Contacts of the helix formed by residues 94 - 124 (chain N) 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 N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35N ARG 5.7 1.3 - - - -
93N LYS* 1.3 76.5 - - - +
95N MET* 1.3 65.6 + - - +
96N ASP* 3.6 10.4 + - - +
97N GLN* 3.2 40.5 + - - +
98N LEU* 3.2 16.4 + - - +
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Residues in contact with MET 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N MET* 3.4 44.4 - - + +
35N ARG 3.4 33.7 + - - +
36N GLY* 4.5 0.9 - - - +
38N ASN* 3.7 38.4 - - + +
39N PHE* 3.7 6.7 - - - +
42N LEU* 3.5 27.1 - - + -
94N THR* 1.3 73.6 - - - +
96N ASP* 1.3 60.9 + - - +
98N LEU* 3.6 7.2 + - - +
99N MET* 3.0 40.1 + - + +
149N PHE* 4.9 4.5 - - + -
37V HIS* 5.5 5.4 - - + -
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Residues in contact with ASP 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94N THR* 3.1 9.5 + - - +
95N MET* 1.3 80.4 - - - +
97N GLN* 1.3 55.3 + - - +
99N MET* 3.5 2.3 + - - +
100N GLU* 3.0 40.1 + - - +
149N PHE* 4.5 4.9 - - - -
150N LEU* 3.7 25.3 - - + +
37V HIS* 3.1 38.2 + - - -
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Residues in contact with GLN 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92N PRO 4.6 2.4 + - - +
93N LYS* 3.7 29.4 - - + +
94N THR* 3.2 41.9 + - - +
96N ASP* 1.3 74.0 - - - +
98N LEU* 1.3 65.9 + - - +
100N GLU* 3.1 31.3 + - - +
101N ASP* 3.2 13.7 + - - +
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Residues in contact with LEU 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N GLN* 5.2 8.1 - - + +
30N ILE* 3.9 40.7 - - + +
33N TYR* 4.4 5.2 - - + +
34N MET* 3.9 33.0 - - + +
35N ARG 5.2 0.2 - - - +
89N TYR* 3.9 28.3 - - + -
93N LYS* 4.1 22.2 - - + +
94N THR 3.2 16.7 + - - +
95N MET* 3.9 5.2 - - - +
97N GLN* 1.3 77.1 - - - +
99N MET* 1.3 65.5 + - + +
101N ASP* 3.3 10.4 + - + +
102N LEU* 3.0 21.3 + - - +
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Residues in contact with MET 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30N ILE* 3.5 31.9 - - + -
34N MET* 4.4 4.7 - - + -
42N LEU* 4.1 21.1 - - + -
46N MET* 4.2 14.6 - - + -
95N MET* 3.0 28.7 + - + +
98N LEU* 1.3 77.2 - - + +
100N GLU* 1.3 55.8 + - - +
102N LEU* 3.3 11.3 + - + +
103N VAL* 2.8 33.2 + - + +
146N PHE* 4.1 27.6 - - + -
149N PHE* 4.1 18.2 - - + -
150N LEU* 3.7 26.0 - - + -
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Residues in contact with GLU 100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96N ASP* 3.0 33.5 + - - +
97N GLN* 3.1 22.4 + - - +
99N MET* 1.3 76.0 - - - +
101N ASP* 1.3 56.4 + - - +
103N VAL* 3.9 6.7 - - - +
104N GLY* 3.0 25.1 + - - -
150N LEU* 4.7 12.7 - - + +
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Residues in contact with ASP 101 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26N LYS* 3.0 40.6 + - - +
29N GLN* 4.7 7.6 + - - -
30N ILE* 5.5 3.0 - - + +
93N LYS* 5.9 1.0 + - - -
97N GLN 3.2 11.0 + - - +
98N LEU* 3.6 13.5 - - + +
99N MET 3.2 0.2 - - - -
100N GLU* 1.3 72.9 - - - +
102N LEU* 1.3 65.7 + - - +
104N GLY* 3.6 1.2 + - - -
105N THR* 2.8 35.5 + - - -
