Contacts of the helix formed by residues 56 - 85 (chain J) in PDB entry 1S7X
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 56 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54J GLN 3.6 3.2 + - - -
55J GLU* 1.3 75.2 + - - +
57J PRO* 1.3 77.3 - - - +
58J GLU* 3.2 3.4 - - - -
59J TYR* 3.1 17.3 + - - +
60J TRP* 3.2 15.1 - - - -
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Residues in contact with PRO 57 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J ARG* 4.6 3.8 + - - +
56J GLY* 1.3 83.3 - - - +
58J GLU* 1.3 61.8 + - - +
59J TYR 3.4 0.3 + - - -
60J TRP* 3.5 10.1 + - + +
61J GLU* 3.2 30.2 + - - +
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Residues in contact with GLU 58 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J GLY 3.1 2.0 + - - -
57J PRO* 1.3 76.4 - - - +
59J TYR* 1.3 60.4 + - - +
61J GLU* 4.1 8.6 - - + +
62J ARG* 3.1 45.3 + - + +
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Residues in contact with TYR 59 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J TYR* 4.4 3.8 + - - -
33J PHE* 4.3 4.0 - - - -
34J VAL* 4.4 3.3 - - + +
52J MET* 3.6 27.2 - - + +
55J GLU* 3.9 20.2 - - + +
56J GLY 3.1 13.4 + - - +
58J GLU* 1.3 78.9 - - - +
60J TRP* 1.3 86.0 + + - +
62J ARG* 3.5 28.1 - - - +
63J GLU* 3.0 52.5 + - + +
167J TRP* 3.8 21.3 - + - -
171J TYR* 2.6 36.0 + + - -
1L LYS* 4.3 4.6 + - + -
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Residues in contact with TRP 60 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J VAL* 3.9 10.1 - - + -
44J ARG* 3.8 18.8 - - - +
45J TYR* 3.6 28.6 - + + +
46J GLU* 3.7 8.3 - - - -
47J PRO* 3.5 44.9 - - + -
52J MET* 3.5 45.8 - - + -
53J GLU* 5.2 1.4 + - - +
55J GLU* 3.3 18.5 + - + -
56J GLY 3.2 25.7 + - - -
57J PRO* 3.5 6.5 + - + +
58J GLU 3.4 0.2 - - - -
59J TYR* 1.3 92.0 - + - +
61J GLU* 1.3 58.6 + - - +
63J GLU* 4.1 1.9 - - + +
64J THR* 2.7 38.2 + - - -
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Residues in contact with GLU 61 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J ARG* 3.8 24.1 + - - +
57J PRO* 3.2 22.1 + - - +
58J GLU* 4.1 9.7 - - + +
60J TRP* 1.3 74.6 - - - +
62J ARG* 1.3 65.7 + - - +
64J THR* 3.7 0.9 - - - -
65J GLN* 3.1 37.7 + - + +
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Residues in contact with ARG 62 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58J GLU* 3.1 33.2 + - + +
59J TYR* 3.5 32.5 + - - +
61J GLU* 1.3 77.0 - - - +
63J GLU* 1.3 91.4 + - - +
65J GLN* 3.4 5.4 + - - +
66J LYS* 3.2 34.9 + - + +
167J TRP* 3.7 17.8 - - - -
1L LYS* 3.6 31.7 - - - +
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Residues in contact with GLU 63 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J TYR* 4.2 2.9 + - - -
45J TYR* 3.3 30.0 - - + -
59J TYR* 3.0 42.7 + - + +
60J TRP* 4.1 3.6 - - - +
62J ARG* 1.3 95.7 + - - +
64J THR* 1.3 61.3 + - - +
66J LYS* 2.6 33.1 + - - +
67J ALA 2.9 23.4 + - - -
1L LYS* 3.1 17.1 - - - +
2L ALA* 3.2 28.2 + - - +
