Contacts of the helix formed by residues 32 - 56 (chain A) in PDB entry 3GNI
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 SER 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ILE* 1.3 78.0 - - - +
33A ASP* 1.3 64.9 + - - +
34A LYS* 3.8 6.5 + - - +
35A LYS* 3.2 26.4 + - - +
36A ALA* 3.0 20.8 + - - +
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Residues in contact with ASP 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE 5.0 1.9 - - - +
32A SER* 1.3 73.1 - - - +
34A LYS* 1.3 59.7 + - + +
36A ALA* 3.5 7.2 + - - +
37A GLU* 2.9 32.9 + - - +
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Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A SER* 3.2 6.6 + - - +
33A ASP* 1.3 78.1 - - + +
35A LYS* 1.3 58.8 + - - +
37A GLU* 3.2 37.2 + - - +
38A LYS* 2.8 32.2 + - - +
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Residues in contact with LYS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A VAL* 4.0 15.1 - - + +
28A LYS* 5.1 5.4 - - - +
31A ILE* 4.3 23.6 - - + +
32A SER* 3.2 26.4 + - - +
34A LYS* 1.3 77.7 - - - +
36A ALA* 1.3 56.3 + - - +
38A LYS* 3.5 13.3 + - + +
39A ALA* 3.1 27.9 + - - +
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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
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26A LEU* 3.6 10.5 - - + +
31A ILE* 3.7 22.1 - - + +
32A SER 3.0 15.9 + - - +
33A ASP* 3.7 7.9 - - - +
35A LYS* 1.3 73.8 - - - +
37A GLU* 1.3 55.9 + - - +
39A ALA* 3.4 2.4 + - - +
40A THR* 2.8 38.8 + - - +
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Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASP* 2.9 19.7 + - - +
34A LYS* 3.2 42.4 + - - +
36A ALA* 1.3 76.5 - - - +
38A LYS* 1.3 57.9 + - - +
40A THR* 3.2 9.3 + - + -
41A GLU* 2.9 36.7 + - + +
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Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LYS 2.8 17.7 + - - +
35A LYS* 3.6 13.9 - - + +
37A GLU* 1.3 75.0 - - - +
39A ALA* 1.3 57.3 + - - +
41A GLU* 3.3 7.3 + - - +
42A GLU* 3.0 60.8 + - - +
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Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A SER* 3.9 11.4 - - - +
25A VAL* 3.6 37.7 - - + -
26A LEU* 3.8 16.8 - - + -
35A LYS 3.1 8.5 + - - +
38A LYS* 1.3 74.6 - - - +
40A THR* 1.3 60.5 - - - +
42A GLU* 3.8 9.8 - - - +
43A VAL* 2.9 35.9 + - - +
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Residues in contact with THR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 3.7 19.8 - - - +
36A ALA* 2.8 20.0 + - - +
37A GLU* 3.2 11.0 + - + +
39A ALA* 1.3 76.4 - - - +
41A GLU* 1.3 73.2 + - - +
43A VAL* 3.6 2.3 + - - +
44A SER* 3.2 23.7 + - - -
89A LEU 4.8 4.5 + - - -
91A ASP* 4.6 20.6 - - + +
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Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLU* 2.9 22.3 + - + +
38A LYS* 3.3 9.6 + - - +
40A THR* 1.3 83.9 - - + +
42A GLU* 1.3 57.2 + - + +
44A SER* 3.5 12.6 + - - -
45A LYS* 3.1 59.5 + - - +
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Residues in contact with GLU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A SER* 3.0 24.6 + - - +
38A LYS* 3.0 57.5 + - - +
39A ALA* 3.9 4.9 - - - +
40A THR 3.3 0.2 - - - -
41A GLU* 1.3 75.0 - - + +
43A VAL* 1.3 65.9 + - - +
45A LYS* 3.3 8.5 + - + +
46A ASN* 2.9 37.0 + - - +
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Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.7 17.3 - - + -
22A SER* 3.6 21.3 - - - -
23A MET* 3.8 20.6 - - - -
26A LEU* 3.9 15.0 - - + -
39A ALA 2.9 21.4 + - - +
40A THR 3.8 3.6 - - - +
42A GLU* 1.3 76.2 - - - +
44A SER* 1.3 64.7 + - - +
46A ASN* 3.3 2.6 + - - +
47A LEU* 2.9 46.9 + - + +
83A LEU* 5.6 0.2 - - + -
90A ILE* 4.0 25.4 - - + -
91A ASP* 5.2 1.1 - - - +
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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
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40A THR* 3.2 16.5 + - - -
41A GLU* 3.5 15.9 + - - -
43A VAL* 1.3 79.9 - - - +
45A LYS* 1.3 59.6 + - - +
47A LEU* 3.5 6.7 + - - +
48A VAL* 3.1 33.8 + - - +
91A ASP* 3.6 28.3 + - - -
94A GLY* 5.4 2.8 - - - -
97A ASP* 4.7 0.9 - - - +
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLU* 3.1 46.9 + - - +
