Contacts of the helix formed by residues 94 - 124 (chain U) 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 U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92U PRO 4.5 0.2 + - - -
93U LYS* 1.3 74.3 - - - +
95U MET* 1.3 70.4 + - + +
96U ASP* 3.5 20.6 - - + +
97U GLN* 3.1 27.8 + - - -
98U LEU* 2.9 24.0 + - - +
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Residues in contact with MET 95 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S HIS* 6.0 0.7 - - + +
34U MET* 3.8 38.6 - - + -
35U ARG 3.3 35.6 + - - +
36U GLY* 4.6 1.6 - - - +
38U ASN* 3.9 17.9 - - + +
39U PHE 3.9 24.2 - - - +
42U LEU* 3.4 28.3 - - + -
93U LYS 4.0 0.2 + - - -
94U THR* 1.3 77.3 - - + +
96U ASP* 1.3 60.4 + - - +
98U LEU* 3.3 8.9 + - - +
99U MET* 2.9 37.8 + - + +
149U PHE* 4.3 11.4 - - + -
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Residues in contact with ASP 96 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S HIS* 3.2 36.4 + - - -
94U THR* 3.3 14.0 - - + +
95U MET* 1.3 78.1 - - - +
97U GLN* 1.3 56.5 + - - +
99U MET* 3.3 1.9 + - - +
100U GLU* 2.8 41.6 + - - +
149U PHE* 4.0 5.0 - - - -
150U LEU* 3.7 29.3 - - + +
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Residues in contact with GLN 97 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92U PRO 4.7 1.2 - - - +
93U LYS* 2.9 47.4 - - + +
94U THR* 3.1 38.7 + - - +
96U ASP* 1.3 74.3 - - - +
98U LEU* 1.3 66.6 + - - +
100U GLU* 3.1 19.5 + - - +
101U ASP* 3.1 21.8 + - - +
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Residues in contact with LEU 98 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29U GLN* 5.3 6.5 - - - +
30U ILE* 3.5 41.9 - - + +
33U TYR* 4.6 1.8 - - + +
34U MET* 3.6 40.6 - - + +
35U ARG 4.9 0.2 - - - +
89U TYR* 4.1 25.8 - - + -
93U LYS* 4.2 18.8 - - + +
94U THR 2.9 21.3 + - - +
95U MET* 3.6 8.5 - - - +
97U GLN* 1.3 74.5 - - - +
99U MET* 1.3 64.5 + - + +
101U ASP* 3.1 11.0 + - + +
102U LEU 3.1 17.2 + - - -
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Residues in contact with MET 99 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30U ILE* 3.5 35.7 - - + -
34U MET* 4.5 8.3 - - + -
42U LEU* 4.1 14.6 - - + -
46U MET* 4.1 13.5 - - + -
95U MET* 2.9 22.6 + - + +
96U ASP 3.7 4.0 - - - +
98U LEU* 1.3 78.6 - - + +
100U GLU* 1.3 57.3 + - - +
102U LEU* 3.3 7.6 - - + +
103U VAL* 2.9 36.7 + - + +
146U PHE* 3.9 34.3 - - + -
149U PHE* 4.0 19.3 - - + -
150U LEU* 4.1 16.4 - - + -
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Residues in contact with GLU 100 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96U ASP* 2.8 28.0 + - - +
97U GLN* 3.1 20.8 + - - +
99U MET* 1.3 77.0 - - - +
101U ASP* 1.3 56.0 + - - +
103U VAL* 3.8 4.1 - - - +
104U GLY* 3.0 24.4 + - - -
150U LEU* 3.9 21.2 - - + +
152U LYS* 4.7 13.5 + - + -
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Residues in contact with ASP 101 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26U LYS* 2.7 40.1 + - - +
29U GLN* 4.9 5.2 + - - -
30U ILE* 5.3 3.0 - - + +
97U GLN 3.1 10.3 + - - +
98U LEU* 3.4 11.4 - - - +
100U GLU* 1.3 74.1 - - - +
102U LEU* 1.3 64.6 + - - +
104U GLY* 3.3 1.9 + - - -
105U THR* 3.0 31.7 + - - -