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Residues in contact with THR 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36J PHE* 4.4 4.6 - - + -
43J PRO 4.0 13.0 - - - +
44J ARG* 3.2 35.2 - - + +
45J TYR* 3.2 26.3 + - - +
60J TRP 2.7 23.5 + - - -
61J GLU 3.7 3.8 - - - -
62J ARG 3.4 0.2 - - - -
63J GLU* 1.3 77.1 - - - +
65J GLN* 1.3 65.3 + - - +
67J ALA* 3.0 5.7 + - - +
68J LYS* 2.9 36.9 + - + +
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Residues in contact with GLN 65 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J ARG* 5.8 1.2 - - - +
61J GLU* 3.1 26.1 + - + +
62J ARG* 3.9 5.4 - - - +
64J THR* 1.3 83.6 - - - +
66J LYS* 1.3 60.3 + - - +
68J LYS* 3.4 26.6 + - - +
69J GLY* 3.2 17.5 + - - -
4L PHE* 5.3 0.5 - - - -
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Residues in contact with LYS 66 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45J TYR* 5.9 0.9 - - + -
62J ARG* 3.2 23.6 + - + +
63J GLU* 2.6 43.2 + - - +
64J THR 3.1 0.6 - - - -
65J GLN* 1.3 75.4 - - - +
67J ALA* 1.3 59.7 + - - +
69J GLY* 3.2 2.4 + - - -
70J GLN* 3.0 33.4 + - + +
163J GLU* 5.3 1.1 - - - -
1L LYS* 3.1 21.3 - - - +
2L ALA* 2.8 34.5 + - + +
3L VAL 4.6 2.0 - - - +
4L PHE* 3.8 33.6 - - + -
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Residues in contact with ALA 67 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J TYR* 3.6 11.0 - - + -
36J PHE* 3.6 35.6 - - + -
45J TYR* 3.6 24.2 - - + +
63J GLU 2.9 6.6 + - - +
64J THR 3.0 8.3 + - - +
66J LYS* 1.3 75.3 - - - +
68J LYS* 1.3 58.1 + - - +
70J GLN* 3.4 9.3 + - - +
71J GLU* 3.0 27.5 + - - +
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Residues in contact with LYS 68 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36J PHE* 4.7 5.4 - - + -
43J PRO* 4.0 36.0 - - - +
64J THR* 2.9 21.1 + - + +
65J GLN* 3.7 30.1 - - - +
66J LYS 3.2 0.2 - - - -
67J ALA* 1.3 77.6 - - - +
69J GLY* 1.3 61.5 + - - +
71J GLU* 3.6 21.5 + - - +
72J GLN* 3.5 24.3 + - - +
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Residues in contact with GLY 69 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65J GLN 3.2 12.3 + - - -
66J LYS 3.2 3.3 + - - -
68J LYS* 1.3 75.9 - - - +
70J GLN* 1.3 63.0 + - - +
72J GLN* 3.1 10.0 + - - +
73J TRP* 3.0 20.7 + - - +
4L PHE* 3.9 21.6 - - - -
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Residues in contact with GLN 70 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J GLU* 2.8 29.5 + - - +
22J TYR* 3.4 18.2 - - + +
66J LYS* 3.0 18.4 + - + +
67J ALA* 3.5 8.1 - - - +
69J GLY* 1.3 75.6 - - - +
71J GLU* 1.3 55.8 + - - +
73J TRP* 3.1 7.6 + - - +
74J PHE* 2.9 37.1 + - - -
97J GLN* 3.9 0.6 - - - +
2L ALA* 6.1 1.6 - - + -
3L VAL* 3.9 15.8 + - - +
4L PHE* 3.7 8.8 - - + -
5L ASN* 2.9 58.1 + - - +
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Residues in contact with GLU 71 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J PRO 4.3 6.2 - - - +
22J TYR* 3.8 26.8 - - + +
36J PHE* 4.4 5.9 - - - -
38J SER* 3.5 30.9 + - - -
43J PRO* 6.0 0.2 - - - +
67J ALA 3.0 15.6 + - - +
