Contacts of the helix formed by residues 58 - 80 (chain A) in PDB entry 2G2Y
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 LYS 58 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLU* 3.3 24.7 + - + +
55A GLU* 2.6 46.7 + - - +
57A ASN* 1.3 76.0 - - - +
59A THR* 1.3 53.7 + - - +
60A TRP* 3.3 41.8 - - + -
61A GLN* 2.7 32.4 + - - +
62A THR 2.8 13.2 + - - -
122A GLN* 5.5 0.2 - - - -
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Residues in contact with THR 59 (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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11A GLN* 2.5 41.8 + - - +
57A ASN 3.6 1.6 + - - -
58A LYS* 1.3 73.4 - - - +
60A TRP* 1.3 62.6 + - + +
62A THR* 3.4 1.6 - - - -
63A GLN* 2.9 44.5 + - - +
118A GLY* 3.6 19.7 - - - +
121A MET* 4.8 5.4 - - + +
122A GLN* 3.3 26.3 + - + +
198A VAL* 4.6 13.0 - - + -
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Residues in contact with TRP 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TYR* 4.4 1.0 + - - -
58A LYS* 3.7 45.1 - - + -
59A THR* 1.3 87.5 - - + +
61A GLN* 1.3 80.9 + - + +
64A PRO* 3.2 19.1 - - - +
115A GLU* 3.6 34.1 - - + +
118A GLY* 3.8 8.1 - - - -
119A LYS* 3.6 38.7 - - + +
122A GLN* 3.4 40.6 - - + -
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Residues in contact with GLN 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TYR* 3.5 32.3 + - + +
44A LEU* 4.4 3.5 - - - +
47A LEU* 4.0 17.1 - - + +
55A GLU* 2.8 52.5 + - - +
56A LEU 4.4 1.1 - - - -
58A LYS* 2.7 20.7 + - - +
60A TRP* 1.3 100.5 - - + +
62A THR* 1.3 64.1 + - - +
63A GLN 3.2 1.3 - - - -
64A PRO* 3.4 3.2 - - - +
65A ALA* 3.1 23.8 + - - +
115A GLU* 5.8 0.2 - - - +
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Residues in contact with THR 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLN* 3.3 38.2 + - + +
14A GLN* 3.5 24.5 - - + +
56A LEU 2.7 25.2 + - - +
57A ASN* 3.2 13.0 - - - -
58A LYS 2.8 17.0 + - - -
59A THR* 3.4 2.2 - - - -
61A GLN* 1.3 77.0 - - - +
63A GLN* 1.3 57.8 + - - +
65A ALA* 3.2 5.4 + - - +
66A LEU* 2.9 36.4 + - + +
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Residues in contact with GLN 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLN* 3.7 11.9 - - + +
59A THR* 2.9 28.7 + - - +
62A THR* 1.3 77.3 - - - +
64A PRO* 1.3 66.8 - - + +
66A LEU* 3.3 1.4 + - - +
67A LEU* 2.8 31.0 + - - +
93A LEU* 3.6 29.9 - - + +
114A VAL* 3.4 22.7 - - + +
117A ARG* 2.8 32.2 + - - +
118A GLY* 3.3 18.6 - - - -
121A MET* 3.5 17.4 - - - +
1001A MLI 3.8 4.8 + - - +
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Residues in contact with PRO 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.0 22.4 - - + -
42A TYR* 4.3 7.6 - - - +
44A LEU* 3.5 2.2 - - + +
60A TRP 3.2 25.4 - - - +
61A GLN* 3.4 12.3 - - - +
63A GLN* 1.3 98.1 - - + +
65A ALA* 1.3 56.4 + - - -
67A LEU* 4.3 2.0 - - + -
68A THR* 2.7 33.8 + - - -
111A VAL* 4.1 13.0 - - + +
114A VAL* 3.5 19.0 - - + -
115A GLU* 4.2 11.2 - - + +
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Residues in contact with ALA 65 (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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14A GLN* 5.8 0.2 - - + -
18A MET* 4.1 7.3 - - + +
33A PHE* 4.0 4.9 - - - -
44A LEU* 3.9 21.3 - - + +
47A LEU* 5.3 0.2 - - + -
48A THR* 4.0 9.0 - - + -
56A LEU* 3.9 25.1 - - + -
61A GLN 3.1 20.6 + - - +
62A THR 3.4 4.9 - - - +
63A GLN 3.1 0.2 - - - -
64A PRO* 1.3 77.1 - - - +
66A LEU* 1.3 58.5 + - + +
68A THR* 3.8 1.9 - - - -