42A GLU* 3.3 7.2 + - + +
44A SER* 1.3 76.7 - - - +
46A ASN* 1.3 59.3 - - - +
48A VAL* 3.5 9.0 + - - +
49A ALA* 3.0 26.9 + - - +
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Residues in contact with ASN 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS* 5.6 3.3 + - - +
15A ILE* 3.8 14.8 - - + +
18A ASN* 3.5 30.7 + - - +
19A LEU* 3.5 39.7 - - + +
22A SER* 4.7 0.2 + - - -
42A GLU* 2.9 32.5 + - - +
43A VAL* 3.6 4.2 - - - +
45A LYS* 1.3 74.6 - - - +
47A LEU* 1.3 58.8 + - - +
49A ALA* 3.2 8.2 + - - +
50A MET* 2.9 34.3 + - - +
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.6 24.2 - - + -
43A VAL* 2.9 38.3 + - + +
44A SER* 3.8 3.8 - - - +
46A ASN* 1.3 72.8 - - - +
48A VAL* 1.3 66.4 + - - +
50A MET* 3.3 1.2 + - - -
51A LYS* 3.0 26.2 + - - +
83A LEU* 4.2 11.2 - - + -
90A ILE* 4.0 5.4 - - + -
94A GLY* 3.5 32.5 - - - +
97A ASP* 4.0 13.9 - - + +
98A VAL* 3.7 18.8 - - + -
101A ILE* 3.5 25.1 - - + +
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A SER* 3.1 22.2 + - - +
45A LYS* 3.7 10.5 - - - +
47A LEU* 1.3 75.1 - - - +
49A ALA* 1.3 57.8 + - - +
51A LYS* 3.5 14.0 + - - +
52A GLU* 3.0 47.9 + - + +
97A ASP* 3.5 17.5 - - - +
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 4.2 21.3 - - + -
45A LYS 3.0 16.0 + - - +
46A ASN* 3.2 12.5 + - - +
48A VAL* 1.3 79.1 - - - +
50A MET* 1.3 60.0 + - - +
52A GLU* 3.4 7.3 + - - +
53A ILE* 3.2 28.7 + - - +
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Residues in contact with MET 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 3.7 15.7 - - + -
16A VAL* 3.7 39.0 - - + -
19A LEU* 3.5 30.5 - - + -
46A ASN 2.9 19.0 + - - +
47A LEU* 3.3 6.3 + - - +
49A ALA* 1.3 72.9 - - - +
51A LYS* 1.3 67.0 - - - +
53A ILE* 3.1 14.0 + - - +
54A LEU* 3.2 19.2 + - - +
70A LEU* 3.9 22.3 - - + +
74A LEU* 4.3 15.5 - - + -
79A LEU* 4.2 6.3 - - + -
83A LEU* 5.5 1.3 - - - -
101A ILE* 3.7 22.7 - - + -
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Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU 3.0 13.1 + - - +
48A VAL* 3.6 15.6 - - - +
50A MET* 1.3 77.0 - - - +
52A GLU* 1.3 62.6 + - + +
54A LEU* 3.2 2.0 + - - -
55A TYR* 2.8 55.4 + - + +
97A ASP* 2.9 33.9 + - - +
100A GLN* 3.5 26.9 + - + +
101A ILE* 3.9 12.8 - - + +
189B MET* 5.8 5.9 - - - +
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LYS* 5.6 7.5 - - - -
48A VAL* 3.0 37.0 + - + +
49A ALA* 3.8 7.7 - - - +
50A MET 3.2 0.4 - - - -
51A LYS* 1.3 81.5 - - + +
53A ILE* 1.3 57.0 + - - +
56A GLY* 2.8 38.2 + - - +
57A THR* 3.8 26.3 - - + +
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Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS 5.1 1.3 - - - +
12A PRO* 4.5 16.4 - - + -
15A ILE* 3.7 27.1 - - + -
49A ALA* 3.2 16.5 + - + +
50A MET* 3.1 8.8 + - - +
52A GLU* 1.3 78.6 - - - +
54A LEU* 1.3 59.6 + - - +
62A PRO* 3.4 18.5 - - - +
63A GLN 4.7 1.4 + - - +
66A ALA* 3.9 36.7 - - + +
67A VAL* 3.5 8.5 - - - +
70A LEU* 3.7 25.4 - - + -
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A MET 3.2 15.7 + - - +
51A LYS 3.2 4.3 + - - +
53A ILE* 1.3 79.5 - - - +
55A TYR* 1.3 63.4 + - + +
62A PRO* 3.4 18.0 - - - +
67A VAL* 3.8 28.4 - - + +
70A LEU* 3.8 23.1 - - + -
101A ILE* 3.8 46.2 - - + +
104A ASN* 3.5 36.2 + - - +
105A ILE* 4.0 17.0 - - + -
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Residues in contact with TYR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LYS* 2.8 32.8 + - + +
54A LEU* 1.3 82.1 - - + +
56A GLY* 1.3 66.2 + - - +
57A THR 3.9 0.3 + - - -
60A LYS 4.5 0.5 - - - +
61A GLU* 4.8 0.3 - - - -
62A PRO* 3.4 15.5 - - - +
100A GLN* 2.7 53.1 + - + +
101A ILE* 4.5 0.9 - - - -
103A ASN* 4.5 4.7 - - - +
104A ASN* 3.5 27.6 + - + +
221B ILE* 5.8 9.9 - - + -
224B GLY* 3.1 30.4 + - - -
225B GLN* 5.3 4.0 - - + -
226B ARG* 3.3 25.9 + - + +
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Residues in contact with GLY 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLU* 2.8 32.4 + - - +
54A LEU 3.5 1.6 - - - -
55A TYR* 1.3 84.1 - - - +
57A THR* 1.3 70.9 + - - +
60A LYS* 3.4 11.2 - - - -
61A GLU 4.3 1.3 - - - -
62A PRO* 3.9 13.2 - - - +
226B ARG* 3.9 3.6 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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