68J LYS* 3.6 27.9 + - - +
69J GLY 3.2 0.2 - - - -
70J GLN* 1.3 76.7 - - - +
72J GLN* 1.3 61.4 + - - +
74J PHE* 3.2 3.3 + - - +
75J ARG* 2.9 64.1 + - + +
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Residues in contact with GLN 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68J LYS 3.5 12.8 + - - +
69J GLY* 3.1 10.6 + - - +
71J GLU* 1.3 77.9 - - - +
73J TRP* 1.3 66.1 + - - +
75J ARG* 3.1 46.8 + - - +
76J VAL* 2.9 34.3 + - + +
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Residues in contact with TRP 73 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69J GLY 3.0 12.2 + - - +
70J GLN* 3.3 16.2 - - - +
72J GLN* 1.3 77.1 - - - +
74J PHE* 1.3 74.2 + + - +
76J VAL* 4.0 1.7 - - - +
77J SER* 2.9 49.7 + - - -
95J LEU* 4.3 9.2 - - + -
116J PHE* 3.6 29.6 - + - -
147J TRP* 4.1 5.2 - + - -
156J TYR* 4.6 0.7 - - - -
4L PHE* 6.4 1.6 - + + -
5L ASN* 3.4 39.7 - - + +
6L PHE 3.0 27.4 + - - -
7L ALA 3.1 23.0 + - - -
8L THR* 3.6 25.0 - - + +
9L MET* 4.1 13.9 - - + -
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Residues in contact with PHE 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J GLU* 3.6 26.7 - - + -
10J THR 4.8 0.2 - - - -
11J ALA* 3.5 33.7 - - + -
22J TYR* 3.7 13.5 - + + -
70J GLN* 2.9 31.3 + - - +
71J GLU 3.7 5.2 - - - +
72J GLN 3.2 0.2 - - - -
73J TRP* 1.3 89.6 - + - +
75J ARG* 1.3 65.8 + - - +
77J SER* 3.8 2.0 - - - -
78J LEU* 2.9 30.5 + - - +
95J LEU* 3.7 40.4 - - + +
97J GLN* 3.2 44.9 - - + -
116J PHE* 5.3 0.4 - + - -
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Residues in contact with ARG 75 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J GLU* 3.4 49.3 + - - +
20J PRO* 4.0 22.9 + - + +
71J GLU* 2.9 41.5 + - + +
72J GLN* 3.1 44.4 + - - +
74J PHE* 1.3 77.8 - - - +
76J VAL* 1.3 65.2 + - + +
78J LEU* 3.3 9.5 + - - +
79J ARG* 3.1 23.5 + - - +
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Residues in contact with VAL 76 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72J GLN* 2.9 24.7 + - + +
73J TRP 4.0 2.7 - - - +
75J ARG* 1.3 79.9 - - + +
77J SER* 1.3 56.5 + - - +
79J ARG* 3.2 11.1 + - - +
80J ASN* 2.9 45.2 + - - +
8L THR* 3.8 18.8 - - + +
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Residues in contact with SER 77 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73J TRP* 2.9 35.9 + - - -
74J PHE 3.8 0.4 - - - -
76J VAL* 1.3 76.1 - - - +
78J LEU* 1.3 56.8 + - - +
80J ASN* 3.1 11.1 + - - +
81J LEU* 2.9 36.1 + - - +
95J LEU* 3.6 15.0 - - - -
8L THR* 3.5 4.0 - - - -
9L MET* 3.1 37.1 + - - +
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Residues in contact with LEU 78 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J ALA* 3.7 27.8 - - + +
13J SER* 4.9 13.5 - - - +
20J PRO* 3.9 26.7 - - + -
74J PHE 2.9 21.2 + - - +
75J ARG* 3.4 4.7 - - - +
77J SER* 1.3 75.3 - - - +
79J ARG* 1.3 61.0 + - - +
81J LEU* 3.4 5.2 + - - +
82J LEU* 3.2 25.7 + - - +
93J HIS* 4.9 3.8 - - + -
94J THR 4.3 4.5 - - - +
95J LEU* 3.4 36.6 - - + +
118J TYR* 4.2 19.7 + - + -
