Contacts of the helix formed by residues 117 - 144 (chain B) in PDB entry 4NSW
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 LEU 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 4.1 21.8 - - + -
31B LEU* 4.8 14.8 - - + -
32B GLU* 3.4 24.5 - - + +
35B LEU* 5.8 0.7 - - + -
112B LEU* 3.1 23.5 + - + +
113B VAL* 4.2 5.6 - - + -
114B LYS 3.5 0.6 + - - -
115B GLU 3.2 0.6 - - - -
116B GLY* 1.3 75.2 - - - +
118B ARG* 1.3 63.8 + - - +
119B GLY 3.5 1.8 - - - -
120B PHE* 3.4 15.4 + - + +
121B ARG* 3.1 60.5 + - + +
180B ILE* 4.0 26.2 - - + -
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Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LYS 3.7 8.1 + - - +
115B GLU* 3.2 44.0 + - - +
116B GLY 3.5 0.4 - - - -
117B LEU* 1.3 74.9 - - - +
119B GLY* 1.3 66.4 + - - +
121B ARG* 3.2 11.0 + - + +
122B GLU* 3.0 43.5 + - - +
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Residues in contact with GLY 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLU 4.8 1.0 + - - -
116B GLY 5.2 1.6 + - - -
117B LEU 3.5 0.4 - - - -
118B ARG* 1.3 75.8 - - - +
120B PHE* 1.3 56.9 + - - +
122B GLU* 3.3 13.4 + - - +
123B ALA* 2.9 31.9 + - - +
176B GLN* 3.6 24.6 - - - +
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Residues in contact with PHE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 3.9 7.9 - - + -
25B GLU* 4.5 6.7 - - + -
28B VAL* 3.5 44.6 - - + -
32B GLU* 5.7 0.9 - - - -
117B LEU* 3.4 25.4 + - + +
118B ARG 3.2 0.2 - - - -
119B GLY* 1.3 74.6 - - - +
121B ARG* 1.3 63.1 + - + +
124B ARG* 2.8 49.5 + - + +
173B TYR* 3.5 28.3 - + - -
176B GLN* 3.9 14.1 - - + +
177B ILE* 3.7 28.0 - - + -
180B ILE* 3.8 27.2 - - + +
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLU* 2.7 36.3 + - - +
113B VAL* 2.8 22.4 + - - +
114B LYS* 3.1 27.3 + - - +
117B LEU* 3.1 40.0 + - - +
118B ARG* 3.2 10.3 + - - +
120B PHE* 1.3 83.0 - - + +
122B GLU* 1.3 57.7 + - - +
124B ARG* 3.7 10.9 - - - +
125B ARG* 3.1 27.3 + - - +
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ARG* 3.0 38.1 + - - +
119B GLY* 3.4 15.3 - - - +
121B ARG* 1.3 74.5 - - - +
123B ALA* 1.3 60.4 + - - +
125B ARG* 3.2 31.5 + - - +
126B ASP* 2.9 38.0 + - - +
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Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLY 2.9 17.9 + - - +
120B PHE 4.0 0.4 - - - +
122B GLU* 1.3 73.2 - - - +
124B ARG* 1.3 67.3 + - - +
126B ASP* 3.2 7.3 + - - +
127B PHE* 2.8 26.2 + - - +
169B ARG* 5.0 1.1 - - - +
172B ASP* 4.3 6.5 - - + +
173B TYR* 3.8 29.6 - - + +
176B GLN* 3.7 20.2 - - + -
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLU* 3.3 48.0 + - - +
120B PHE* 2.8 30.5 + - + +
121B ARG* 3.7 11.2 - - - +
123B ALA* 1.3 75.0 - - - +
125B ARG* 1.3 64.5 + - - +
127B PHE* 3.6 1.2 - - - +
128B TRP* 3.1 46.2 + - + +
173B TYR* 3.4 21.3 - - + +
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Residues in contact with ARG 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ARG 3.1 17.8 + - - +
122B GLU* 3.2 29.8 + - - +
124B ARG* 1.3 82.6 - - - +
126B ASP* 1.3 93.0 + - - +
128B TRP* 3.5 4.2 + - - +
129B ARG* 3.2 54.6 + - - +
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Residues in contact with ASP 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B GLU* 2.9 22.9 + - - +
123B ALA* 3.9 6.1 - - - +
125B ARG* 1.3 105.8 + - - +
127B PHE* 1.3 63.3 + - - +
129B ARG* 4.2 9.7 + - - -
130B GLY 3.1 7.6 + - - -
169B ARG* 2.6 50.3 + - + +
