Contacts of the helix formed by residues 94 - 123 (chain Y) in PDB entry 2BKC
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 94 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93Y LYS* 1.3 77.5 - - - +
95Y MET* 1.3 62.0 + - - +
96Y ASP* 3.4 18.2 - - + +
97Y GLN* 3.1 44.6 + - + +
98Y LEU* 3.1 24.5 + - - +
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Residues in contact with MET 95 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Q HIS* 6.1 2.7 - - + +
34Y MET* 3.7 43.7 - - + -
35Y ARG 3.1 39.6 + - - +
36Y GLY* 4.5 3.1 - - - -
38Y ASN* 4.1 11.7 - - + +
39Y PHE 3.8 22.9 - - - +
42Y LEU* 4.0 24.0 - - + -
94Y THR* 1.3 75.2 + - - +
96Y ASP* 1.3 63.7 + - - +
98Y LEU* 3.7 7.9 + - - +
99Y MET* 3.1 33.7 + - - +
149Y PHE* 4.3 9.6 - - + -
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Residues in contact with ASP 96 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Q HIS* 3.2 29.4 + - - -
94Y THR* 3.2 13.1 - - + +
95Y MET* 1.3 77.4 - - - +
97Y GLN* 1.3 58.1 + - - +
99Y MET* 3.2 2.6 + - - +
100Y GLU* 2.9 46.2 + - - +
149Y PHE* 3.9 7.4 - - - -
150Y LEU* 3.8 26.3 - - + +
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Residues in contact with GLN 97 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92Y PRO 4.5 2.1 - - - +
93Y LYS* 3.6 21.8 - - + +
94Y THR* 3.1 44.5 + - + +
96Y ASP* 1.3 75.3 - - - +
98Y LEU* 1.3 61.4 + - - +
100Y GLU* 3.3 21.7 + - - +
101Y ASP* 3.1 22.0 + - - +
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Residues in contact with LEU 98 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29Y GLN* 5.6 7.0 - - + +
30Y ILE* 3.8 40.5 - - + +
33Y TYR* 4.7 4.7 - - + +
34Y MET* 4.0 34.1 - - + +
35Y ARG 5.2 0.4 - - - +
89Y TYR* 4.4 15.9 - - + -
93Y LYS* 4.3 23.8 - - + +
94Y THR 3.1 20.2 + - - +
95Y MET* 3.9 8.5 - - - +
97Y GLN* 1.3 77.6 - - - +
99Y MET* 1.3 60.4 + - + +
101Y ASP* 3.2 9.5 + - + +
102Y LEU* 2.9 24.6 + - - +
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Residues in contact with MET 99 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Y ILE* 3.7 30.1 - - + -
34Y MET* 4.6 4.5 - - + -
42Y LEU* 4.1 17.5 - - + -
46Y MET* 4.3 12.8 - - + -
95Y MET* 3.1 21.3 - - + +
96Y ASP 3.2 5.4 + - - +
98Y LEU* 1.3 77.7 - - + +
100Y GLU* 1.3 61.1 + - - +
102Y LEU* 3.3 8.4 - - + +
103Y VAL* 2.8 34.9 + - + +
146Y PHE* 3.8 33.2 - - + -
149Y PHE* 3.9 18.2 - - + -
150Y LEU* 3.9 17.3 - - + -
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Residues in contact with GLU 100 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96Y ASP* 2.9 33.0 + - - +
97Y GLN* 3.4 24.9 - - - +
99Y MET* 1.3 77.0 - - - +
101Y ASP* 1.3 56.4 + - - +
103Y VAL* 4.1 5.6 - - - +
104Y GLY* 2.9 26.3 + - - -
150Y LEU* 4.4 15.4 - - + +
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Residues in contact with ASP 101 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Y LYS* 3.0 36.3 + - + +
29Y GLN* 5.0 4.2 + - - -
30Y ILE* 5.3 2.1 - - + +
97Y GLN 3.1 12.6 + - - +
98Y LEU* 3.5 12.6 - - + +
99Y MET 3.2 0.2 - - - -
100Y GLU* 1.3 73.6 - - - +
102Y LEU* 1.3 67.1 + - - +
104Y GLY* 3.8 1.4 - - - -
