Contacts of the helix formed by residues 55 - 84 (chain J) in PDB entry 2XQL
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 55 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I ARG* 4.7 6.1 - - - +
78I ILE 3.0 14.4 + - - +
79I ILE* 3.7 22.0 - - - +
80I PRO* 3.7 2.8 - - - +
54J ILE* 1.3 75.4 - - - +
56J SER* 1.3 55.3 + - - +
57J LYS* 3.9 6.0 + - - +
58J ALA* 3.0 25.2 + - - +
59J MET* 2.7 34.1 + - - +
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Residues in contact with SER 56 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54J ILE 3.9 0.4 + - - -
55J SER* 1.3 72.9 - - - +
57J LYS* 1.3 57.8 + - - +
59J MET* 3.1 10.5 + - - +
60J GLY* 2.9 24.8 + - - -
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Residues in contact with LYS 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G GLU* 4.3 1.4 + - - -
80I PRO* 4.1 17.7 - - + -
103I ALA* 5.2 4.5 - - + +
104I GLN* 3.0 39.1 - - + +
55J SER* 3.2 7.1 - - - +
56J SER* 1.3 77.9 - - - +
58J ALA* 1.3 62.1 + - - +
60J GLY* 3.2 10.3 + - - +
61J ILE* 3.3 16.2 + - + +
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Residues in contact with ALA 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I ILE 3.2 18.8 - - - +
79I ILE* 4.0 1.1 - - - -
80I PRO* 3.7 21.9 - - + +
83I LEU* 3.6 13.5 - - + +
54J ILE* 3.7 11.9 - - + -
55J SER* 3.0 24.5 + - - +
57J LYS* 1.3 75.1 - - - +
59J MET* 1.3 64.6 + - - +
61J ILE* 3.2 5.7 + - - +
62J MET* 3.1 20.4 + - - +
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Residues in contact with MET 59 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J SER* 3.5 43.7 - - - +
41J VAL* 3.2 43.3 - - + -
42J TYR* 3.8 12.1 - - + +
54J ILE* 4.0 26.7 - - + +
55J SER 2.7 14.8 + - - +
56J SER* 3.2 14.4 - - - +
58J ALA* 1.3 76.0 - - - +
60J GLY* 1.3 64.9 + - - +
62J MET* 3.3 4.6 + - - +
63J ASN* 3.0 32.1 + - - +
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Residues in contact with GLY 60 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J SER 2.9 13.3 + - - -
57J LYS* 3.2 5.6 + - - -
58J ALA 3.1 0.8 - - - -
59J MET* 1.3 76.6 - - - +
61J ILE* 1.3 62.6 + - - +
63J ASN* 3.2 9.9 + - - +
64J SER* 3.0 23.0 + - - -
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Residues in contact with ILE 61 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I PRO* 3.4 24.7 - - + -
83I LEU* 3.5 17.3 - - + -
102I ILE* 3.2 49.1 - - + -
103I ALA* 3.4 27.4 - - + +
57J LYS* 3.3 7.9 + - + +
58J ALA 3.2 7.6 + - - +
59J MET 3.2 0.2 - - - -
60J GLY* 1.3 74.6 - - - +
62J MET* 1.3 60.5 + - - +
64J SER* 2.8 26.4 + - - -
65J PHE* 2.9 14.9 + - + +
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Residues in contact with MET 62 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I THR* 3.7 32.8 - - + +
62I ILE* 3.4 39.0 - - + -
63I LEU* 4.1 20.2 - - + -
83I LEU* 4.0 18.2 - - + -
41J VAL* 4.0 21.1 - - + -
54J ILE* 4.2 7.0 - - + -
58J ALA 3.1 13.9 + - - +
59J MET* 3.3 8.7 + - - +
61J ILE* 1.3 77.9 - - - +
63J ASN* 1.3 57.1 + - - +
65J PHE* 3.1 10.9 + - + +
66J VAL* 2.9 35.0 + - + +
