Contacts of the helix formed by residues 94 - 123 (chain S) 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 S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35S ARG 5.3 0.9 - - - -
93S LYS* 1.3 78.2 - - - +
95S MET* 1.3 69.0 + - - +
96S ASP* 3.7 14.2 + - + +
97S GLN* 3.2 45.8 + - + +
98S LEU* 3.2 20.2 + - - +
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Residues in contact with MET 95 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P HIS* 5.5 0.7 - - + +
34S MET* 3.5 42.2 - - + -
35S ARG 3.5 30.9 + - - +
36S GLY* 5.1 1.8 - - - -
38S ASN* 4.1 28.7 - - + +
39S PHE 4.2 1.1 - - - +
42S LEU* 3.4 33.9 - - + -
94S THR* 1.3 77.4 + - - +
96S ASP* 1.3 67.8 + - - +
98S LEU* 3.1 9.9 + - - +
99S MET* 3.0 31.8 + - - +
149S PHE* 4.1 14.4 - - + -
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Residues in contact with ASP 96 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P HIS* 2.8 38.5 + - - -
94S THR* 3.2 13.1 + - + +
95S MET* 1.3 81.1 - - - +
97S GLN* 1.3 55.8 + - + +
99S MET* 3.5 1.0 + - - -
100S GLU* 2.9 37.3 + - - +
149S PHE* 4.4 1.3 - - - -
150S LEU* 3.6 28.9 - - + +
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Residues in contact with GLN 97 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91S LYS* 4.5 18.0 + - - +
92S PRO 5.0 1.2 - - - +
93S LYS* 4.1 26.6 + - + +
94S THR* 3.2 41.2 + - + +
95S MET 3.2 0.4 - - - -
96S ASP* 1.3 75.1 - - + +
98S LEU* 1.3 63.5 + - - +
100S GLU* 3.6 19.5 - - - +
101S ASP* 3.3 20.6 + - - +
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Residues in contact with LEU 98 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29S GLN* 5.6 5.2 - - - +
30S ILE* 3.9 36.1 - - + +
33S TYR* 4.3 5.4 - - + +
34S MET* 3.8 37.7 - - + +
35S ARG 5.1 0.2 - - - +
89S TYR* 4.2 12.3 - - + +
93S LYS* 3.8 36.6 - - + +
94S THR 3.2 15.5 + - - +
95S MET* 3.1 10.7 + - - +
97S GLN* 1.3 72.1 - - - +
99S MET* 1.3 65.9 + - + +
101S ASP* 3.1 10.5 + - + +
102S LEU* 2.9 25.3 + - - +
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Residues in contact with MET 99 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30S ILE* 3.4 35.4 - - + -
34S MET* 4.6 1.1 - - + -
42S LEU* 3.6 25.6 - - + -
46S MET* 4.3 12.3 - - - -
95S MET* 3.0 21.7 + - - +
96S ASP 3.7 4.3 - - - +
98S LEU* 1.3 77.0 - - + +
100S GLU* 1.3 55.3 + - - +
102S LEU* 3.0 7.9 + - + +
103S VAL* 2.8 40.8 + - + +
146S PHE* 3.8 28.9 - - + -
149S PHE* 3.8 21.8 - - + -
150S LEU* 4.1 17.0 - - + -
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Residues in contact with GLU 100 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96S ASP* 2.9 23.6 + - - +
97S GLN* 3.6 29.6 - - - +
98S LEU 3.3 0.4 - - - -
99S MET* 1.3 72.2 - - - +
101S ASP* 1.3 58.5 + - - +
103S VAL* 3.4 3.8 + - - +
104S GLY* 3.0 26.5 + - - -
150S LEU* 4.2 23.6 - - + +
152S LYS* 4.8 18.0 + - - +
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Residues in contact with ASP 101 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26S LYS* 2.2 44.4 + - - +
29S GLN* 5.2 3.1 + - - -
30S ILE* 5.1 3.8 - - + +
85S GLU 5.2 0.3 - - - +
93S LYS* 5.4 9.6 - - - +
97S GLN 3.3 9.2 + - - +
98S LEU* 3.1 12.6 + - + +
100S GLU* 1.3 74.9 - - - +
102S LEU* 1.3 62.5 + - - +
104S GLY* 3.7 1.9 + - - +