69A ALA* 3.0 28.6 + - - +
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Residues in contact with LEU 66 (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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9A PRO* 4.9 4.9 - - + +
10A GLY* 3.3 35.4 - - - +
11A GLN* 3.7 12.3 - - + +
13A SER* 4.2 2.5 - - - -
14A GLN* 3.3 44.6 - - + +
18A MET* 4.1 4.5 - - + -
62A THR* 2.9 21.8 + - + +
63A GLN 3.9 1.8 - - - +
65A ALA* 1.3 75.1 - - - +
67A LEU* 1.3 66.1 + - - +
69A ALA* 3.2 4.0 + - - +
70A SER* 3.0 27.5 + - - +
93A LEU* 4.0 14.4 - - + -
277A PRO* 3.8 22.1 - - + +
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLN 2.8 18.7 + - - +
64A PRO* 3.9 7.0 - - + +
66A LEU* 1.3 76.3 - - - +
68A THR* 1.3 58.2 + - - +
70A SER* 3.4 0.5 + - - -
71A VAL* 3.0 42.6 + - + +
93A LEU* 3.9 5.2 - - + +
96A TYR* 3.5 35.2 - - + +
97A SER* 3.2 28.7 - - - +
100A VAL* 4.5 3.6 - - + -
107A PHE* 4.9 5.8 - - + -
110A ALA* 4.2 16.4 - - + -
111A VAL* 5.2 4.5 - - + -
114A VAL* 4.1 15.9 - - + -
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Residues in contact with THR 68 (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 THR* 4.0 2.8 - - + +
33A PHE* 3.5 45.1 - - + -
36A ALA* 3.4 17.5 - - + +
44A LEU* 3.3 12.1 - - - +
64A PRO 2.7 22.3 + - - -
65A ALA 3.8 4.0 - - - -
67A LEU* 1.3 73.4 - - - +
69A ALA* 1.3 68.0 + - - +
71A VAL* 3.8 1.0 - - - +
72A ALA* 2.9 23.7 + - - +
107A PHE* 4.0 15.3 - - + -
111A VAL* 3.9 9.7 - - - +
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Residues in contact with ALA 69 (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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18A MET* 4.5 8.3 - - + -
19A LEU* 3.6 17.9 - - + +
33A PHE* 3.6 19.6 - - + -
65A ALA 3.0 18.3 + - - +
66A LEU* 3.2 7.8 + - - +
68A THR* 1.3 77.2 - - - +
70A SER* 1.3 61.7 + - - +
72A ALA* 3.5 2.4 - - - +
73A LEU* 3.1 29.6 + - - +
277A PRO* 4.2 15.9 - - + -
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Residues in contact with SER 70 (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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8A PHE* 3.8 19.0 - - - +
9A PRO* 4.0 10.9 + - - +
66A LEU 3.0 17.5 + - - -
67A LEU 3.8 3.8 - - - -
69A ALA* 1.3 74.0 - - - +
71A VAL* 1.3 62.3 + - - +
73A LEU* 3.3 1.4 + - - -
74A TYR* 2.9 26.2 + - - +
97A SER* 3.9 12.0 + - - -
275A VAL* 2.7 36.0 + - - +
276A GLY* 3.7 8.5 - - - -
277A PRO* 4.7 0.9 - - - +
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Residues in contact with VAL 71 (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 THR* 4.3 1.8 - - + -
67A LEU* 3.0 36.7 + - + +
68A THR 3.9 2.9 - - - +
70A SER* 1.3 76.9 - - - +
72A ALA* 1.3 58.6 + - - +
74A TYR* 3.2 8.3 + - + +
75A ARG* 2.8 54.3 + - + +
97A SER* 4.7 1.3 - - - +
100A VAL* 3.7 26.2 - - + -
101A CYS* 4.3 9.4 - - - -
107A PHE* 3.9 26.0 - - + -
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.7 1.3 - - + -
28A ILE* 4.6 1.0 - - - +
29A VAL* 4.1 28.9 - - + +
32A THR* 4.0 27.3 - - + +
33A PHE* 4.4 4.0 - - + -
68A THR 2.9 19.1 + - - +
69A ALA* 3.5 5.2 - - - +
71A VAL* 1.3 76.3 - - - +
73A LEU* 1.3 63.2 + - - +
75A ARG* 3.1 4.0 + - - +
76A VAL* 2.9 27.9 + - - +
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Residues in contact with LEU 73 (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 22.0 - - + -
22A MET* 3.8 30.3 - - + -
29A VAL* 5.4 0.2 - - + -
69A ALA 3.1 14.1 + - - +
70A SER 3.6 6.1 - - - +
72A ALA* 1.3 73.9 - - - +
74A TYR* 1.3 66.6 + - - +