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Residues in contact with ASN 63 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36J SER* 3.6 11.1 - - - +
37J TYR* 2.7 40.8 + - - +
38J SER* 3.1 28.3 + - - +
41J VAL* 5.2 0.9 - - - -
59J MET* 3.0 27.1 + - - +
60J GLY* 3.4 11.3 - - - +
61J ILE 3.1 0.2 - - - -
62J MET* 1.3 76.4 - - - +
64J SER* 1.3 63.5 + - - +
66J VAL* 3.3 6.2 + - - +
67J ASN* 3.1 33.2 + - - +
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Residues in contact with SER 64 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H GLU* 4.7 15.2 + - - -
109H HIS* 6.0 0.5 - - - -
60J GLY 3.0 12.6 + - - -
61J ILE* 2.8 13.7 + - - -
63J ASN* 1.3 77.2 - - - +
65J PHE* 1.3 58.5 + - - +
67J ASN* 3.4 4.5 + - - +
68J ASP* 2.8 31.9 + - - +
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Residues in contact with PHE 65 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I LEU* 4.9 1.8 - - - -
58I LEU* 3.7 35.2 - - + -
59I THR* 4.2 11.0 - - - -
62I ILE* 3.9 34.3 - - + -
87I ILE* 5.9 0.7 - - + -
96I LEU* 4.6 4.7 - - + -
97I LEU* 3.9 34.1 - - + -
61J ILE* 2.9 13.5 + - + +
62J MET* 3.3 15.3 - - + +
64J SER* 1.3 75.5 - - - +
66J VAL* 1.3 78.7 + - + +
68J ASP* 3.2 6.0 + - + -
69J ILE* 3.1 50.7 + - + +
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Residues in contact with VAL 66 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I PHE* 3.8 16.2 - - + -
55I LEU* 4.2 14.7 - - + +
59I THR* 3.7 23.3 - - + +
37J TYR* 3.4 49.8 - - + +
41J VAL* 5.7 1.8 - - + -
62J MET* 2.9 24.7 + - + +
63J ASN 3.3 4.0 + - - +
65J PHE* 1.3 83.0 - - + +
67J ASN* 1.3 63.9 + - - +
69J ILE* 3.8 4.3 + - - +
70J PHE* 3.2 21.0 + - - +
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Residues in contact with ASN 67 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I LEU* 5.2 6.3 - - - +
36J SER* 4.9 6.2 + - - -
37J TYR* 3.4 32.4 + - - -
63J ASN* 3.1 23.8 + - - +
64J SER* 3.9 4.7 - - - +
66J VAL* 1.3 74.9 - - - +
68J ASP* 1.3 64.6 + - - +
70J PHE* 3.3 8.4 + - - +
71J GLU* 2.9 38.3 + - + +
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Residues in contact with ASP 68 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108H LYS* 5.4 6.7 + - - -
97I LEU* 5.0 2.1 - - - +
100I VAL* 4.3 10.6 - - - +
64J SER 2.8 20.1 + - - +
65J PHE* 3.2 7.6 + - - +
67J ASN* 1.3 75.5 - - - +
69J ILE* 1.3 63.0 + - + +
71J GLU* 2.9 31.5 + - - +
72J ARG* 2.9 50.3 + - - +
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Residues in contact with ILE 69 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I VAL* 4.7 0.4 - - + -
55I LEU* 3.3 23.8 - - + -
58I LEU* 3.4 26.5 - - + -
96I LEU* 4.9 8.5 - - + -
97I LEU* 4.8 7.0 - - + -
65J PHE* 3.1 45.6 + - + +
66J VAL* 4.3 1.8 - - - +
68J ASP* 1.3 81.0 - - - +
70J PHE* 1.3 58.4 + - - +
72J ARG* 3.7 15.7 - - + +
73J ILE* 3.0 68.7 + - + +
102J LEU* 5.1 4.0 - - + -
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Residues in contact with PHE 70 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I VAL* 4.0 10.5 - - + -
33I LEU* 3.4 39.3 - - + -
34I LEU* 3.7 29.8 - - + -
39I TYR* 4.5 14.6 - + - -
51I LEU* 3.8 17.3 - - + +