105S THR* 3.0 31.7 + - - -
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Residues in contact with LEU 102 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23S PHE* 3.4 36.8 - - + -
26S LYS* 5.6 1.6 - - + -
27S ILE* 4.3 6.3 - - + -
30S ILE* 3.8 24.6 - - + +
46S MET* 4.1 18.6 - - + -
49S LEU* 4.0 22.9 - - + -
98S LEU 2.9 12.8 + - - +
99S MET* 3.0 13.7 + - + +
101S ASP* 1.3 74.3 - - - +
103S VAL* 1.3 58.9 + - - +
105S THR* 3.2 4.7 + - - -
106S LEU* 2.8 44.3 + - + +
146S PHE* 4.2 20.2 - - + -
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Residues in contact with VAL 103 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99S MET 2.8 21.4 + - - +
100S GLU* 3.7 6.7 - - - +
102S LEU* 1.3 71.9 - - + +
104S GLY* 1.3 57.0 + - - +
106S LEU* 3.1 10.9 + - + +
107S GLU* 2.9 50.1 + - + +
143S ILE* 4.9 7.9 - - + +
146S PHE* 3.7 30.3 - - + -
147S LYS* 3.6 32.1 - - + +
150S LEU* 4.2 15.7 - - + -
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Residues in contact with GLY 104 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100S GLU 3.0 16.8 + - - -
101S ASP* 4.0 2.0 - - - -
102S LEU 3.3 0.2 - - - -
103S VAL* 1.3 76.8 - - - +
105S THR* 1.3 57.8 + - - +
107S GLU* 3.4 15.8 + - - +
108S LEU* 3.1 24.8 + - - +
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Residues in contact with THR 105 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23S PHE* 3.9 26.7 - - + -
26S LYS* 3.9 15.3 - - + -
84S VAL* 3.7 36.4 - - + +
85S GLU 5.1 1.0 + - - -
101S ASP* 3.0 22.3 + - - -
102S LEU 3.7 3.6 - - - -
104S GLY* 1.3 74.8 - - - +
106S LEU* 1.3 64.5 + - - +
107S GLU 3.2 0.4 - - - -
108S LEU* 3.3 6.3 + - + +
109S LEU* 3.1 25.3 + - + +
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Residues in contact with LEU 106 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23S PHE* 3.4 31.9 - - + -
49S LEU* 4.9 2.0 - - + -
53S PHE* 4.1 19.3 - - + -
102S LEU* 2.8 37.6 + - + +
103S VAL* 3.1 13.0 + - + +
105S THR* 1.3 78.1 - - - +
107S GLU* 1.3 55.0 + - - +
109S LEU* 3.5 4.9 + - + +
110S ARG* 3.1 20.3 + - - +
139S ILE* 3.3 22.1 - - + +
142S HIS* 3.9 33.0 - - + -
143S ILE* 3.9 14.8 - - + +
146S PHE* 4.6 4.7 - - + -
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Residues in contact with GLU 107 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103S VAL* 2.9 20.7 + - - +
104S GLY* 3.6 17.6 - - - +
105S THR 3.2 0.2 - - - -
106S LEU* 1.3 74.7 - - - +
108S LEU* 1.3 66.2 + - - +
110S ARG* 4.0 22.9 + - - +
111S ASP* 3.1 32.2 + - - +
143S ILE* 4.0 18.5 - - + +
147S LYS* 2.6 33.3 + - - -
154S PRO 4.5 1.6 - - - +
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Residues in contact with LEU 108 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19S ASN* 4.1 3.8 - - - +
83S SER* 4.2 19.7 - - - +
84S VAL* 3.7 32.1 - - + +
85S GLU* 5.8 2.2 - - - +
104S GLY 3.1 16.3 + - - +
105S THR* 3.3 6.7 + - + +
107S GLU* 1.3 79.4 - - - +
109S LEU* 1.3 63.8 + - + +
111S ASP* 3.6 5.1 + - - +
112S GLU* 3.0 48.7 + - + +
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Residues in contact with LEU 109 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16S GLN* 3.8 10.8 - - - +
19S ASN* 3.7 36.1 - - + +
20S LEU* 4.3 15.0 - - + -