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Residues in contact with PHE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PHE* 3.8 23.1 - + - -
18B ARG* 4.3 11.9 - - - -
21B ILE* 3.9 15.3 - - + -
123B ALA 2.8 17.3 + - - +
124B ARG 3.6 2.2 - - - +
126B ASP* 1.3 75.2 - - - +
128B TRP* 1.3 96.9 + + - +
130B GLY* 2.9 4.9 + - - -
131B ALA* 2.8 32.3 + - + +
166B TYR* 3.6 35.7 - + - -
169B ARG* 3.8 16.1 - - + +
170B ALA* 3.9 21.5 - - + -
173B TYR* 3.6 23.6 - + + -
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Residues in contact with TRP 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG* 3.7 35.2 - - - -
21B ILE* 4.0 8.5 - - + -
22B GLU* 4.5 16.6 - - + -
25B GLU* 2.6 38.9 + - - -
124B ARG* 3.1 43.4 + - + +
125B ARG* 4.2 3.6 - - - +
127B PHE* 1.3 96.3 - + - +
129B ARG* 1.3 65.3 + - - +
131B ALA* 3.8 9.9 - - + +
132B GLU* 3.1 30.0 + - - +
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Residues in contact with ARG 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ARG* 3.2 52.7 + - - +
126B ASP* 3.6 12.9 + - - +
128B TRP* 1.3 77.9 - - - +
130B GLY* 1.3 59.3 + - - +
132B GLU* 3.5 10.0 + - - +
133B SER* 3.2 23.4 + - - -
169B ARG* 4.1 11.9 - - - +
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Residues in contact with GLY 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASP 3.1 11.4 + - - -
127B PHE 2.9 7.7 + - - -
129B ARG* 1.3 75.7 - - - +
131B ALA* 1.3 57.5 + - - +
133B SER* 3.4 7.1 + - - -
134B LEU* 2.9 31.5 + - - +
162B ALA 4.9 0.5 - - - +
165B GLY 5.8 0.2 - - - -
166B TYR* 3.8 14.7 - - - +
169B ARG* 3.9 16.8 - - - +
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG* 3.9 22.4 + - - +
127B PHE* 2.8 19.5 + - + +
128B TRP* 3.4 18.8 + - + +
130B GLY* 1.3 70.4 - - - +
132B GLU* 1.3 64.6 + - - +
134B LEU* 4.0 2.0 - - - +
135B GLU* 3.1 25.6 + - - +
166B TYR* 3.6 25.0 - - + -
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B TRP* 3.1 21.8 + - - +
129B ARG* 3.6 8.3 - - - +
131B ALA* 1.3 75.8 - - - +
133B SER* 1.3 64.1 + - - +
135B GLU* 3.4 5.9 + - - +
136B ALA* 3.2 21.1 + - - +
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Residues in contact with SER 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ARG 3.2 12.1 + - - -
130B GLY* 3.7 8.5 + - - -
132B GLU* 1.3 79.7 - - - +
134B LEU* 1.3 64.5 + - - +
136B ALA* 3.5 9.0 + - - +
137B ALA* 3.2 21.7 + - - +
162B ALA* 4.0 14.7 + - - +
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A GLU* 4.8 1.1 - - - +
13B ASP* 4.3 5.4 - - - +
18B ARG* 5.9 0.7 - - - +
130B GLY 2.9 17.5 + - - +
131B ALA* 4.1 3.1 - - - +
132B GLU 3.3 0.2 - - - -
133B SER* 1.3 77.2 + - - +
135B GLU* 1.3 58.5 + - - +
137B ALA* 3.0 4.4 + - + -
138B LEU* 2.9 49.2 + - + +
159B LEU* 4.6 3.6 - - + +
162B ALA* 3.9 14.6 - - + +
163B ARG* 3.6 53.8 - - + +
166B TYR* 3.5 39.3 - - + -
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Residues in contact with GLU 135 (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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285A ARG* 6.3 2.2 - - - -
131B ALA 3.1 19.5 + - - +
132B GLU* 3.8 6.2 - - - +
134B LEU* 1.3 76.2 - - - +
136B ALA* 1.3 58.1 + - - +
138B LEU* 4.2 12.8 - - + +
139B THR* 3.1 37.4 + - + +
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLU 3.2 12.7 + - - +
133B SER* 3.6 12.3 - - - +
134B LEU 3.1 0.6 - - - -
135B GLU* 1.3 77.1 - - - +
137B ALA* 1.3 58.8 + - - +
139B THR* 3.0 18.7 + - - -