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Residues in contact with LEU 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23N PHE* 3.5 33.4 - - + -
26N LYS* 5.4 1.1 - - - -
27N ILE* 4.7 2.7 - - + -
30N ILE* 3.7 23.7 - - + +
46N MET* 4.1 14.1 - - + -
49N LEU* 4.1 10.1 - - + -
98N LEU 3.0 13.6 + - - +
99N MET* 3.3 15.5 - - + +
101N ASP* 1.3 76.4 - - - +
103N VAL* 1.3 62.1 + - - +
105N THR* 3.2 5.5 + - - -
106N LEU* 3.1 24.5 + - + +
146N PHE* 3.9 44.4 - - + -
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Residues in contact with VAL 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99N MET 2.8 23.1 + - - +
100N GLU* 3.9 5.6 - - - +
102N LEU* 1.3 69.2 - - + +
104N GLY* 1.3 66.5 + - - +
105N THR 3.1 0.2 + - - -
106N LEU* 3.1 12.6 + - + +
107N GLU* 3.0 35.6 + - + +
143N ILE* 5.2 7.0 - - + +
146N PHE* 4.0 24.2 - - + -
147N LYS* 3.8 34.8 - - + -
150N LEU* 3.9 21.1 - - + -
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Residues in contact with GLY 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100N GLU 3.0 20.3 + - - -
101N ASP* 4.0 1.6 - - - -
103N VAL* 1.3 73.2 - - - +
105N THR* 1.3 56.5 + - - +
107N GLU* 3.5 16.0 + - - +
108N LEU* 3.1 28.7 + - - +
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Residues in contact with THR 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23N PHE* 3.4 35.0 - - + -
26N LYS* 3.5 10.1 - - - -
84N VAL* 3.6 29.8 - - + +
101N ASP* 2.8 31.2 + - - -
102N LEU* 3.5 4.7 - - - -
103N VAL 3.1 0.6 - - - -
104N GLY* 1.3 75.0 - - - +
106N LEU* 1.3 63.5 + - - +
108N LEU* 3.3 8.6 + - + +
109N LEU* 3.1 25.4 + - + +
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Residues in contact with LEU 106 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23N PHE* 3.4 33.0 - - + -
49N LEU* 5.0 3.4 - - + -
53N PHE* 3.9 22.2 - - + -
102N LEU* 3.1 23.7 + - + +
103N VAL* 3.7 10.1 - - - +
105N THR* 1.3 77.8 - - - +
107N GLU* 1.3 50.6 + - - +
109N LEU* 3.4 4.7 + - + +
110N ARG* 2.8 34.3 + - - +
139N ILE* 3.5 13.1 - - + +
142N HIS* 3.9 31.6 - - + +
143N ILE* 3.9 15.7 - - + -
146N PHE* 4.3 16.6 - - + -
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Residues in contact with GLU 107 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103N VAL* 3.0 24.8 + - + +
104N GLY* 3.5 17.7 - - - +
106N LEU* 1.3 73.4 - - - +
108N LEU* 1.3 65.1 + - - +
110N ARG* 3.5 30.1 + - - +
111N ASP* 3.1 32.3 + - - +
143N ILE* 4.0 14.2 - - + +
147N LYS* 3.8 26.2 + - - +
154N PRO 4.7 3.6 - - - +
155N LEU 6.0 0.5 - - - -
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Residues in contact with LEU 108 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19N ASN* 4.4 0.4 - - - +
83N SER* 4.0 21.5 - - - +
84N VAL* 4.1 27.4 - - + -
85N GLU* 5.5 2.2 - - - +
104N GLY 3.1 16.7 + - - +
105N THR* 3.5 8.3 - - - +
106N LEU 3.3 0.2 - - - -
107N GLU* 1.3 78.2 - - - +
109N LEU* 1.3 59.6 + - - +
111N ASP* 3.3 4.4 + - - +
112N GLU* 3.0 56.6 + - + +
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Residues in contact with LEU 109 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16N GLN* 3.5 22.9 - - - +
19N ASN* 3.9 24.5 - - + +
20N LEU* 3.9 18.4 - - + -
23N PHE* 3.7 38.6 - - + -
53N PHE* 4.5 7.9 - - + -
84N VAL* 4.1 9.0 - - + -
105N THR* 3.1 21.8 + - + +
