Contacts of the helix formed by residues 160 - 179 (chain B) in PDB entry 2G5W
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 GLU 160 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ARG* 2.8 41.6 + - - -
156B LEU* 3.8 17.8 - - + +
157B GLU* 2.8 43.4 + - + +
159B SER* 1.3 80.9 + - - +
161B ILE* 1.3 66.2 + - - +
162B PRO 3.4 0.9 - - - -
163B ARG* 3.1 34.5 + - - +
164B VAL* 3.5 9.8 + - - +
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Residues in contact with ILE 161 (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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156B LEU* 4.3 15.7 - - + -
157B GLU 3.4 10.1 + - - +
158B ALA* 3.8 4.3 - - - +
160B GLU* 1.3 77.2 - - - +
162B PRO* 1.4 66.9 - - + +
164B VAL* 3.0 21.0 + - - +
165B VAL* 3.1 11.1 + - + +
196B PHE* 4.1 16.8 - - + -
204B ARG* 3.8 19.1 - - - +
208B TYR* 3.6 52.5 - - + +
218B PHE* 3.3 26.4 - - + -
221B GLN* 3.9 9.9 - - - +
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Residues in contact with PRO 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO* 4.5 7.9 - - + +
98A ALA 3.3 27.4 - - - +
99A LYS* 3.6 17.5 - - + +
100A GLY* 3.5 17.7 - - - +
158B ALA 3.4 15.7 - - - +
159B SER 3.5 15.5 - - - +
160B GLU 3.5 0.2 - - - -
161B ILE* 1.4 91.2 - - + +
163B ARG* 1.3 57.2 + - + +
164B VAL 3.3 0.2 - - - -
165B VAL* 3.5 14.0 + - + +
166B GLU* 3.0 25.8 + - - +
208B TYR* 4.9 0.2 - - - +
221B GLN* 4.6 1.8 - - - +
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Residues in contact with ARG 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASP 4.9 5.1 + - - -
24A SER* 3.1 29.3 + - - -
56A PRO* 3.8 21.6 - - + +
57A GLY* 3.5 21.8 - - - +
100A GLY 5.1 0.4 + - - -
159B SER* 4.1 14.9 + - - +
160B GLU* 3.1 24.0 + - - +
162B PRO* 1.3 74.7 - - - +
164B VAL* 1.3 66.8 + - + +
166B GLU* 3.3 14.7 + - - +
167B ASP* 3.1 27.3 + - - +
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Residues in contact with VAL 164 (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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109B HIS* 4.5 11.2 - - + +
126B ILE* 4.2 21.5 - - + -
156B LEU* 4.4 15.7 - - + -
160B GLU 3.8 12.3 - - - +
161B ILE 3.0 7.8 + - - +
163B ARG* 1.3 74.7 - - + +
165B VAL* 1.3 65.4 + - - +
167B ASP* 3.0 23.5 + - + +
168B TYR* 3.1 38.0 + - + -
192B LEU* 4.0 18.8 - - + -
218B PHE* 4.0 8.7 - - + -
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Residues in contact with VAL 165 (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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161B ILE 3.1 14.0 + - - +
162B PRO* 3.6 10.5 - - + +
163B ARG 3.3 0.2 - - - -
164B VAL* 1.3 75.4 - - - +
166B GLU* 1.3 63.0 + - - +
168B TYR* 3.0 13.4 + - - +
169B CYS* 3.0 32.1 + - - -
218B PHE* 4.4 6.3 - - + -
221B GLN* 3.7 52.0 - - + +
222B VAL* 4.0 20.2 - - + +
225B GLY* 4.7 2.9 - - - -
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Residues in contact with GLU 166 (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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56A PRO* 3.4 30.9 - - + +
357A LYS* 5.6 4.2 + - - -
162B PRO 3.0 14.2 + - - +
163B ARG* 3.4 14.5 + - - +
164B VAL 3.2 0.2 - - - -
165B VAL* 1.3 76.2 - - - +
167B ASP* 1.3 57.7 + - - +
169B CYS* 3.2 12.2 + - + +
170B LEU* 3.0 51.9 + - + +
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Residues in contact with ASP 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 3.6 20.8 - - + +
68B SER* 3.9 22.6 + - - +
109B HIS* 6.4 0.2 - - + -
163B ARG* 3.1 19.6 + - - +
164B VAL* 3.0 21.8 + - + +
166B GLU* 1.3 73.8 - - - +
168B TYR* 1.3 56.2 + - - +
170B LEU* 4.0 15.9 - - - +
171B SER* 2.7 34.8 + - - -
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Residues in contact with TYR 168 (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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67B VAL* 4.0 24.7 - - + -
107B LEU* 3.9 20.8 - - + +
109B HIS* 3.4 28.3 + - + +
164B VAL* 3.1 45.8 + - + -
165B VAL 3.0 8.3 + - - +
167B ASP* 1.3 74.8 - - - +
169B CYS* 1.3 57.6 + - - +
171B SER* 3.3 6.1 + - - -
172B ALA* 2.8 30.8 + - - +
185B ILE* 3.9 13.9 - - + -
186B HIS 4.7 1.7 + - - -
192B LEU* 4.9 2.3 - - + +
193B ILE* 3.7 25.7 - - + +
218B PHE* 4.7 2.2 - + - -
222B VAL* 3.7 37.2 - - + +
226B VAL* 3.9 14.8 - - + +
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Residues in contact with CYS 169 (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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165B VAL* 3.0 22.5 + - - -
166B GLU* 3.4 14.1 - - + +
168B TYR* 1.3 76.7 - - - +
170B LEU* 1.3 64.1 + - + +
172B ALA* 3.3 7.7 + - - +
173B LEU* 3.1 32.5 + - + +
225B GLY* 3.5 39.3 - - - -
226B VAL* 4.0 3.8 - - - -
229B ALA* 4.4 8.4 - - + +
