Contacts of the helix formed by residues 125 - 148 (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 ASP 125 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9N THR* 3.7 20.9 - - - +
63N ARG* 2.9 26.9 + - - -
67N ILE* 4.1 10.7 - - - +
120N THR* 3.0 15.4 + - - +
123N GLU* 3.4 7.5 + - - +
124N GLY* 1.3 73.9 - - - +
126N ASP* 1.3 61.5 + - - +
127N VAL* 3.1 2.4 + - - +
128N THR* 2.7 31.6 + - - -
129N ASN* 3.2 19.6 + - - +
136S LYS* 5.1 2.6 + - - +
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Residues in contact with ASP 126 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124N GLY* 2.8 25.1 + - - +
125N ASP* 1.3 71.1 + - - +
127N VAL* 1.3 58.9 + - + +
129N ASN* 3.5 9.8 - - - +
130N ASP* 3.1 27.0 + - - +
114S LYS* 4.4 14.6 + - - +
117S ILE* 3.5 27.6 - - + +
129S ASN* 5.3 0.5 + - - -
133S ILE* 3.5 29.4 - - + +
136S LYS* 5.8 4.2 + - + +
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Residues in contact with VAL 127 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63N ARG* 3.2 40.6 - - - +
125N ASP* 3.1 1.4 + - - +
126N ASP* 1.3 76.5 - - + +
128N THR* 1.3 65.6 + - - +
130N ASP* 3.2 3.6 + - - +
131N MET* 3.0 21.5 + - + +
133S ILE* 3.6 33.7 - - + +
136S LYS* 4.0 25.0 - - + +
137S ALA* 3.6 29.4 - - + +
140S ASP* 4.3 0.2 - - - +
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Residues in contact with THR 128 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9N THR* 4.2 2.5 - - + -
13N LEU* 3.5 39.9 - - + +
63N ARG* 2.9 20.8 + - - +
67N ILE* 4.6 1.0 - - - +
120N THR* 4.0 17.9 - - + -
125N ASP* 2.7 32.7 + - - -
127N VAL* 1.3 76.0 - - - +
129N ASN* 1.3 62.6 + - - +
131N MET* 3.1 12.3 + - + +
132N LEU* 3.0 25.8 + - + +
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Residues in contact with ASN 129 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117N ILE* 3.0 29.8 + - - +
120N THR* 2.7 30.1 + - - +
121N ASP* 3.5 21.7 + - - +
125N ASP 3.2 16.9 + - - +
126N ASP* 3.5 11.7 - - - +
128N THR* 1.3 76.2 - - - +
130N ASP* 1.3 60.9 + - - +
132N LEU* 3.3 5.7 + - - +
133N ILE* 3.1 40.4 + - - +
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Residues in contact with ASP 130 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126N ASP 3.1 15.3 + - - +
127N VAL 3.2 4.7 + - - +
129N ASN* 1.3 79.9 + - - +
131N MET* 1.3 65.2 + - - +
133N ILE* 3.5 9.0 + - - +
134N ALA* 3.3 23.8 + - - +
130S ASP* 3.6 12.7 - - - +
133S ILE* 4.0 19.6 - - + +
134S ALA* 5.9 3.4 - - - +
130Y ASP* 3.6 22.1 - - - +
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Residues in contact with MET 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13N LEU* 3.9 18.2 - - + -
59N GLU* 3.9 17.9 - - - +
60N VAL* 3.9 7.0 - - + -
63N ARG* 3.7 28.3 - - + -
127N VAL* 3.0 14.3 + - + +
128N THR* 3.3 13.9 - - + +
130N ASP* 1.3 79.0 + - - +
132N LEU* 1.3 83.7 + - + +
134N ALA* 3.5 4.9 + - - +
135N PHE* 3.3 55.6 + - + -
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Residues in contact with LEU 132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N PHE* 3.9 22.2 - - + -
13N LEU* 4.1 9.9 - - + -
16N GLN* 5.7 1.1 - - + -
60N VAL* 5.3 1.6 - - + -
113N TYR* 4.0 24.3 - - + +
116N GLY 3.6 30.7 - - - +
117N ILE* 3.6 19.4 - - + +
120N THR* 4.0 12.6 - - + +
128N THR* 3.0 20.3 + - + +
129N ASN 3.7 1.6 - - - +
130N ASP 3.2 0.2 - - - -
131N MET* 1.3 96.2 - - + +
133N ILE* 1.3 66.5 + - - +
134N ALA 3.3 0.2 + - - -
135N PHE* 3.3 9.8 + - + +
136N LYS* 3.0 23.4 + - - +
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Residues in contact with ILE 133 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117N ILE* 3.8 27.4 - - + -