76A VAL* 3.0 7.0 + - + +
77A TRP* 3.0 21.2 + - - +
275A VAL* 3.7 10.3 - - + -
276A GLY* 3.3 42.0 - - - +
297A LEU 3.6 24.7 - - - +
298A ASN* 3.9 9.0 - - + -
303A MET* 4.0 6.5 - - + +
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Residues in contact with TYR 74 (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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6A PHE* 3.7 37.2 - + - -
8A PHE* 4.7 1.8 - + - -
70A SER 2.9 10.1 + - - +
71A VAL* 3.4 9.0 - - + +
73A LEU* 1.3 75.3 - - - +
75A ARG* 1.3 68.8 + - + +
77A TRP* 3.1 10.4 + + - +
78A GLN* 2.9 60.3 + - + +
84A ALA* 5.1 5.9 - - - +
85A PRO* 4.5 9.4 - - + +
88A MET* 3.9 12.3 - - + +
101A CYS* 3.4 59.8 + - + -
225A THR* 5.7 0.5 + - - -
226A VAL* 5.3 1.7 - - - +
275A VAL* 3.7 6.9 - - + +
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Residues in contact with ARG 75 (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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28A ILE* 3.8 25.5 - - + +
32A THR* 3.3 28.0 + - - +
35A GLU* 3.1 34.8 + - - -
71A VAL* 2.8 31.0 + - + +
72A ALA* 3.1 6.7 + - - +
74A TYR* 1.3 84.1 - - + +
76A VAL* 1.3 56.9 + - - +
78A GLN* 3.4 7.8 + - - +
79A GLN* 2.9 31.8 + - - +
100A VAL* 5.9 0.4 - - - +
107A PHE* 3.7 31.3 - - - +
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Residues in contact with VAL 76 (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 MET* 4.4 6.3 - - + -
26A TYR* 3.8 44.4 - - + -
28A ILE* 3.6 23.6 - - + -
29A VAL* 4.0 11.2 - - + -
72A ALA 2.9 18.9 + - - +
73A LEU* 3.0 7.6 + - - +
75A ARG* 1.3 73.7 - - - +
77A TRP* 1.3 66.9 + - - +
79A GLN* 3.2 3.5 + - - +
80A GLN* 2.9 25.6 + - + +
303A MET* 3.8 27.6 - - + -
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Residues in contact with TRP 77 (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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4A PHE* 4.0 17.9 - + - -
6A PHE* 3.5 29.2 - + + -
73A LEU 3.0 11.0 + - - +
74A TYR* 3.2 15.5 - + - +
76A VAL* 1.3 79.3 - - - +
78A GLN* 1.3 68.1 + - + +
80A GLN* 3.3 5.9 + - - +
81A GLY 3.4 0.3 + - - -
82A GLY* 2.8 46.1 + - - -
83A LYS 2.7 31.6 + - - -
85A PRO* 5.4 0.4 - - + -
273A TYR* 4.9 8.1 - + - -
297A LEU* 4.2 12.6 - - + -
303A MET* 3.9 20.2 - - + -
306A ALA* 3.8 40.2 - - + -
307A LEU* 3.6 28.6 - - + +
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Residues in contact with GLN 78 (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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74A TYR* 2.9 55.5 + - + +
75A ARG* 3.8 7.0 - - - +
77A TRP* 1.3 81.7 - - + +
79A GLN* 1.3 64.7 + - - +
81A GLY* 2.9 15.8 + - - -
82A GLY 4.4 10.0 + - - +
84A ALA* 5.8 6.5 - - - +
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Residues in contact with GLN 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 4.3 11.3 - - - +
27A PRO* 5.8 1.6 - - - +
28A ILE* 3.7 43.5 + - + +
31A GLU* 5.3 1.6 + - - -
75A ARG 2.9 19.1 + - - +
76A VAL* 3.2 3.6 + - - +
78A GLN* 1.3 77.4 - - - +
80A GLN* 1.3 74.9 + - - +
81A GLY* 3.2 3.5 + - - -
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Residues in contact with GLN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 3.6 34.4 + - + -
76A VAL* 2.9 20.3 + - + +
77A TRP 3.3 1.8 + - - +
78A GLN 3.1 0.4 - - - -
79A GLN* 1.3 97.7 - - + +
81A GLY* 1.3 58.8 + - - +
82A GLY 3.4 2.0 + - - -
307A LEU* 3.3 36.2 - - + +
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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