105Y THR* 2.9 33.5 + - - -
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Residues in contact with LEU 102 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Y PHE* 3.5 33.7 - - + -
26Y LYS* 5.4 0.9 - - - -
27Y ILE* 4.7 4.3 - - + -
30Y ILE* 4.1 17.9 - - + +
46Y MET* 3.9 9.6 - - + -
49Y LEU* 3.6 28.0 - - + -
98Y LEU 2.9 13.3 + - - +
99Y MET* 3.2 14.1 + - + +
101Y ASP* 1.3 80.4 - - - +
103Y VAL* 1.3 57.2 + - - +
105Y THR* 3.1 3.9 + - - -
106Y LEU* 3.0 28.0 + - + +
146Y PHE* 3.8 36.3 - - + -
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Residues in contact with VAL 103 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99Y MET 2.8 21.9 + - - +
100Y GLU* 4.1 4.7 - - - +
102Y LEU* 1.3 69.9 - - - +
104Y GLY* 1.3 61.6 + - - +
106Y LEU* 3.2 13.0 + - + +
107Y GLU* 2.9 38.5 + - - +
143Y ILE* 4.6 8.4 - - + +
146Y PHE* 3.3 41.3 - - + -
147Y LYS* 3.7 35.7 - - + +
150Y LEU* 4.4 7.4 - - + -
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Residues in contact with GLY 104 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100Y GLU 2.9 18.4 + - - -
101Y ASP* 3.8 1.3 - - - -
103Y VAL* 1.3 76.1 - - - +
105Y THR* 1.3 59.3 + - - +
107Y GLU* 3.5 17.1 + - - +
108Y LEU* 3.2 20.6 + - - +
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Residues in contact with THR 105 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Y PHE* 3.6 33.2 - - + -
26Y LYS* 3.7 16.4 - - - -
84Y VAL* 3.9 32.1 - - + +
101Y ASP* 2.9 18.0 + - - -
102Y LEU* 3.4 8.7 - - - -
104Y GLY* 1.3 74.0 - - - +
106Y LEU* 1.3 62.4 + - - +
107Y GLU 3.2 0.2 - - - -
108Y LEU* 3.3 9.9 + - + +
109Y LEU* 3.1 25.6 + - + +
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Residues in contact with LEU 106 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Y PHE* 4.0 16.1 - - + -
49Y LEU* 5.4 1.8 - - + -
53Y PHE* 3.8 31.6 - - + -
102Y LEU* 3.0 27.0 + - + +
103Y VAL* 3.2 15.0 + - + +
105Y THR* 1.3 74.1 - - - +
107Y GLU* 1.3 58.6 + - - +
109Y LEU* 3.9 5.2 - - + +
110Y ARG* 2.9 28.9 + - - +
139Y ILE* 3.5 18.5 - - + +
142Y HIS* 4.1 26.7 - - + +
143Y ILE* 3.7 21.8 - - + +
146Y PHE* 4.5 11.0 - - + -
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Residues in contact with GLU 107 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103Y VAL* 2.9 22.8 + - + +
104Y GLY* 3.5 19.5 + - - +
105Y THR 3.2 0.2 - - - -
106Y LEU* 1.3 73.4 - - - +
108Y LEU* 1.3 65.8 + - - +
110Y ARG* 3.6 28.1 + - - +
111Y ASP* 3.1 33.5 + - - +
143Y ILE* 4.0 15.0 - - + +
147Y LYS* 3.5 25.8 + - - -
154Y PRO 4.6 0.9 - - - +
156Y GLU* 3.6 22.6 - - - +
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Residues in contact with LEU 108 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Y ASN* 4.5 1.6 - - - +
83Y SER* 3.9 25.8 - - - +
84Y VAL* 4.0 24.7 - - + -
85Y GLU* 5.5 6.1 - - + +
104Y GLY 3.2 10.4 + - - +
105Y THR* 3.3 10.9 + - + +
107Y GLU* 1.3 78.2 - - - +
109Y LEU* 1.3 62.8 + - + +
111Y ASP* 3.2 6.6 + - - +
112Y GLU* 2.8 58.3 + - + +
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Residues in contact with LEU 109 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16Y GLN* 3.7 23.1 - - - +