106N LEU* 3.8 5.8 - - - +
108N LEU* 1.3 73.6 - - + +
110N ARG* 1.3 66.9 + - - +
112N GLU* 4.5 2.0 - - - +
113N TYR* 3.0 35.9 + - + -
139N ILE* 4.0 13.2 - - + -
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Residues in contact with ARG 110 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106N LEU 2.8 22.1 + - - +
107N GLU* 3.5 31.4 + - - +
108N LEU 3.3 0.2 - - - -
109N LEU* 1.3 74.2 - - - +
111N ASP* 1.3 80.8 + - - +
113N TYR* 3.5 5.8 + - - +
114N LYS* 3.2 22.6 + - + +
136N LYS* 4.2 22.7 - - + +
139N ILE* 3.9 14.8 - - + +
140N ASP* 3.3 25.3 + - - +
143N ILE* 4.0 18.7 - - + +
154N PRO 5.1 1.4 + - - -
155N LEU* 4.0 25.1 - - - +
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Residues in contact with ASP 111 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107N GLU* 3.1 16.8 + - - +
108N LEU* 3.9 4.3 - - - +
110N ARG* 1.3 104.5 + - - +
112N GLU* 1.3 68.5 + - + +
113N TYR 3.2 0.2 - - - -
114N LYS* 3.3 13.1 - - + +
115N GLN* 3.3 20.6 + - - +
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Residues in contact with GLU 112 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N PHE* 3.1 13.7 - - + -
15N HIS* 3.3 9.2 - - - -
16N GLN* 2.9 21.3 + - - +
19N ASN* 2.8 25.4 + - - -
83N SER* 2.5 27.8 + - - -
108N LEU* 3.0 30.9 + - + +
109N LEU* 4.1 3.6 - - - +
111N ASP* 1.3 79.3 - - - +
113N TYR* 1.3 56.4 + - - +
115N GLN* 3.1 8.7 + - + +
116N GLY 3.0 22.7 + - - -
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Residues in contact with TYR 113 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N PHE* 4.0 6.7 - + - -
16N GLN* 3.4 36.2 - - + +
20N LEU* 3.4 27.8 - - + +
56N GLN* 3.1 18.4 + - - -
60N VAL* 5.0 1.0 - - + +
109N LEU* 3.0 32.6 + - + +
110N ARG* 3.7 5.6 - - - +
112N GLU* 1.3 76.4 - - - +
114N LYS* 1.3 52.6 + - - +
116N GLY* 3.0 1.7 + - - -
117N ILE* 2.8 48.5 + - + +
132N LEU* 4.0 19.5 - - + +
135N PHE* 3.4 44.1 - + + -
136N LYS* 4.3 8.5 - - + -
139N ILE* 4.0 14.8 - - + -
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Residues in contact with LYS 114 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110N ARG* 3.2 12.5 + - + +
111N ASP* 3.3 17.3 - - + +
113N TYR* 1.3 76.7 - - - +
115N GLN* 1.3 56.3 + - - +
117N ILE* 3.5 10.8 + - + +
118N GLU* 3.1 50.9 + - + +
136N LYS* 4.6 19.0 - - + +
124Y GLY* 3.6 25.9 + - - -
126Y ASP* 3.9 12.0 + - - +
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Residues in contact with GLN 115 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7N VAL* 5.5 7.1 + - - +
12N PHE* 4.5 7.1 - - + -
111N ASP 3.3 8.5 + - - +
112N GLU* 3.1 12.9 + - + +
114N LYS* 1.3 76.0 - - - +
116N GLY* 1.3 60.3 + - - +
118N GLU* 3.3 13.8 + - - +
119N LEU* 3.0 37.6 + - - +
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Residues in contact with GLY 116 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N PHE* 3.3 36.0 - - - -
112N GLU 3.0 11.3 + - - -
113N TYR 3.0 2.0 + - - -
115N GLN* 1.3 76.2 - - - +
117N ILE* 1.3 57.6 + - - +
119N LEU* 3.5 5.0 + - - +
120N THR* 3.0 35.7 + - - +
132N LEU* 3.6 6.7 - - - -
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Residues in contact with ILE 117 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113N TYR* 2.8 25.2 + - + +