140B HIS* 3.1 19.1 + - - +
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B SER 3.2 11.3 + - - +
134B LEU* 3.0 10.1 + - + +
136B ALA* 1.3 78.2 - - - +
138B LEU* 1.3 59.1 + - - +
140B HIS* 4.0 5.7 - - - +
141B ASN* 3.0 31.8 + - - +
155B ALA 5.0 1.6 - - - +
158B ALA* 4.4 5.8 - - + +
159B LEU* 3.9 21.3 - - - +
162B ALA* 3.7 20.9 - - + -
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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
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254A GLU* 3.4 33.2 - - - +
273A PHE* 3.5 16.0 - - + -
285A ARG* 3.5 31.4 - - - +
343A ASP* 3.6 20.1 - - - +
13B ASP* 5.7 1.6 - - - +
134B LEU* 2.9 40.7 + - + +
135B GLU* 4.3 11.0 - - + +
137B ALA* 1.3 78.0 - - - +
139B THR* 1.3 56.6 + - + +
141B ASN* 3.6 2.6 + - - +
142B ALA* 3.0 26.7 + - - +
159B LEU* 4.2 9.4 - - + +
163B ARG* 4.2 3.8 - - - +
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Residues in contact with THR 139 (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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273A PHE* 3.9 24.7 - - + -
283A TRP 5.9 1.3 - - - +
135B GLU* 3.1 31.2 + - + +
136B ALA* 3.0 13.5 + - - -
138B LEU* 1.3 73.5 - - + +
140B HIS* 1.3 60.9 + - - +
142B ALA* 3.1 3.2 + - - +
143B GLU* 2.8 51.2 + - - +
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Residues in contact with HIS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ALA 3.1 16.0 + - - +
137B ALA* 4.0 6.1 - - - +
139B THR* 1.3 82.1 + - - +
141B ASN* 1.3 59.1 + - - +
143B GLU* 4.0 4.1 - - - +
144B VAL* 3.0 48.5 + - + +
151B GLU* 4.2 17.8 + - - +
155B ALA* 3.6 34.6 + - + +
158B ALA* 5.6 5.2 - - + -
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Residues in contact with ASN 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ARG* 2.7 54.3 + - - +
327A PHE* 4.8 2.1 - - - -
341A GLN* 5.0 0.3 - - - +
343A ASP* 3.1 26.6 + - - +
137B ALA 3.0 19.5 + - - +
138B LEU 3.8 3.3 - - - +
140B HIS* 1.3 76.1 - - - +
142B ALA* 1.3 61.2 + - - +
144B VAL 4.3 0.3 + - - -
155B ALA* 4.1 11.4 - - - +
156B GLY* 3.5 27.9 - - - +
159B LEU* 3.5 20.8 - - + +
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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
----------------------------------------------------------
273A PHE* 3.8 22.7 - - + -
283A TRP* 5.9 1.1 - - + -
325A ARG* 3.0 15.5 - - - +
326A ARG* 4.8 1.2 + - - +
341A GLN* 2.9 40.5 - - - +
342A ALA 5.8 0.4 - - - +
343A ASP* 5.3 1.6 - - - +
138B LEU 3.0 18.2 + - - +
139B THR* 3.1 5.6 + - - +
141B ASN* 1.3 79.9 + - - +
143B GLU* 1.3 63.9 + - + +
144B VAL 3.3 4.3 + - - +
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Residues in contact with GLU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A TRP* 4.9 14.3 - - + +
325A ARG* 2.6 47.8 + - - +
139B THR* 2.8 32.6 + - - +
140B HIS* 4.3 4.0 + - - +
142B ALA* 1.3 73.4 - - + +
144B VAL* 1.3 62.8 + - - +
145B PRO* 3.2 6.4 - - - +
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Residues in contact with VAL 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ARG* 4.6 1.0 - - - -
326A ARG* 3.2 34.1 + - - +
140B HIS* 3.0 47.3 + - + +
142B ALA 3.3 6.5 - - - +
143B GLU* 1.3 76.1 - - - +
145B PRO* 1.4 80.9 - - + +
149B ALA* 4.4 0.7 - - + -
151B GLU* 4.3 18.4 - - + +
152B ALA* 3.5 31.9 - - + +
155B ALA* 4.3 5.4 - - + -
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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