19Y ASN* 3.8 23.6 - - + +
20Y LEU* 4.5 13.7 - - + -
23Y PHE* 3.9 35.4 - - + -
53Y PHE* 4.9 5.4 - - + -
84Y VAL* 4.5 4.9 - - + -
105Y THR* 3.1 23.0 + - + +
106Y LEU* 4.1 7.0 - - + +
107Y GLU 3.4 0.2 - - - -
108Y LEU* 1.3 77.2 - - + +
110Y ARG* 1.3 57.4 + - - +
112Y GLU* 4.4 3.1 - - - +
113Y TYR* 2.7 51.2 + - + +
139Y ILE* 4.4 11.7 - - + -
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Residues in contact with ARG 110 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106Y LEU 2.9 19.3 + - - +
107Y GLU* 3.6 30.8 + - - +
109Y LEU* 1.3 76.7 - - - +
111Y ASP* 1.3 84.3 + - - +
113Y TYR* 3.4 6.0 + - - +
114Y LYS* 3.1 26.7 + - + +
136Y LYS* 4.2 21.5 - - + +
139Y ILE* 3.8 16.5 - - + +
140Y ASP* 3.2 26.0 + - - +
143Y ILE* 4.1 17.4 - - + +
154Y PRO 5.5 0.8 + - - -
155Y LEU* 3.8 26.9 - - - +
156Y GLU* 5.6 2.4 + - - -
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Residues in contact with ASP 111 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107Y GLU* 3.1 21.1 + - - +
108Y LEU* 3.9 4.6 - - - +
110Y ARG* 1.3 104.4 + - - +
112Y GLU* 1.3 66.1 + - + +
114Y LYS* 3.5 12.0 + - - +
115Y GLN* 3.4 22.7 + - - +
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Residues in contact with GLU 112 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Y PHE* 3.1 12.6 - - + -
15Y HIS* 3.3 9.7 + - - -
16Y GLN* 3.0 27.4 + - - +
19Y ASN* 3.0 13.3 + - - -
83Y SER* 2.4 30.9 + - - -
108Y LEU* 2.8 30.5 + - + +
109Y LEU* 3.9 5.8 - - - +
111Y ASP* 1.3 76.1 - - + +
113Y TYR* 1.3 58.9 + - - +
115Y GLN* 3.1 10.0 + - + +
116Y GLY 3.0 22.2 + - - -
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Residues in contact with TYR 113 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Y PHE* 3.9 16.2 - + - -
16Y GLN* 3.7 31.0 - - + +
20Y LEU* 3.5 24.3 - - - +
56Y GLN* 3.0 18.3 + - - -
60Y VAL* 4.9 1.4 - - + +
109Y LEU* 2.7 31.5 + - + +
110Y ARG* 3.6 5.8 - - - +
112Y GLU* 1.3 70.2 - - - +
114Y LYS* 1.3 53.3 + - - +
116Y GLY* 3.2 1.4 + - - -
117Y ILE* 2.7 40.7 + - - +
132Y LEU* 4.2 21.9 - - + +
135Y PHE* 3.6 38.5 - + + -
136Y LYS* 4.5 9.0 - - + -
139Y ILE* 3.6 25.8 - - + -
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Residues in contact with LYS 114 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124S GLY 4.8 6.3 - - - +
126S ASP* 3.4 23.4 + - - +
110Y ARG* 3.1 13.2 + - + +
111Y ASP* 3.7 14.6 - - - +
112Y GLU 3.3 0.4 - - - -
113Y TYR* 1.3 74.8 - - - +
115Y GLN* 1.3 60.1 + - + +
117Y ILE* 3.2 23.0 + - + +
118Y GLU* 3.0 35.2 + - - +
136Y LYS* 3.9 29.6 - - + +
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Residues in contact with GLN 115 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Y PHE* 4.7 3.6 - - + -
111Y ASP 3.4 12.0 + - - +
112Y GLU* 3.1 11.5 + - - +
114Y LYS* 1.3 78.5 - - + +
116Y GLY* 1.3 58.9 + - - +
118Y GLU* 3.2 21.6 + - - +
119Y LEU* 2.8 33.9 + - - +
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Residues in contact with GLY 116 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Y PHE* 3.5 36.4 - - - -
112Y GLU 3.0 10.9 + - - -
113Y TYR 3.2 4.0 + - - -
