + +
26A LYS* 3.7 6.5 - - - +
28A PHE* 1.3 74.3 - - + +
30A GLU* 1.3 61.7 + - - +
32A PHE* 2.8 22.0 + - + +
33A ASN* 2.9 24.0 + - - +
93A VAL* 4.5 10.1 - - + +
96A GLN* 4.0 26.2 - - + +
97A LEU* 4.0 33.0 - - + +
100A LEU* 4.2 19.1 - - + -
391A LEU* 3.9 28.0 - - + -
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Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 2.8 35.3 + - + +
27A THR* 3.9 12.3 + - + +
29A LEU* 1.3 71.9 - - - +
31A THR* 1.3 62.6 + - - +
33A ASN* 3.3 10.6 + - - +
34A TYR* 3.1 47.6 + - + -
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Residues in contact with THR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 3.2 17.7 + - - +
28A PHE* 3.6 10.8 - - - -
29A LEU 3.3 0.6 - - - -
30A GLU* 1.3 77.8 - - - +
32A PHE* 1.3 64.6 + - - +
34A TYR* 3.6 7.4 + - - +
35A GLU* 3.1 25.6 + - + +
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Residues in contact with PHE 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 3.1 12.2 + - + +
29A LEU* 2.8 14.4 + - + +
31A THR* 1.3 74.8 - - - +
33A ASN* 1.3 70.7 + - - +
35A GLU* 2.8 4.9 + - - +
36A ALA* 2.6 54.9 + - + +
69A TRP* 4.6 1.6 - + - -
72A PHE* 3.6 22.2 - + - -
73A LEU* 4.2 20.4 - - + -
76A GLN* 3.5 38.8 + - + +
100A LEU* 3.7 29.4 - - + -
390A PHE* 4.2 6.3 - + - -
391A LEU* 3.9 29.8 - - + -
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Residues in contact with ASN 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 2.9 24.9 + - - +
30A GLU* 3.3 10.1 + - - +
32A PHE* 1.3 88.3 - - - +
34A TYR* 1.3 61.1 + - + +
36A ALA* 3.7 3.0 - - - +
37A GLN* 2.9 41.6 + - - +
96A GLN* 3.8 24.4 + - - +
389A PRO* 4.9 2.6 - - - +
390A PHE* 3.6 30.8 + - + +
391A LEU* 4.1 5.9 - - - +
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Residues in contact with TYR 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 3.1 42.8 + - + +
31A THR* 4.0 6.3 - - - +
32A PHE 3.1 0.6 - - - -
33A ASN* 1.3 82.4 - - + +
35A GLU* 1.3 63.2 + - - +
37A GLN* 3.3 34.3 + - - +
38A GLU* 3.7 13.7 - - - +
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Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A THR* 3.1 20.7 + - + +
32A PHE 2.8 5.3 + - - -
34A TYR* 1.3 71.1 - - - +
36A ALA* 1.3 66.7 + - - +
38A GLU* 3.3 12.6 + - - +
39A LEU* 3.3 44.0 + - - +
72A PHE* 3.7 23.7 - - + -
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 2.6 47.6 + - + +
33A ASN 3.7 2.9 - - - +
35A GLU* 1.3 70.6 - - - +
37A GLN* 1.3 64.1 + - - +
40A SER* 2.9 31.0 + - - -
69A TRP* 3.6 23.1 - - + -
72A PHE* 4.0 3.7 - - + -
390A PHE* 3.7 14.1 - - + -
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Residues in contact with GLN 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASN* 2.9 32.7 + - - +
34A TYR* 3.6 26.1 - - - +
35A GLU 3.3 0.6 - - - -
36A ALA* 1.3 76.3 - - - +
38A GLU* 1.3 66.1 + - - +
40A SER* 4.4 0.4 - - - -
41A TYR* 3.0 29.6 + - - +
353A LYS* 3.9 23.8 + - + +
390A PHE* 4.1 24.3 - - + +
393A ARG* 4.6 17.6 - - - +
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Residues in contact with GLU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR 3.7 12.9 - - - +