23S PHE* 3.4 40.8 - - + -
53S PHE* 4.8 6.5 - - + -
84S VAL* 3.9 10.3 - - + -
105S THR* 3.1 18.0 + - + +
106S LEU* 4.1 7.0 - - + +
108S LEU* 1.3 74.6 - - + +
110S ARG* 1.3 60.3 + - - +
112S GLU* 4.4 3.6 - - - -
113S TYR* 2.8 41.3 + - + -
139S ILE* 4.1 12.1 - - + -
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Residues in contact with ARG 110 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106S LEU 3.1 18.2 + - - +
107S GLU* 3.8 25.5 + - - +
108S LEU 3.3 0.2 - - - -
109S LEU* 1.3 74.3 - - - +
111S ASP* 1.3 78.9 + - - +
113S TYR* 3.1 7.9 + - - +
114S LYS* 2.8 36.7 + - + +
136S LYS* 4.0 20.2 - - + +
139S ILE* 4.0 15.8 - - + +
140S ASP* 3.3 26.2 + - - +
143S ILE* 3.6 28.4 - - - +
154S PRO 4.9 2.2 + - - -
155S LEU* 4.3 23.5 - - - +
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Residues in contact with ASP 111 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107S GLU* 3.1 18.0 + - - +
108S LEU* 3.9 5.6 - - - +
110S ARG* 1.3 105.2 + - - +
112S GLU* 1.3 59.6 + - + +
114S LYS* 3.2 25.7 - - - +
115S GLN* 3.4 14.5 + - - +
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Residues in contact with GLU 112 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12S PHE* 3.2 13.2 - - + -
15S HIS* 3.6 7.9 - - - -
16S GLN* 2.9 27.2 + - - +
19S ASN* 3.1 16.7 + - - -
83S SER* 2.7 25.6 + - - -
108S LEU* 3.0 32.9 + - + +
109S LEU* 3.9 5.2 - - - +
111S ASP* 1.3 75.5 - - + +
113S TYR* 1.3 64.4 + - - +
114S LYS 3.1 1.8 - - - -
115S GLN* 3.2 20.4 + - - +
116S GLY 3.1 16.6 + - - -
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Residues in contact with TYR 113 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12S PHE* 4.2 8.5 - + - -
16S GLN* 3.7 38.5 - - + +
20S LEU* 3.3 23.2 - - - +
56S GLN* 2.7 28.7 + - - -
60S VAL* 5.0 1.0 - - + +
109S LEU* 2.8 27.6 + - + +
110S ARG* 3.6 4.7 - - - +
112S GLU* 1.3 70.3 - - - +
114S LYS* 1.3 64.8 + - - +
116S GLY* 3.3 0.9 + - - -
117S ILE* 3.0 37.9 + - + +
132S LEU* 4.3 18.9 - - + +
135S PHE* 3.5 29.9 - + + -
136S LYS* 4.3 6.1 - - + -
139S ILE* 3.5 27.8 - - + +
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Residues in contact with LYS 114 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124N GLY 5.4 4.0 - - - +
126N ASP* 4.4 12.7 + - - +
110S ARG* 2.8 15.0 + - + +
111S ASP* 3.2 17.5 - - - +
112S GLU 3.1 0.2 - - - -
113S TYR* 1.3 75.6 - - - +
115S GLN* 1.3 61.2 + - + +
117S ILE* 3.3 18.8 + - + +
118S GLU* 3.3 37.2 + - - +
136S LYS* 3.8 31.8 - - + +
----------------------------------------------------------
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Residues in contact with GLN 115 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12S PHE* 4.6 5.2 - - + -
111S ASP* 3.4 14.6 + - - +
112S GLU* 3.2 24.0 + - - +
114S LYS* 1.3 76.9 - - + +
116S GLY* 1.3 58.0 + - - +
118S GLU* 3.5 10.7 - - - +
119S LEU* 2.9 30.2 + - + +
----------------------------------------------------------
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Residues in contact with GLY 116 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12S PHE* 3.6 33.3 - - - -
112S GLU 3.1 10.3 + - - -
113S TYR 3.3 1.9 + - - -
115S GLN* 1.3 73.2 - - - +
117S ILE* 1.3 60.4 + - - +
119S LEU* 4.2 3.8 - - - -
120S THR* 2.9 35.9 + - - -