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Residues in contact with LEU 170 (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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80B ILE 5.0 0.2 - - - -
81B TYR* 5.9 6.3 - - + +
166B GLU* 3.0 38.7 + - + +
167B ASP* 4.0 17.5 - - - +
169B CYS* 1.3 76.0 - - + +
171B SER* 1.3 58.0 + - - +
173B LEU* 3.4 15.1 + - + +
174B ASN* 2.9 37.1 + - - +
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Residues in contact with SER 171 (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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67B VAL* 3.2 35.5 + - - -
80B ILE* 3.6 33.2 + - - +
81B TYR* 4.5 3.0 - - - +
107B LEU* 3.9 5.8 - - - -
167B ASP 2.7 23.5 + - - -
168B TYR 3.5 4.7 - - - -
169B CYS 3.3 0.2 - - - -
170B LEU* 1.3 78.2 - - - +
172B ALA* 1.3 56.8 + - - +
174B ASN* 3.2 2.6 + - - +
175B ALA* 2.9 30.0 + - - +
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Residues in contact with ALA 172 (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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107B LEU* 4.1 11.1 - - + +
168B TYR 2.8 20.1 + - - +
169B CYS* 3.3 6.0 + - - +
171B SER* 1.3 72.9 - - - +
173B LEU* 1.3 62.3 + - - +
175B ALA* 3.4 5.0 + - - +
176B ILE* 3.4 25.5 + - - +
183B ILE* 4.3 7.3 - - + +
226B VAL* 3.9 31.6 - - + +
229B ALA* 5.0 0.7 - - + -
230B ILE* 3.8 16.4 - - + +
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Residues in contact with LEU 173 (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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387A PRO* 3.7 31.2 - - + -
169B CYS* 3.1 26.7 + - + +
170B LEU* 3.7 16.6 - - + +
172B ALA* 1.3 73.4 - - - +
174B ASN* 1.3 66.5 + - - +
176B ILE* 3.1 8.5 + - + +
177B ARG* 3.1 26.8 + - - +
229B ALA* 3.9 29.8 - - + +
230B ILE* 4.1 7.2 - - + +
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Residues in contact with ASN 174 (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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80B ILE* 3.2 30.4 + - - +
81B TYR* 3.4 20.8 + - - +
82B SER 4.0 3.4 + - - -
83B ASP* 4.4 2.7 + - - +
86B VAL* 3.4 25.3 - - + +
170B LEU* 2.9 21.6 + - - +
171B SER 3.2 1.5 + - - +
173B LEU* 1.3 77.7 - - - +
175B ALA* 1.3 61.1 + - - +
177B ARG* 3.2 33.1 + - - +
178B ALA* 3.1 17.7 + - - +
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Residues in contact with ALA 175 (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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80B ILE* 3.7 13.4 - - + +
105B CYS* 4.3 5.6 - - + -
107B LEU* 5.1 0.4 - - + -
171B SER 2.9 12.8 + - - +
172B ALA 3.4 10.8 - - - +
173B LEU 3.2 0.2 - - - -
174B ASN* 1.3 73.9 - - - +
176B ILE* 1.3 64.2 + - + +
178B ALA 3.1 9.7 + - - -
180B PHE* 3.2 43.1 + - + +
183B ILE* 3.6 24.0 - - + -
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Residues in contact with ILE 176 (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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172B ALA 3.4 14.6 - - - +
173B LEU* 3.1 8.4 + - - +
175B ALA* 1.3 75.0 - - + +
177B ARG* 1.3 61.2 + - + +
179B GLY* 3.0 18.7 + - - -
180B PHE 3.6 20.8 - - - +
181B ASP 4.5 3.4 - - - +
182B GLY* 4.2 22.4 - - - +
230B ILE* 3.7 27.8 - - + -
234B LYS* 4.6 20.6 - - + +
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Residues in contact with ARG 177 (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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83B ASP* 3.2 31.3 + - - +
86B VAL* 3.5 24.7 - - + +
87B GLU* 4.5 9.7 + - - -
90B LYS* 3.7 17.0 - - - -
173B LEU* 3.1 16.6 + - - +
174B ASN* 3.2 43.2 + - - +
175B ALA 3.2 0.4 - - - -
176B ILE* 1.3 76.2 - - + +
178B ALA* 1.3 61.4 + - - +
179B GLY* 3.4 0.7 + - - -
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Residues in contact with ALA 178 (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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80B ILE* 4.5 2.9 - - + -
86B VAL* 3.7 25.5 - - + +
89B TRP* 3.7 19.7 - - + -
90B LYS* 3.4 27.3 - - - +
93B VAL* 4.0 7.7 - - + +
94B GLU* 5.5 0.9 - - - +
174B ASN 3.1 11.6 + - - +
175B ALA* 3.1 13.9 + - - +
177B ARG* 1.3 76.7 - - - +
179B GLY* 1.3 57.3 + - - +
180B PHE* 3.9 10.1 - - + -
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Residues in contact with GLY 179 (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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93B VAL* 3.5 10.1 - - - -
97B HIS* 3.2 24.3 + - - -
176B ILE 3.0 13.4 + - - -
177B ARG 3.2 1.2 - - - -
178B ALA* 1.3 78.0 - - - +
180B PHE* 1.3 67.5 + - - +
181B ASP* 4.5 1.0 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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