35A GLU* 3.3 16.3 + - - +
36A ALA 3.2 0.4 - - - -
37A GLN* 1.3 81.8 - - - +
39A LEU* 1.3 70.0 + - + +
41A TYR* 3.2 3.4 + - - +
42A GLN* 2.9 36.1 + - - +
353A LYS* 2.5 40.5 + - - -
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU* 3.3 29.4 + - - +
38A GLU* 1.3 76.5 - - + +
40A SER* 1.3 52.4 + - - +
42A GLN* 3.1 16.7 + - - +
43A SER* 2.7 36.5 + - - -
65A ALA 4.7 1.6 - - - +
68A LYS* 3.6 44.6 - - + +
69A TRP* 3.7 21.5 - - + +
72A PHE* 3.3 44.6 - - + -
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Residues in contact with SER 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA 2.9 20.9 + - - -
37A GLN 4.4 0.9 - - - -
39A LEU* 1.3 79.2 - - - +
41A TYR* 1.3 55.7 + - - -
43A SER* 3.4 3.7 - - - -
44A SER* 2.9 35.9 + - - -
69A TRP* 3.7 32.9 + - - -
351A LEU 4.6 5.0 + - - -
390A PHE* 3.8 18.0 - - - -
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Residues in contact with TYR 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLN 3.0 23.0 + - - +
38A GLU* 3.2 3.3 + - - +
40A SER* 1.3 74.8 - - - +
42A GLN* 1.3 68.9 + - + +
44A SER* 3.3 0.9 + - - -
45A VAL* 3.0 48.4 + - + +
351A LEU* 3.5 25.5 + - + +
352A GLY* 3.8 16.4 - - - -
353A LYS* 3.8 40.4 - - + -
355A ASP* 2.9 30.2 + - + +
357A ARG* 4.6 1.4 + - - -
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Residues in contact with GLN 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLU* 2.9 27.5 + - - +
39A LEU* 3.5 16.7 - - - +
41A TYR* 1.3 78.4 - - + +
43A SER* 1.3 68.3 + - - +
45A VAL* 4.2 3.4 - - - +
46A ALA* 3.1 25.3 + - - +
65A ALA* 3.6 11.3 - - + +
68A LYS* 5.3 3.8 + - - +
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Residues in contact with SER 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU 2.7 20.3 + - - -
40A SER 3.3 5.6 + - - -
42A GLN* 1.3 73.3 - - - +
44A SER* 1.3 57.2 + - - +
46A ALA* 3.6 2.4 - - - +
47A SER* 2.9 30.5 + - - -
62A MET* 5.2 1.9 - - - +
65A ALA* 3.7 19.8 - - - +
66A GLY* 3.8 15.2 - - - -
69A TRP* 3.6 28.2 - - - -
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Residues in contact with SER 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A SER* 2.9 20.5 + - - -
41A TYR 3.8 2.0 - - - -
42A GLN 3.3 0.2 - - - -
43A SER* 1.3 74.0 - - - +
45A VAL* 1.3 54.3 + - - +
47A SER* 3.1 7.4 + - - -
48A TRP* 2.7 37.7 + - - +
349A TRP* 3.8 7.8 - - - -
350A ASP 4.7 2.3 + - - -
351A LEU* 3.6 39.3 + - - -
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Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 3.0 58.1 + - + +
42A GLN* 4.2 4.0 - - - +
44A SER* 1.3 73.3 - - - +
46A ALA* 1.3 59.2 + - - +
48A TRP* 3.2 7.0 + - - +
49A ASN* 2.8 48.1 + - - +
351A LEU* 4.0 11.0 - - + -
355A ASP* 4.9 0.2 - - - +
357A ARG* 5.5 6.1 - - - +
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN 3.1 17.6 + - - +
43A SER 3.6 3.1 - - - +
45A VAL* 1.3 79.2 - - - +
47A SER* 1.3 61.9 + - - +
49A ASN* 3.4 8.1 + - - +
50A TYR* 3.2 22.3 + - - +
58A ASN* 4.9 2.3 - - - +
61A ASN* 3.8 32.6 - - + +
62A MET* 3.9 11.2 + - - +
65A ALA* 4.0 6.5 - - + -