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Residues in contact with LEU 102 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23U PHE* 3.4 36.6 - - + -
26U LYS* 5.4 1.8 - - - -
27U ILE* 4.9 3.4 - - + -
30U ILE* 3.9 24.7 - - + +
46U MET* 4.0 17.3 - - + -
49U LEU* 3.9 12.6 - - + -
98U LEU 3.1 7.1 + - - +
99U MET* 3.3 14.4 - - - +
101U ASP* 1.3 72.8 - - - +
103U VAL* 1.3 64.9 + - - +
105U THR* 2.9 7.3 + - - -
106U LEU* 2.9 27.2 + - + +
146U PHE* 4.0 41.1 - - + -
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Residues in contact with VAL 103 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99U MET 2.9 25.7 + - - +
100U GLU* 3.8 5.8 - - - +
102U LEU* 1.3 72.2 - - - +
104U GLY* 1.3 57.7 + - - +
106U LEU* 3.2 11.6 + - + +
107U GLU* 2.9 49.0 + - + +
143U ILE* 4.8 7.6 - - + +
146U PHE* 3.9 32.3 - - + -
147U LYS* 4.0 25.1 - - + +
150U LEU* 4.3 14.4 - - + -
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Residues in contact with GLY 104 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100U GLU 3.0 17.3 + - - -
101U ASP* 3.8 2.9 - - - -
102U LEU 3.1 0.4 + - - -
103U VAL* 1.3 75.8 - - - +
105U THR* 1.3 57.5 + - - +
107U GLU* 3.3 16.5 + - - +
108U LEU* 3.1 23.4 + - - +
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Residues in contact with THR 105 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23U PHE* 3.7 28.3 - - + -
26U LYS* 4.0 15.5 + - - -
84U VAL* 3.6 39.5 - - + +
85U GLU 5.3 0.7 + - - -
101U ASP* 3.0 19.7 + - - -
102U LEU* 2.9 4.8 + - - -
104U GLY* 1.3 75.1 - - - +
106U LEU* 1.3 63.5 + - - +
107U GLU 3.1 1.3 - - - -
108U LEU* 3.3 7.2 + - + +
109U LEU* 3.1 24.7 + - + +
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Residues in contact with LEU 106 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23U PHE* 3.9 18.6 - - + -
49U LEU* 5.2 1.8 - - + -
53U PHE* 3.6 33.2 - - + -
102U LEU* 2.9 33.9 + - + +
103U VAL* 3.6 11.7 - - - +
105U THR* 1.3 76.5 - - - +
107U GLU* 1.3 57.0 + - - +
109U LEU* 3.6 4.6 + - + +
110U ARG* 2.9 23.0 + - - +
139U ILE* 3.3 23.9 - - + +
142U HIS* 3.8 30.7 - - + +
143U ILE* 3.9 18.4 - - + -
146U PHE* 4.5 4.0 - - + -
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Residues in contact with GLU 107 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103U VAL* 2.9 23.5 + - + +
104U GLY* 3.4 17.6 - - - +
105U THR 3.1 0.2 - - - -
106U LEU* 1.3 75.6 - - - +
108U LEU* 1.3 64.7 + - - +
110U ARG* 3.3 34.3 + - - +
111U ASP* 3.1 32.7 + - - +
143U ILE* 4.1 10.0 - - + +
147U LYS* 3.1 33.4 + - - -
154U PRO 4.6 2.8 - - - +
155U LEU 6.1 0.2 - - - -
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Residues in contact with LEU 108 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19U ASN* 4.1 3.8 - - - +
83U SER* 3.9 29.4 - - - +
84U VAL* 3.9 26.5 - - + -
85U GLU* 5.2 1.1 - - + +
104U GLY 3.1 12.4 + - - +
105U THR* 3.3 12.3 + - + +
107U GLU* 1.3 77.2 - - - +
109U LEU* 1.3 66.0 - - + +
111U ASP* 3.3 5.4 + - - +
112U GLU* 3.0 51.6 + - + +
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Residues in contact with LEU 109 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16U GLN* 3.9 20.9 - - - +
19U ASN* 4.1 19.7 - - + +
20U LEU* 4.1 13.9 - - + -
23U PHE* 3.8 35.9 - - + -
53U PHE* 4.1 17.0 - - + -
84U VAL* 4.5 7.2 - - + -
105U THR* 3.1 19.0 + - + +
106U LEU* 3.7 8.5 - - - +