132S LEU* 3.4 10.0 - - - +
----------------------------------------------------------
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Residues in contact with ILE 117 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126N ASP* 3.5 32.3 - - - +
113S TYR 3.0 32.1 + - - +
114S LYS* 3.5 13.5 - - + +
115S GLN 3.2 0.2 - - - -
116S GLY* 1.3 76.8 - - - +
118S GLU* 1.3 59.5 + - + +
121S ASP* 2.9 27.5 + - + +
129S ASN* 3.0 25.7 + - - +
132S LEU* 3.7 30.1 - - + +
133S ILE* 4.1 18.8 - - + -
136S LYS* 3.9 24.9 - - + -
----------------------------------------------------------
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Residues in contact with GLU 118 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114S LYS* 3.3 31.9 + - - +
115S GLN* 3.5 11.1 - - - +
117S ILE* 1.3 78.6 - - + +
119S LEU* 1.3 58.5 + - - +
121S ASP* 3.6 6.2 + - - +
122S LYS* 2.8 44.1 + - + +
----------------------------------------------------------
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Residues in contact with LEU 119 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7S VAL* 3.5 29.6 - - + +
8S ASP 3.5 25.6 - - - +
9S THR* 4.7 2.9 - - - +
12S PHE* 4.0 25.8 - - + -
115S GLN* 2.9 18.0 + - + +
116S GLY* 3.8 2.9 - - - +
117S ILE 3.2 0.2 - - - -
118S GLU* 1.3 74.5 - - - +
120S THR* 1.3 62.7 + - - +
122S LYS* 3.4 9.9 + - + +
123S GLU* 3.1 38.3 + - + +
----------------------------------------------------------
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Residues in contact with THR 120 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S THR* 3.6 17.9 + - - +
12S PHE* 5.7 2.6 - - - +
116S GLY 2.9 19.9 + - - -
117S ILE 3.7 2.7 - - - -
119S LEU* 1.3 75.0 - - - +
121S ASP* 1.3 63.6 + - - +
123S GLU* 3.6 1.6 + - - +
124S GLY 3.2 2.6 + - - -
125S ASP* 2.8 68.9 + - + +
128S THR* 3.8 15.7 - - - +
129S ASN* 3.1 25.6 - - + +
132S LEU* 4.2 2.6 - - - +
----------------------------------------------------------
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Residues in contact with ASP 121 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117S ILE* 2.9 17.2 + - + +
118S GLU* 3.7 9.9 - - - +
119S LEU 3.3 0.2 - - - -
120S THR* 1.3 77.4 - - - +
122S LYS* 1.3 76.5 + - - +
124S GLY* 3.1 18.5 + - - -
129S ASN* 3.8 15.1 + - - +
----------------------------------------------------------
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Residues in contact with LYS 122 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118S GLU* 2.8 37.7 + - + +
119S LEU* 3.4 10.7 + - + +
120S THR 3.4 0.2 - - - -
121S ASP* 1.3 92.1 + - - +
123S GLU* 1.3 60.6 + - - +
124S GLY 3.3 1.2 + - - -
----------------------------------------------------------
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Residues in contact with GLU 123 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8S ASP* 3.4 18.7 - - - +
9S THR* 2.9 49.6 + - - +
119S LEU* 3.1 23.7 + - + +
120S THR 3.6 3.3 + - - +
121S ASP 3.3 0.4 - - - -
122S LYS* 1.3 76.3 - - - +
124S GLY* 1.3 60.0 + - - +
125S ASP* 3.5 6.4 + - + +
----------------------------------------------------------
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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