129N ASN* 3.1 35.7 + - - +
130N ASP* 4.0 9.0 - - - +
132N LEU* 1.3 78.3 - - - +
134N ALA* 1.3 56.3 + - - +
136N LYS* 3.5 1.9 + - - -
137N ALA* 3.0 25.9 + - + +
126Y ASP* 3.7 45.8 - - + +
127Y VAL* 3.7 11.7 - - + +
130Y ASP* 4.1 19.7 - - + +
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Residues in contact with ALA 134 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130N ASP* 3.3 18.5 + - - +
131N MET* 3.7 6.7 - - - +
132N LEU 3.2 0.6 - - - -
133N ILE* 1.3 79.4 - - - +
135N PHE* 1.3 66.7 + - + +
137N ALA* 3.4 8.6 - - - +
138N SER* 3.4 19.1 + - - -
130Y ASP* 5.7 5.2 - - - +
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Residues in contact with PHE 135 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56N GLN* 3.6 47.6 + - + +
59N GLU* 3.4 27.4 - - + -
60N VAL* 3.6 25.6 - - + -
113N TYR* 3.4 33.0 - + + -
131N MET* 3.3 39.4 + - + -
132N LEU* 3.6 6.5 - - + +
134N ALA* 1.3 80.3 - - + +
136N LYS* 1.3 60.5 + - - +
138N SER* 3.2 5.3 + - - -
139N ILE* 2.8 32.9 + - - +
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Residues in contact with LYS 136 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110N ARG* 4.2 28.7 - - + +
113N TYR* 4.3 8.5 - - + -
114N LYS* 4.6 16.4 - - + +
117N ILE* 4.4 18.8 - - + -
132N LEU 3.0 16.9 + - - +
133N ILE* 3.9 6.1 - - - +
134N ALA 3.4 0.2 - - - -
135N PHE* 1.3 72.9 - - - +
137N ALA* 1.3 58.3 + - - +
139N ILE* 3.6 10.0 - - - +
140N ASP* 2.7 67.7 + - - +
63Y ARG* 4.0 7.9 - - - +
125Y ASP* 4.9 3.4 + - - +
126Y ASP* 5.9 3.0 - - + +
127Y VAL* 3.8 15.8 - - + +
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Residues in contact with ALA 137 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133N ILE* 3.0 12.8 + - + +
134N ALA* 3.4 13.9 - - - +
136N LYS* 1.3 78.8 - - - +
138N SER* 1.3 60.9 + - - +
140N ASP* 3.5 4.8 + - - +
141N LYS* 3.3 23.9 + - - +
63Y ARG* 4.8 1.4 + - - -
127Y VAL* 3.5 32.8 - - + +
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Residues in contact with SER 138 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52N GLU* 2.5 32.2 + - - -
53N PHE* 5.1 0.2 - - - -
56N GLN* 4.7 2.3 + - - -
134N ALA 3.4 7.9 + - - -
135N PHE* 3.2 9.7 + - - -
136N LYS 3.2 0.4 - - - -
137N ALA* 1.3 79.0 - - - +
139N ILE* 1.3 65.3 + - - +
141N LYS* 3.3 12.2 + - - +
142N HIS* 3.1 30.5 + - - -
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Residues in contact with ILE 139 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53N PHE* 3.8 31.9 - - + -
56N GLN* 4.2 2.2 - - - +
106N LEU* 3.5 28.9 - - + +
109N LEU* 4.0 23.6 - - + -
110N ARG* 3.9 15.3 - - + -
113N TYR* 4.0 27.6 - - + -
135N PHE 2.8 21.4 + - - +
136N LYS* 3.6 5.8 - - - +
138N SER* 1.3 77.5 - - - +
140N ASP* 1.3 56.8 + - - +
142N HIS* 3.3 8.9 + - - +
143N ILE* 3.0 31.3 + - + +
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Residues in contact with ASP 140 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110N ARG* 3.3 33.1 + - - +
136N LYS* 2.7 50.8 + - - +
137N ALA 3.6 2.5 - - - +
139N ILE* 1.3 72.3 - - - +
141N LYS* 1.3 62.7 + - - +
143N ILE* 3.6 8.5 + - - +
144N TRP 3.2 15.8 + - - -
63Y ARG* 2.9 31.7 + - - +
66Y ALA* 3.7 18.8 - - + +
127Y VAL* 3.9 1.4 - - - +
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Residues in contact with LYS 141 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137N ALA 3.3 12.6 + - - +
138N SER* 3.3 13.0 + - - +
140N ASP* 1.3 79.6 - - - +
142N HIS* 1.3 57.0 + - + +
144N TRP* 3.1 26.1 + - + +