114N LYS* 3.7 12.8 - - + +
116N GLY* 1.3 74.3 - - - +
118N GLU* 1.3 66.4 + - + +
120N THR* 3.6 5.6 - - - -
121N ASP* 3.1 11.5 + - + +
129N ASN* 3.0 31.8 + - - +
132N LEU* 3.6 23.3 - - + +
133N ILE* 3.8 33.0 - - + +
136N LYS* 4.4 16.6 - - + -
126Y ASP* 3.7 30.1 - - + +
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Residues in contact with GLU 118 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114N LYS* 3.1 44.3 + - - +
115N GLN* 3.3 14.9 + - - +
117N ILE* 1.3 77.3 - - + +
119N LEU* 1.3 62.0 + - - +
121N ASP* 3.6 6.8 + - - +
122N LYS* 3.4 26.2 + - - +
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Residues in contact with LEU 119 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7N VAL* 3.7 40.2 - - + +
8N ASP 3.8 30.7 - - - +
9N THR* 4.1 7.2 - - - +
12N PHE* 4.3 14.6 - - + -
115N GLN* 3.0 24.6 + - - +
116N GLY 3.6 5.2 - - - +
117N ILE 3.2 0.2 - - - -
118N GLU* 1.3 76.7 - - - +
120N THR* 1.3 60.2 + - + +
122N LYS* 3.5 3.6 + - - +
123N GLU* 3.1 32.6 + - - +
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Residues in contact with THR 120 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9N THR* 3.7 24.5 - - + +
12N PHE* 5.8 2.5 - - + -
116N GLY* 3.0 26.2 + - - +
117N ILE* 3.6 1.0 - - - -
119N LEU* 1.3 75.2 - - + +
121N ASP* 1.3 59.7 + - - +
123N GLU* 3.7 1.5 - - - -
124N GLY* 2.9 23.4 + - - -
125N ASP* 3.0 20.2 + - + +
128N THR* 4.0 17.5 - - + -
129N ASN* 2.7 43.4 + - - -
132N LEU* 4.0 13.9 - - + -
----------------------------------------------------------
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Residues in contact with ASP 121 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117N ILE* 3.1 20.2 + - + +
118N GLU* 3.6 8.5 - - - +
119N LEU 3.2 0.2 - - - -
120N THR* 1.3 80.6 + - - +
122N LYS* 1.3 71.0 + - + +
124N GLY* 3.6 8.7 + - - -
129N ASN* 3.5 15.7 + - - +
----------------------------------------------------------
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Residues in contact with LYS 122 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118N GLU 3.4 17.0 + - - +
119N LEU* 3.5 3.8 + - - +
120N THR 3.3 0.4 - - - -
121N ASP* 1.3 89.3 + - - +
123N GLU* 1.3 65.2 + - - +
124N GLY* 3.2 2.3 + - - -
----------------------------------------------------------
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Residues in contact with GLU 123 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7N VAL 4.8 1.4 - - - +
8N ASP* 3.6 13.9 - - - +
9N THR* 3.1 45.8 + - - +
119N LEU* 3.1 20.3 + - - +
120N THR 4.2 2.7 - - - +
122N LYS* 1.3 77.8 - - - +
124N GLY* 1.3 58.9 + - - +
125N ASP* 3.4 6.2 + - - +
----------------------------------------------------------
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Residues in contact with GLY 124 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120N THR 2.9 8.3 + - - -
121N ASP 3.6 7.5 + - - -
122N LYS 3.2 5.8 - - - -
123N GLU* 1.3 76.2 - - - +
125N ASP* 1.3 59.3 + - - +
126N ASP* 2.8 25.5 - - - +
114S LYS* 5.4 4.5 - - - +
----------------------------------------------------------
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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