55I LEU* 4.0 24.7 - - + -
37J TYR* 4.6 10.8 - - - +
66J VAL 3.2 20.3 + - - +
67J ASN* 3.3 11.7 - - - +
68J ASP 3.0 0.4 + - - -
69J ILE* 1.3 78.0 - - - +
71J GLU* 1.3 67.0 + - + +
73J ILE* 3.3 1.2 + - - +
74J ALA* 2.9 39.7 + - + +
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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
----------------------------------------------------------
108H LYS* 5.3 6.8 + - - -
39I TYR* 4.1 19.3 + - - +
67J ASN* 2.9 25.1 + - + +
68J ASP* 2.9 17.4 + - - +
70J PHE* 1.3 86.3 - - + +
72J ARG* 1.3 56.4 + - + +
74J ALA* 4.2 0.7 - - - +
75J GLY* 3.0 26.0 + - - -
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Residues in contact with ARG 72 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96I LEU* 3.0 46.8 + - - +
97I LEU* 4.0 11.8 - - - +
100I VAL* 4.1 10.7 - - - +
68J ASP* 2.9 46.9 + - - +
69J ILE* 3.7 14.5 - - + +
71J GLU* 1.3 78.3 - - + +
73J ILE* 1.3 62.8 + - + +
75J GLY* 3.3 2.5 + - - -
76J GLU* 3.1 19.4 + - - +
79J ARG* 5.5 0.2 + - - -
101J LEU* 3.3 32.4 + - + +
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Residues in contact with ILE 73 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I LEU* 4.3 18.4 - - + -
54I VAL* 4.2 9.9 - - + -
69J ILE* 3.0 41.5 + - + +
70J PHE 3.9 1.8 - - - +
72J ARG* 1.3 78.0 - - + +
74J ALA* 1.3 60.0 + - - +
76J GLU 3.5 0.7 + - - -
77J ALA* 2.9 26.3 + - - +
94J ILE* 4.1 26.7 - - + +
97J ALA* 3.6 16.5 - - + +
98J VAL* 3.9 21.3 - - + -
101J LEU* 3.5 18.2 - - + -
102J LEU* 4.8 9.2 - - + -
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Residues in contact with ALA 74 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I LEU* 4.0 23.6 - - + -
39I TYR* 3.3 28.8 - - + +
51I LEU* 4.7 4.7 - - + +
70J PHE* 2.9 24.9 + - + +
71J GLU 4.2 0.2 - - - +
73J ILE* 1.3 74.7 - - - +
75J GLY* 1.3 60.8 + - - +
77J ALA* 3.7 7.4 - - - +
78J SER* 3.0 30.5 + - - -
89J ILE* 4.5 0.5 - - - +
94J ILE* 5.6 0.4 - - - -
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Residues in contact with GLY 75 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I TYR* 3.8 11.0 - - - -
71J GLU 3.0 19.0 + - - -
72J ARG 3.3 1.8 + - - -
73J ILE 3.2 0.2 - - - -
74J ALA* 1.3 77.1 - - - +
76J GLU* 1.3 56.0 + - - +
78J SER* 3.3 4.6 + - - -
79J ARG* 2.9 46.0 + - - +
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Residues in contact with GLU 76 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72J ARG 3.1 12.7 + - - +
75J GLY* 1.3 71.9 - - - +
77J ALA* 1.3 57.5 + - - +
79J ARG* 2.6 38.9 + - - +
80J LEU* 2.7 40.6 + - - +
83J TYR* 5.6 2.4 - - - -
97J ALA* 3.9 18.2 - - + -
100J LEU* 3.9 25.4 - - + +
101J LEU* 3.7 30.5 - - + +
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Residues in contact with ALA 77 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73J ILE 2.9 19.4 + - - +
74J ALA* 3.7 7.0 - - - +
75J GLY 3.3 0.2 - - - -
76J GLU* 1.3 76.4 - - - +
78J SER* 1.3 63.6 + - - +
80J LEU* 3.2 5.9 + - - +
81J ALA* 3.1 21.8 + - - +
89J ILE* 4.2 10.5 - - + -
93J GLU* 3.9 23.1 - - + +
94J ILE* 4.0 26.2 - - + -
97J ALA* 3.7 7.9 - - + +
