Contacts of the helix formed by residues 131 - 153 (chain B) in PDB entry 2YW7
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 131 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ARG* 3.8 11.6 + - - +
17B VAL* 3.5 24.7 - - + +
71B ARG* 3.0 23.9 + - - -
75B LEU* 3.4 17.2 - - - +
127B LEU* 3.2 11.7 + - + +
130B LEU* 1.3 80.7 - - - +
132B LEU* 1.3 58.5 + - - +
133B VAL* 3.2 7.6 + - - +
134B SER* 3.0 29.1 + - - +
135B GLN* 3.0 27.5 + - - +
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 4.4 7.5 - - - +
124A ILE* 3.8 22.2 - - + -
128A GLU* 4.6 7.6 - - - +
135A GLN* 4.1 13.0 - - - +
139A ILE* 3.5 35.1 - - + +
128B GLU* 3.4 46.7 - - - +
130B LEU 4.2 0.4 - - - -
131B ASP* 1.3 71.2 + - - +
133B VAL* 1.3 66.2 + - + +
135B GLN* 3.5 12.6 + - + +
136B ASP* 3.1 21.7 + - - +
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 3.3 21.5 - - - +
124A ILE* 5.1 2.5 - - + -
139A ILE* 4.3 13.2 - - + +
142A ALA* 3.8 17.9 - - + -
143A GLY* 3.8 23.8 - - - +
146A GLU* 3.6 14.8 - - - +
71B ARG* 3.5 26.2 - - - +
131B ASP* 3.2 7.3 + - - +
132B LEU* 1.3 75.5 - - + +
134B SER* 1.3 66.9 + - - +
136B ASP* 3.2 21.0 + - + +
137B LEU* 3.4 5.4 + - - +
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Residues in contact with SER 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 3.8 2.9 - - - +
21B LEU* 3.7 29.2 - - - +
71B ARG* 2.8 30.6 + - - +
127B LEU* 4.3 5.6 - - - -
131B ASP* 3.0 28.3 + - - -
133B VAL* 1.3 74.7 - - - +
135B GLN* 1.3 55.6 + - - +
137B LEU* 2.7 36.5 + - - +
138B LEU* 3.1 8.5 + - - +
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Residues in contact with GLN 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ILE* 2.6 41.9 + - + +
127B LEU* 3.2 13.3 - - + +
128B GLU* 2.9 37.8 - - - +
131B ASP 3.0 18.9 + - - +
132B LEU* 3.5 15.1 - - + +
133B VAL 3.3 0.2 - - - -
134B SER* 1.3 75.6 - - - +
136B ASP* 1.3 52.5 + - - +
138B LEU* 2.9 7.5 + - - +
139B ILE* 2.8 54.6 + - + +
132D LEU* 3.3 18.2 - - - +
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Residues in contact with ASP 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ASP* 4.8 1.7 - - - +
139A ILE* 3.1 32.7 - - + +
140A ALA* 3.9 14.4 - - - +
132B LEU 3.1 12.5 + - - +
133B VAL* 3.2 12.8 - - + +
135B GLN* 1.3 75.9 - - - +
137B LEU* 1.3 61.2 + - - +
139B ILE* 3.3 10.5 + - - +
140B ALA* 3.1 22.0 + - - +
136D ASP* 3.7 22.9 - - - +
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 5.2 3.4 - - + -
67B GLU* 3.0 57.9 - - + +
68B VAL* 4.4 10.1 - - + -
71B ARG* 3.9 26.7 - - + -
133B VAL 3.4 4.8 + - - +
134B SER* 2.7 20.6 + - - +
136B ASP* 1.3 74.9 - - - +
138B LEU* 1.3 57.9 + - + +
140B ALA* 3.4 9.1 - - + +
141B HIS* 3.0 47.0 - - + +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU 5.4 1.8 - - - +
21B LEU* 3.9 22.7 - - + -
24B GLN* 3.7 24.5 - - + +
28B TYR* 3.4 24.9 - - - +
68B VAL* 4.2 11.7 - - + -
120B THR* 3.9 6.0 - - + +
123B SER* 4.1 25.8 - - - -
124B ILE* 3.5 16.4 - - + +
127B LEU* 4.2 13.7 - - + -
134B SER 3.1 6.8 + - - +
135B GLN* 2.9 8.2 + - - +
137B LEU* 1.3 75.7 - - + +
139B ILE* 1.3 59.3 + - - +
140B ALA 3.2 1.6 - - - -
141B HIS* 3.9 8.1 - - - +
142B ALA* 3.0 28.1 + - - +