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Residues in contact with SER 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A SER* 2.9 19.3 + - - -
44A SER* 3.5 6.7 - - - -
46A ALA* 1.3 76.4 - - - +
48A TRP* 1.3 63.3 + - - +
50A TYR* 3.4 3.3 - - - +
51A ASN* 2.8 32.4 + - - +
62A MET* 3.4 26.5 - - - +
349A TRP* 3.7 15.9 - - - -
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Residues in contact with TRP 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A SER 2.7 20.3 + - - +
45A VAL* 3.5 7.6 - - + +
47A SER* 1.3 68.7 - - - +
49A ASN* 1.3 84.6 + - - +
50A TYR 2.9 3.1 + - - -
51A ASN* 3.0 12.6 + - - +
52A THR* 3.0 38.9 + - + +
330A ASN 3.6 13.3 + - - -
332A MET* 4.0 11.7 - - + -
349A TRP* 3.4 60.1 - + + -
351A LEU* 4.4 3.6 - - + -
357A ARG* 3.3 52.7 - - + +
358A ILE 3.8 12.1 - - - -
359A LEU* 3.6 22.4 - - + -
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Residues in contact with ASN 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 2.8 41.5 + - - +
46A ALA* 3.8 7.5 - - - +
48A TRP* 1.3 84.9 + - - +
50A TYR* 1.3 52.5 - - - +
52A THR* 3.1 7.2 + - - -
53A ASN* 2.7 33.1 + - + +
58A ASN* 3.2 23.6 + - - +
357A ARG* 5.2 0.7 + - - -
----------------------------------------------------------
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Residues in contact with TYR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA 3.2 12.7 + - - +
47A SER 3.4 8.1 - - - +
48A TRP 2.9 0.8 + - - -
49A ASN* 1.3 70.6 - - - +
51A ASN* 1.3 87.0 + - - +
52A THR 2.7 14.6 + - - -
53A ASN 2.8 20.7 + - - -
54A ILE* 3.3 38.5 + - + +
55A THR 4.8 1.1 - - - -
58A ASN* 3.8 13.8 - - + +
59A VAL* 4.2 36.5 - - + +
62A MET* 4.2 26.5 - - + -
343A VAL* 4.8 8.8 - - + +
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Residues in contact with ASN 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 2.8 24.4 + - - +
48A TRP 3.0 10.0 + - - +
50A TYR* 1.3 93.6 - - - +
52A THR* 1.3 57.3 + - - +
54A ILE* 4.9 0.2 - - - -
62A MET* 5.2 0.5 - - - +
342A ALA* 3.2 5.7 - - - +
343A VAL* 3.1 60.5 + - + +
349A TRP* 3.8 20.0 - - + -
359A LEU* 3.8 19.4 - - + +
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Residues in contact with THR 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TRP* 3.0 57.3 + - + +
49A ASN* 3.1 10.2 + - - -
50A TYR 2.7 4.8 + - - -
51A ASN* 1.3 78.4 - - - +
53A ASN* 1.3 58.8 + - - +
54A ILE 4.1 0.2 - - - -
332A MET* 3.5 33.8 - - + +
340A GLN* 4.0 12.5 + - - +
341A LYS 4.1 0.6 - - - +
342A ALA* 3.9 14.6 - - - +
359A LEU* 4.0 17.5 - - + -
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Residues in contact with ASN 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ASN* 2.7 17.0 + - + +
50A TYR 2.8 3.9 + - - +
52A THR* 1.3 76.5 - - - +
54A ILE* 1.3 59.0 + - - +
55A THR* 2.8 37.2 + - - -
57A GLU* 5.2 4.2 + - - -
58A ASN* 2.8 25.9 + - - +
340A GLN* 3.1 36.3 + - - +
341A LYS 4.1 2.7 - - - -
----------------------------------------------------------
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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