145N MET* 3.0 48.7 + - + +
59Y GLU* 5.9 6.7 + - - +
62Y GLU* 4.1 29.1 + - + +
63Y ARG* 5.6 2.6 - - - +
66Y ALA* 4.5 6.2 - - + +
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Residues in contact with HIS 142 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45N LYS* 4.6 7.6 - - - -
48N ASP* 6.6 0.2 - - + -
49N LEU* 3.4 27.7 - - + +
52N GLU* 2.7 26.5 + - - -
53N PHE* 4.1 10.3 - + - -
106N LEU* 3.9 18.4 - - + -
138N SER* 3.1 34.9 + - - -
139N ILE* 3.3 7.4 + - - +
141N LYS* 1.3 72.8 - - + +
143N ILE* 1.3 60.4 + - - +
145N MET* 3.7 25.9 - - + +
146N PHE* 2.9 46.5 + - + +
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Residues in contact with ILE 143 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103N VAL* 4.9 5.4 - - + +
106N LEU* 3.9 25.8 - - + +
107N GLU* 4.0 35.2 - - + +
110N ARG* 4.0 29.8 - - - +
139N ILE* 3.0 23.5 + - + +
140N ASP* 3.7 7.9 - - - +
142N HIS* 1.3 74.6 - - - +
144N TRP* 1.3 64.2 + - - +
146N PHE* 5.1 1.6 - - - -
147N LYS* 3.1 33.6 + - + +
154N PRO* 3.8 24.9 - - + +
155N LEU* 5.6 2.0 - - + -
66Y ALA 5.9 0.7 - - - +
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Residues in contact with TRP 144 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140N ASP 3.2 12.3 + - - +
141N LYS* 3.1 21.0 + - + +
143N ILE* 1.3 77.7 - - - +
145N MET* 1.3 82.9 + - + +
147N LYS* 4.2 0.7 - - - +
148N ALA* 3.2 31.0 + - + +
154N PRO* 4.0 27.1 - - + +
31V HIS* 4.9 13.2 - + - -
32V TRP* 4.2 11.0 + + - -
34V MET 5.8 0.2 + - - -
39V PHE* 4.1 22.1 - + - -
62Y GLU* 3.6 50.5 - - + -
65Y LEU* 3.7 41.6 - - + +
66Y ALA* 4.0 15.5 - - + -
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Residues in contact with MET 145 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45N LYS* 4.5 8.7 - - - +
141N LYS* 3.0 33.6 + - + +
142N HIS* 3.7 33.0 - - + +
144N TRP* 1.3 95.7 - - + +
146N PHE* 1.3 66.1 + - + +
148N ALA 3.6 7.8 - - - +
149N PHE* 3.5 15.8 - - - +
39V PHE* 3.8 28.6 - - + -
40V PHE* 4.0 25.4 - - + -
62Y GLU* 5.9 0.4 - - - +
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Residues in contact with PHE 146 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42N LEU* 4.5 4.5 - - + -
45N LYS* 4.1 15.0 - - + -
46N MET* 3.7 30.7 - - + -
49N LEU* 4.4 10.5 - - + -
99N MET* 4.1 20.9 - - - +
102N LEU* 3.9 17.0 - - + -
103N VAL* 4.0 18.4 - - + -
106N LEU* 4.3 3.8 - - + -
142N HIS* 2.9 50.3 + - + +
145N MET* 1.3 77.1 - - + +
147N LYS* 1.3 57.4 + - - +
149N PHE* 3.2 9.1 - + - +
150N LEU* 3.1 32.6 + - + +
40V PHE* 3.5 31.9 - + - -
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Residues in contact with LYS 147 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103N VAL* 3.8 31.2 - - + -
107N GLU* 3.8 12.9 + - - -
143N ILE* 3.1 23.9 + - + +
144N TRP 4.2 1.6 - - - +
146N PHE* 1.3 70.6 - - - +
148N ALA* 1.3 50.5 + - - +
149N PHE 2.9 8.7 + - - -
150N LEU* 3.3 11.6 + - + -
151N GLY 3.0 3.6 + - - -
152N LYS* 2.5 49.1 + - + +
153N ALA 3.5 7.0 - - - +
154N PRO* 3.2 28.1 + - + +
155N LEU 4.6 0.2 - - - -
156N GLU* 3.1 38.9 - - - +
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Residues in contact with ALA 148 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144N TRP* 3.2 30.4 + - + +
145N MET 3.6 3.1 - - - +
147N LYS* 1.3 71.4 - - - +
149N PHE* 1.3 57.6 + - - +
151N GLY 4.1 0.4 - - - -
152N LYS 3.3 10.6 + - - +
34V MET 4.0 7.0 - - - +
35V ARG* 3.7 24.2 - - + +
36V GLY 3.7 10.3 + - - -
39V PHE* 3.2 34.1 - - + +
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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