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Residues in contact with ARG 79 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75J ARG 3.1 11.3 + - - +
76J VAL* 3.2 13.2 - - - +
78J LEU* 1.3 77.2 - - - +
80J ASN* 1.3 69.5 + - - +
82J LEU* 3.1 29.8 + - + +
83J GLY* 3.3 4.2 + - - -
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Residues in contact with ASN 80 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76J VAL* 2.9 31.9 + - - +
77J SER* 3.1 7.1 + - - +
79J ARG* 1.3 77.9 - - - +
81J LEU* 1.3 58.3 + - - +
83J GLY* 3.2 4.7 + - - -
84J TYR* 3.0 45.7 + - + -
146J LYS* 3.7 5.6 - - - +
8L THR* 3.4 18.6 + - - -
9L MET* 2.7 29.5 + - - +
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Residues in contact with LEU 81 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77J SER 2.9 20.4 + - - +
78J LEU* 3.7 5.8 - - - +
79J ARG 3.2 0.2 - - - -
80J ASN* 1.3 73.7 - - - +
82J LEU* 1.3 65.4 + - - +
84J TYR* 3.2 8.2 + - + -
85J TYR* 3.0 36.7 + - + +
87J GLN* 4.2 2.0 - - - -
95J LEU* 4.0 24.7 - - + -
118J TYR* 3.6 39.3 - - + -
123J TYR* 3.4 46.4 - - + +
9L MET* 4.1 15.0 - - + -
----------------------------------------------------------
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Residues in contact with LEU 82 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78J LEU 3.2 13.8 + - - +
79J ARG* 3.1 21.3 + - + +
81J LEU* 1.3 76.9 - - - +
83J GLY* 1.3 61.6 + - - +
85J TYR 3.5 0.2 + - - -
86J ASN* 3.1 18.2 + - - -
87J GLN* 3.1 50.0 + - + +
88J SER 4.1 11.7 - - - +
89J ALA* 5.8 2.5 - - - -
93J HIS* 3.6 32.5 - - + +
118J TYR* 3.9 4.0 - - - +
----------------------------------------------------------
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Residues in contact with GLY 83 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79J ARG 3.3 4.9 + - - -
80J ASN 3.2 7.5 + - - -
82J LEU* 1.3 78.0 - - - +
84J TYR* 1.3 67.2 + - - +
86J ASN* 3.1 14.4 + - - +
----------------------------------------------------------
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Residues in contact with TYR 84 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80J ASN* 3.0 30.8 + - + +
81J LEU* 3.2 14.6 + - + +
83J GLY* 1.3 77.3 - - - +
85J TYR* 1.3 62.2 + - + +
86J ASN* 3.7 0.9 + - - +
123J TYR* 3.3 18.4 - - - -
139J ALA* 4.0 28.6 - - + +
142J ILE* 3.8 39.0 - - + +
143J THR* 3.5 9.4 - - - -
146J LYS* 3.5 10.7 + - - +
9L MET* 2.7 41.4 + - - -
----------------------------------------------------------
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Residues in contact with TYR 85 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81J LEU* 3.0 26.5 + - + +
84J TYR* 1.3 77.7 - - + +
86J ASN* 1.3 71.5 + - - +
87J GLN* 3.0 27.0 + - + +
118J TYR* 3.6 31.5 - + - +
123J TYR* 3.3 32.6 - + - -
137J ASP* 2.6 32.8 + - + +
139J ALA* 3.6 20.6 - - + +
----------------------------------------------------------
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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