----------------------------------------------------------
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Residues in contact with SER 78 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I TYR* 2.6 45.7 + - - -
74J ALA 3.0 19.1 + - - -
75J GLY* 3.5 5.4 - - - -
77J ALA* 1.3 75.7 - - - +
79J ARG* 1.3 62.5 + - - +
81J ALA* 3.4 2.5 + - - +
82J HIS* 3.2 38.1 + - - -
89J ILE* 3.9 10.9 - - - +
----------------------------------------------------------
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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
----------------------------------------------------------
72J ARG 5.5 0.2 + - - -
75J GLY* 2.9 28.5 + - - +
76J GLU* 2.6 61.8 + - - +
78J SER* 1.3 77.0 - - - +
80J LEU* 1.3 62.2 + - - +
82J HIS* 3.3 7.4 + - - +
83J TYR* 3.1 71.9 + - + +
----------------------------------------------------------
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Residues in contact with LEU 80 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76J GLU* 2.7 26.0 + - - +
77J ALA* 3.3 7.9 - - - +
79J ARG* 1.3 73.6 - - - +
81J ALA* 1.3 60.5 + - - +
83J TYR* 3.5 14.1 + - + +
84J ASN* 3.1 39.0 + - - +
93J GLU* 3.6 27.4 - - + +
96J THR* 3.5 42.2 - - + -
97J ALA* 3.7 9.6 - - + +
100J LEU* 4.4 10.1 - - + -
----------------------------------------------------------
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Residues in contact with ALA 81 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77J ALA 3.1 11.7 + - - +
78J SER* 3.7 8.7 - - - +
79J ARG 3.2 0.4 - - - -
80J LEU* 1.3 75.8 - - - +
82J HIS* 1.3 66.9 + - + +
84J ASN* 3.3 2.4 + - - -
85J LYS 3.2 3.8 + - - -
86J ARG* 2.9 46.6 + - + +
87J SER 5.7 0.2 - - - -
88J THR 4.2 16.2 - - - +
89J ILE* 4.5 10.5 - - + -
93J GLU* 4.4 11.7 - - + -
----------------------------------------------------------
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Residues in contact with HIS 82 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I TYR 3.8 15.4 + - - -
40I ALA* 5.5 1.4 - - - -
78J SER* 3.2 28.0 + - - -
79J ARG* 3.3 8.6 + - - +
81J ALA* 1.3 80.2 - - + +
83J TYR* 1.3 68.7 + - + +
85J LYS* 2.9 22.0 + - - +
86J ARG 4.6 6.7 - - - -
87J SER* 6.3 0.2 - - - -
----------------------------------------------------------
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Residues in contact with TYR 83 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76J GLU* 5.6 2.7 - - - -
79J ARG* 3.1 53.9 + - + +
80J LEU* 3.7 18.6 - - + +
82J HIS* 1.3 81.2 - - + +
84J ASN* 1.3 65.4 + - - +
85J LYS* 3.4 8.5 + - - +
----------------------------------------------------------
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Residues in contact with ASN 84 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80J LEU* 3.1 31.3 + - - +
81J ALA* 3.4 2.0 - - - +
82J HIS 3.2 0.4 - - - -
83J TYR* 1.3 82.9 + - - +
85J LYS* 1.3 70.5 + - - +
86J ARG* 3.0 23.9 + - + +
93J GLU* 5.7 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
------------------------------------------------------------
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