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Residues in contact with ILE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ILE* 3.8 18.8 - - + -
135B GLN* 2.8 48.5 + - + +
136B ASP* 3.3 11.9 + - - +
138B LEU* 1.3 76.2 - - - +
140B ALA* 1.3 64.0 + - - +
142B ALA* 3.8 0.9 - - - +
143B GLY* 3.4 17.2 + - - -
132D LEU* 4.2 17.0 - - + +
133D VAL* 3.9 24.4 - - + +
136D ASP* 3.7 33.9 - - + +
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Residues in contact with ALA 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TYR* 4.2 1.1 + - - -
67B GLU* 5.4 1.8 - - - +
136B ASP* 3.1 12.4 + - - +
137B LEU* 3.4 15.5 - - + +
138B LEU 3.2 0.2 - - - -
139B ILE* 1.3 78.5 - - - +
141B HIS* 1.3 69.4 + - + +
143B GLY* 3.9 1.0 + - - -
144B GLU* 3.6 21.0 + - - +
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Residues in contact with HIS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B TYR* 2.5 39.1 + + - +
64B TYR* 3.3 61.2 - + + -
67B GLU* 3.0 24.1 + - - -
68B VAL* 4.0 6.1 - - + -
120B THR* 5.2 0.7 - - + -
137B LEU* 3.0 30.6 + - + +
138B LEU* 3.7 5.8 + - + +
140B ALA* 1.3 77.4 - - + +
142B ALA* 1.3 68.6 + - - +
144B GLU* 2.9 2.9 + - - +
145B LEU* 2.9 32.0 + - + +
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 6.0 2.2 - - + -
120B THR* 3.9 16.6 - - + +
121B ARG* 5.8 2.2 - - + +
124B ILE* 3.7 20.0 - - + -
138B LEU 3.0 21.0 + - - +
139B ILE 3.8 4.0 - - - +
140B ALA 3.4 0.2 - - - -
141B HIS* 1.3 76.2 - - - +
143B GLY* 1.3 62.7 + - - +
145B LEU* 3.9 4.4 - - - +
146B GLU* 2.9 38.0 + - - +
133D VAL* 3.9 11.2 - - + -
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Residues in contact with GLY 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ILE 3.4 9.3 + - - -
140B ALA 4.4 1.3 - - - -
141B HIS 3.3 0.4 - - - -
142B ALA* 1.3 79.5 - - - +
144B GLU* 1.3 59.9 + - - +
146B GLU* 4.0 6.8 - - - +
147B LYS* 3.4 31.1 + - - +
71D ARG* 5.1 3.8 + - - -
133D VAL* 3.4 23.9 - - - +
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Residues in contact with GLU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B GLN* 4.7 2.3 - - - +
60B LEU* 3.3 22.5 - - + +
64B TYR* 3.0 29.2 - - + +
140B ALA 3.6 10.9 + - - +
141B HIS 2.9 7.3 + - - +
143B GLY* 1.3 74.1 - - - +
145B LEU* 1.3 66.6 + - - +
146B GLU 3.1 1.1 - - - -
147B LYS* 3.0 33.7 + - - +
148B PHE* 3.2 10.6 + - - +
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TYR* 4.4 17.3 - - + +
31B LEU* 4.8 4.3 - - + -
57B GLN* 4.1 12.3 - - - +
60B LEU* 5.5 0.2 - - + -
61B VAL* 4.2 13.2 - - + -
64B TYR* 4.0 18.8 - - + -
113B TYR* 3.7 32.9 - - + -
116B VAL* 4.6 10.3 - - + -
117B ILE* 4.4 9.4 - - + -
120B THR* 4.5 13.0 - - + +
141B HIS* 2.9 40.4 + - + +
142B ALA* 3.9 6.5 - - - +
144B GLU* 1.3 70.9 - - - +
146B GLU* 1.3 62.9 + - - +
148B PHE* 3.0 14.2 + - - +
149B GLN* 3.1 10.4 + - - +
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ILE* 3.1 44.3 - - + +
121B ARG* 4.1 19.8 + - - +
142B ALA* 2.9 28.2 + - - +
143B GLY* 4.0 5.6 - - - +
144B GLU 3.1 0.2 - - - -
145B LEU* 1.3 77.3 - - - +
147B LYS* 1.3 60.5 + - - +
149B GLN* 3.4 5.0 + - - +
150B TRP 3.1 15.4 + - - -
71D ARG* 3.0 33.1 + - - +
74D THR* 3.3 18.4 - - + +