115Y GLN* 1.3 77.2 - - - +
117Y ILE* 1.3 55.8 + - - +
119Y LEU* 3.8 4.1 - - - +
120Y THR* 2.8 32.6 + - - +
132Y LEU* 3.5 8.2 - - - +
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Residues in contact with ILE 117 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126S ASP* 3.9 19.3 - - + +
113Y TYR 2.7 28.8 + - - +
114Y LYS* 3.2 24.4 + - + +
116Y GLY* 1.3 73.0 - - - +
118Y GLU* 1.3 60.6 + - - +
120Y THR* 3.1 12.4 - - - +
121Y ASP* 3.2 6.1 + - + +
129Y ASN* 2.8 33.8 + - - +
132Y LEU* 3.8 30.3 - - + +
133Y ILE* 3.6 28.3 - - + -
136Y LYS* 4.1 23.6 - - + -
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Residues in contact with GLU 118 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114Y LYS* 3.0 27.5 + - - +
115Y GLN* 3.6 24.2 + - - +
117Y ILE* 1.3 74.4 - - - +
119Y LEU* 1.3 64.7 + - - +
121Y ASP* 3.2 8.4 + - - +
122Y LYS* 3.1 26.7 + - - +
----------------------------------------------------------
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Residues in contact with LEU 119 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Y VAL* 3.7 33.2 - - + +
8Y ASP 3.6 22.0 - - - +
9Y THR* 4.4 3.4 - - - +
12Y PHE* 3.8 19.5 - - + -
115Y GLN 2.8 20.8 + - - +
116Y GLY* 3.8 2.9 - - - +
118Y GLU* 1.3 72.6 - - - +
120Y THR* 1.3 63.2 + - - +
122Y LYS* 3.1 38.1 + - + +
123Y GLU* 3.2 33.9 + - - +
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Residues in contact with THR 120 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Y THR* 3.9 18.4 - - - -
116Y GLY 2.8 32.6 + - - +
117Y ILE* 3.1 15.7 - - - +
119Y LEU* 1.3 73.9 - - - +
121Y ASP* 1.3 60.0 + - - +
123Y GLU 3.7 0.8 + - - +
124Y GLY 3.3 2.4 + - - -
125Y ASP* 2.6 57.3 + - - +
128Y THR* 4.0 5.8 - - - -
129Y ASN* 3.1 32.5 + - - +
132Y LEU* 4.0 8.1 - - + -
----------------------------------------------------------
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Residues in contact with ASP 121 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117Y ILE* 3.2 14.2 + - + +
118Y GLU* 3.2 12.5 + - - +
120Y THR* 1.3 74.1 - - - +
122Y LYS* 1.3 68.7 + - - +
124Y GLY* 3.2 11.7 + - - -
126Y ASP* 5.5 2.9 - - - +
129Y ASN* 4.2 13.9 - - - +
----------------------------------------------------------
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Residues in contact with LYS 122 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Y VAL 5.3 3.0 + - - -
118Y GLU 3.1 21.9 + - - +
119Y LEU* 3.3 29.9 - - + +
121Y ASP* 1.3 77.4 - - - +
123Y GLU* 1.3 63.2 + - - +
124Y GLY* 3.1 6.4 + - - -
----------------------------------------------------------
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Residues in contact with GLU 123 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Y ASP* 3.1 21.6 - - - +
9Y THR* 2.8 53.4 + - - +
119Y LEU* 3.2 21.2 + - + +
120Y THR 4.2 2.7 - - - +
121Y ASP 3.4 0.2 - - - -
122Y LYS* 1.3 83.3 + - + +
124Y GLY* 1.3 60.0 + - - +
125Y ASP* 3.2 9.0 + - + +
----------------------------------------------------------
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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