108U LEU* 1.3 81.2 - - + +
110U ARG* 1.3 56.4 + - - +
112U GLU* 4.7 2.5 - - - -
113U TYR* 2.9 41.9 + - + +
139U ILE* 4.0 11.4 - - + -
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Residues in contact with ARG 110 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106U LEU 2.9 18.6 + - - +
107U GLU* 3.3 27.3 + - - +
109U LEU* 1.3 74.3 - - - +
111U ASP* 1.3 87.1 + - - +
113U TYR* 3.6 6.3 - - - +
114U LYS* 3.0 25.7 + - + +
136U LYS* 4.1 21.8 - - + +
139U ILE* 3.9 15.0 - - + +
140U ASP* 3.1 27.1 + - - +
143U ILE* 3.9 21.2 - - + +
154U PRO 5.2 0.8 + - - -
155U LEU* 4.3 21.8 - - - +
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Residues in contact with ASP 111 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107U GLU* 3.1 20.6 + - - +
108U LEU* 3.8 5.5 - - - +
110U ARG* 1.3 107.5 + - - +
112U GLU* 1.3 66.4 + - - +
114U LYS* 3.1 22.3 + - - +
115U GLN* 3.2 14.1 + - - +
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Residues in contact with GLU 112 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12U PHE* 3.3 12.4 - - + -
15U HIS* 3.4 9.9 + - - -
16U GLN* 2.7 34.8 + - - +
19U ASN* 2.8 15.0 + - - -
83U SER* 2.5 26.7 + - - -
108U LEU* 3.0 31.1 + - + +
109U LEU* 4.0 3.6 - - - +
111U ASP* 1.3 74.9 - - + +
113U TYR* 1.3 63.8 + - - +
115U GLN* 3.0 24.5 + - - +
116U GLY 2.9 17.7 + - - -
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Residues in contact with TYR 113 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12U PHE* 4.1 8.7 - + - -
16U GLN* 3.6 38.8 - - + +
20U LEU* 3.6 25.8 - - + +
56U GLN* 3.0 15.8 + - - -
60U VAL* 4.9 1.5 - - + +
109U LEU* 2.9 26.6 + - + +
110U ARG* 3.6 6.5 - - - +
112U GLU* 1.3 74.9 - - - +
114U LYS* 1.3 57.7 + - - +
116U GLY* 3.2 1.0 + - - -
117U ILE* 2.9 41.7 + - + +
132U LEU* 4.3 18.6 - - + +
135U PHE* 3.6 37.2 - + + -
136U LYS* 4.3 7.6 - - + -
139U ILE* 3.6 26.2 - - + +
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Residues in contact with LYS 114 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124Q GLY* 3.7 16.2 + - - -
126Q ASP* 2.8 29.2 + - - +
110U ARG* 3.0 14.6 + - + +
111U ASP* 3.2 16.6 - - - +
112U GLU 3.1 0.6 - - - -
113U TYR* 1.3 77.0 - - - +
115U GLN* 1.3 58.8 + - + +
117U ILE* 3.4 12.4 + - + +
118U GLU* 3.3 46.3 + - - +
136U LYS* 4.5 19.3 - - - +
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Residues in contact with GLN 115 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122G LYS* 4.3 28.3 + - - +
12U PHE* 4.4 5.4 - - + -
111U ASP* 3.2 9.8 + - - +
112U GLU* 3.0 31.4 + - - +
114U LYS* 1.3 74.2 - - + +
116U GLY* 1.3 59.0 + - - +
118U GLU* 3.3 9.0 + - - +
119U LEU* 2.9 31.2 + - - +
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Residues in contact with GLY 116 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12U PHE* 3.4 36.9 - - - -
112U GLU 2.9 11.1 + - - -
113U TYR 3.2 1.7 + - - -
115U GLN* 1.3 74.6 - - - +
117U ILE* 1.3 56.8 + - - +
119U LEU* 3.6 4.0 - - - +
120U THR* 2.8 34.7 + - - -
132U LEU* 3.5 7.9 - - - -
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Residues in contact with ILE 117 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126Q ASP* 3.5 31.6 - - + +
113U TYR 2.9 26.3 + - - +
114U LYS* 3.5 15.9 - - + +
115U GLN 3.2 0.2 - - - -