75D LEU* 4.7 6.1 - - - +
133D VAL* 4.7 0.6 - - - +
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Residues in contact with LYS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B GLY 3.4 18.1 + - - +
144B GLU* 3.0 25.1 + - - +
146B GLU* 1.3 74.1 - - - +
148B PHE* 1.3 54.3 + - - +
150B TRP* 2.9 11.9 + - + +
151B PHE* 2.6 35.1 + - - +
67D GLU* 5.5 12.6 - - - +
70D GLU* 4.2 29.2 + - - +
71D ARG* 6.0 4.7 - - - +
74D THR* 4.0 19.5 - - + +
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Residues in contact with PHE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU* 4.8 2.5 - - + -
53B MET* 3.4 52.9 - - + -
54B ILE* 4.6 10.1 - - + -
57B GLN* 3.2 51.6 - - + +
109B LEU* 4.3 8.5 - - + -
113B TYR* 3.4 26.9 - + - -
144B GLU* 3.2 5.3 + - - +
145B LEU 3.0 7.5 + - - +
147B LYS* 1.3 78.7 - - - +
149B GLN* 1.3 52.2 + - - +
151B PHE* 3.0 17.2 - + - +
152B VAL* 2.6 49.2 + - + +
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Residues in contact with GLN 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ASP* 3.0 31.0 + - - +
113B TYR* 3.9 14.6 - - + -
114B ASN* 3.1 34.2 - - - +
117B ILE* 3.1 30.7 - - + +
145B LEU 3.1 6.4 + - - +
146B GLU 3.7 7.5 - - - +
147B LYS 3.1 0.2 - - - -
148B PHE* 1.3 73.5 - - - +
150B TRP* 1.3 59.9 + - - +
152B VAL* 3.3 6.9 + - - +
153B ARG* 2.8 62.0 + - - +
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Residues in contact with TRP 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B GLU 3.1 5.7 + - - -
147B LYS* 2.9 13.7 + - + +
149B GLN* 1.3 74.6 - - - +
151B PHE* 1.3 90.7 + + + +
153B ARG* 3.0 33.3 + - + +
73D ALA* 3.4 34.2 + - + +
74D THR* 3.8 32.5 - - + +
40I TRP 5.3 7.6 - - - -
41I ASN 6.1 0.2 - - - -
42I VAL 4.9 1.6 - - - -
43I VAL* 3.5 25.3 - - + +
47I PHE* 3.7 37.2 - + - -
51I HIS* 4.8 6.7 - + - -
99I ARG* 3.7 23.9 - - - +
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Residues in contact with PHE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLY 5.9 0.4 - - - -
53B MET* 3.6 45.5 - - + -
147B LYS 2.6 15.9 + - - +
148B PHE* 3.0 24.5 - + - +
150B TRP* 1.3 85.4 - + + +
152B VAL* 1.3 64.0 + - - +
153B ARG 3.3 0.2 - - - -
154B ALA* 2.9 21.5 + - + +
47I PHE* 3.6 33.7 - + - -
48I ILE* 4.3 14.8 - - + -
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Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B MET* 3.7 14.7 - - + +
106B LEU* 3.5 28.7 - - + +
109B LEU* 4.5 14.1 - - + -
110B ASP* 3.5 36.3 - - + +
113B TYR* 5.5 2.2 - - + -
148B PHE* 2.6 46.2 + - + +
149B GLN* 3.4 11.4 - - - +
151B PHE* 1.3 70.6 - - - +
153B ARG* 1.3 52.2 + - - +
154B ALA* 2.5 17.0 + - - +
155B HIS 3.5 12.2 - - - +
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Residues in contact with ARG 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASP* 3.2 22.5 + - - +
114B ASN* 3.7 17.4 + - - +
149B GLN* 2.8 53.3 + - - +
150B TRP* 3.3 22.8 + - + +
151B PHE 2.9 4.8 + - - -
152B VAL* 1.3 70.9 - - + +
154B ALA* 1.3 54.5 + - - +
155B HIS* 3.1 11.3 + - - +
74D THR 5.4 5.5 + - - -
43I VAL* 4.9 11.8 - - - +
99I ARG* 5.8 3.1 + - - -
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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