116U GLY* 1.3 77.9 - - - +
118U GLU* 1.3 56.5 + - + +
120U THR* 3.6 6.5 - - - -
121U ASP* 3.1 13.3 + - + +
129U ASN* 2.8 33.1 + - - +
132U LEU* 3.7 20.9 - - + +
133U ILE* 3.8 30.7 - - + +
136U LYS* 4.2 19.1 - - + -
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Residues in contact with GLU 118 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G GLU* 2.7 32.9 - - - +
122G LYS* 4.4 17.5 + - - -
114U LYS* 3.3 40.0 + - - +
115U GLN* 3.7 9.4 - - - +
116U GLY 3.3 0.4 - - - -
117U ILE* 1.3 77.4 - - + +
119U LEU* 1.3 65.8 + - - +
121U ASP* 3.4 6.1 + - - +
122U LYS* 3.1 22.7 + - - +
----------------------------------------------------------
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Residues in contact with LEU 119 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7U VAL 3.0 31.9 - - - +
8U ASP 3.5 21.5 - - - +
9U THR* 4.1 4.3 - - - +
12U PHE* 3.8 24.5 - - + -
115U GLN 2.9 17.9 + - - +
116U GLY* 3.6 3.1 - - - +
118U GLU* 1.3 79.2 - - - +
120U THR* 1.3 57.9 + - - +
122U LYS* 3.2 17.4 + - + +
123U GLU* 3.1 47.1 + - + +
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Residues in contact with THR 120 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9U THR* 4.0 14.5 + - - -
116U GLY 2.8 22.8 + - - +
117U ILE* 3.3 4.5 - - - +
119U LEU* 1.3 76.8 - - - +
121U ASP* 1.3 63.8 + - - +
123U GLU* 3.5 1.5 + - - +
124U GLY 3.3 2.8 + - - -
125U ASP* 3.1 52.4 + - - +
128U THR* 3.5 10.3 - - - +
129U ASN* 3.1 46.8 + - - +
132U LEU* 4.4 5.6 - - + -
----------------------------------------------------------
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Residues in contact with ASP 121 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117U ILE* 3.1 20.9 + - + +
118U GLU* 3.7 7.4 - - - +
119U LEU 3.4 0.4 - - - -
120U THR* 1.3 78.8 - - - +
122U LYS* 1.3 61.9 + - - +
124U GLY* 3.4 10.6 + - - -
129U ASN* 3.8 12.5 + - - +
----------------------------------------------------------
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Residues in contact with LYS 122 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G ASP* 5.9 3.2 - - - +
115G GLN* 3.3 39.7 - - - +
118U GLU 3.1 13.4 + - - +
119U LEU* 3.2 20.4 - - + +
121U ASP* 1.3 76.8 - - - +
123U GLU* 1.3 65.2 + - + +
124U GLY 3.3 1.3 + - - -
----------------------------------------------------------
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Residues in contact with GLU 123 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7U VAL 4.4 0.2 - - - +
8U ASP* 3.4 31.6 - - - +
9U THR* 3.1 30.8 + - - +
119U LEU* 3.1 25.4 + - + +
120U THR 3.5 4.2 + - - +
121U ASP 3.3 0.4 - - - -
122U LYS* 1.3 79.7 - - + +
124U GLY* 1.3 60.9 + - - +
125U ASP* 3.6 5.7 + - + +
----------------------------------------------------------
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Residues in contact with GLY 124 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114M LYS* 3.6 24.3 + - - +
120U THR 3.3 4.4 + - - -
121U ASP* 3.4 7.0 + - - -
122U LYS 3.3 5.5 + - - -
123U GLU* 1.3 78.4 - - - +
125U ASP* 1.3 58.2 + - - +
126U ASP* 3.2 14.2 + - - +
----------------------------------------------------------
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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