Contacts of the strand formed by residues 176 - 187 (chain B) in PDB entry 2VIG
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 SER 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172B ALA* 3.6 5.7 - - - +
173B GLU 3.1 33.2 + - - +
174B GLY 3.2 3.6 + - - +
175B ASP* 1.3 86.5 + - - +
177B TRP* 1.3 71.0 + - - +
178B VAL* 5.0 0.2 - - - -
247B ARG* 4.0 22.9 + - - +
248B ILE 3.1 18.9 + - - -
249B PRO* 4.4 0.9 - - - +
250B LYS* 4.0 3.7 - - - +
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Residues in contact with TRP 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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170B ALA* 4.0 21.3 - - + -
171B ARG 3.4 20.2 - - - -
172B ALA* 3.7 26.7 - - + -
176B SER* 1.3 74.6 - - - +
178B VAL* 1.3 61.5 + - - +
179B LEU* 4.0 10.1 - - + -
201B THR* 4.1 17.5 - - + -
213B PHE* 3.5 23.6 - + + -
246B CYS 3.5 0.9 - - - +
247B ARG* 3.4 4.0 - - - -
248B ILE* 2.7 44.0 + - + +
249B PRO 3.7 7.2 - - - -
250B LYS* 3.2 38.0 + - + +
253B ILE* 4.0 24.3 - - + +
257B PRO* 5.3 10.1 - - + -
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Residues in contact with VAL 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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169B THR* 3.6 1.7 + - - +
170B ALA* 3.3 2.6 - - - -
171B ARG* 2.7 42.3 + - + +
173B GLU* 3.7 30.3 - - + +
176B SER* 5.0 0.2 - - - -
177B TRP* 1.3 77.0 - - - +
179B LEU* 1.3 63.5 + - - +
180B ASN* 3.8 18.5 + - - +
245B ASP* 3.1 33.4 - - - +
246B CYS 3.4 3.1 - - - +
247B ARG* 3.8 25.1 - - + +
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Residues in contact with LEU 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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168B THR* 5.1 1.8 - - + -
169B THR 3.2 7.6 - - - +
170B ALA* 4.0 13.0 - - + -
177B TRP* 4.0 24.5 - - + -
178B VAL* 1.3 79.8 - - - +
180B ASN* 1.3 67.9 + - - +
197B VAL* 4.6 12.1 - - + -
199B ALA* 4.8 5.4 - - + -
213B PHE* 4.8 9.4 - - + -
215B VAL* 3.9 27.6 - - + -
243B PHE* 3.7 31.9 - - + +
245B ASP 3.4 1.6 + - - -
246B CYS* 2.9 36.2 + - + +
248B ILE* 4.2 15.3 - - + -
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Residues in contact with ASN 180 (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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167B SER 4.5 0.9 - - - +
168B THR* 3.4 5.1 - - - +
169B THR* 2.9 44.3 + - - +
178B VAL* 3.8 21.8 + - - +
179B LEU* 1.3 83.2 + - - +
181B GLY* 1.3 58.3 + - - +
243B PHE* 3.4 4.4 - - - +
244B GLU* 3.6 7.1 - - - +
245B ASP* 2.7 24.6 + - - +
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Residues in contact with GLY 181 (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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167B SER 5.5 0.9 - - - -
168B THR* 3.7 14.1 - - - -
180B ASN* 1.3 75.8 - - - +
182B THR* 1.3 60.2 + - - -
242B ILE* 5.2 0.4 - - - -
243B PHE* 2.7 48.6 + - - +
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Residues in contact with THR 182 (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 GLU* 3.5 12.3 - - - +
157B PRO* 3.4 28.5 - - + +
168B THR* 3.7 3.1 + - - -
181B GLY* 1.3 73.8 - - - -
183B LYS* 1.3 76.3 + - - +
240B ASN* 3.6 27.8 - - + +
241B LEU 3.2 7.6 - - - +
242B ILE* 3.9 21.7 - - + +
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Residues in contact with LYS 183 (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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153B ALA* 3.4 40.2 - - + -
154B LEU* 2.9 28.5 + - - +
155B SER 3.3 7.4 - - - +
156B GLU* 2.6 24.7 + - - +
166B ALA* 4.1 4.2 - - - +
168B THR* 3.2 26.2 - - + +
182B THR* 1.3 74.4 - - - +
184B ALA* 1.3 61.5 + - - +
186B ILE* 4.0 6.7 - - + -
197B VAL* 4.2 2.9 - - + -
198B PHE* 2.9 22.1 + - - +
240B ASN* 3.1 9.7 - - - +
241B LEU* 2.7 33.6 + - + +
243B PHE* 4.0 20.4 - - + -
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Residues in contact with ALA 184 (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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155B SER* 2.9 20.1 + - - +
156B GLU 3.5 5.2 - - - -
157B PRO* 3.4 35.0 - - + -
183B LYS* 1.3 73.6 - - - +
185B TRP* 1.3 85.2 + - + +
186B ILE* 3.3 13.3 - - - +
240B ASN* 3.2 14.8 - - - +
501B FAD 4.1 0.3 + - - -
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Residues in contact with TRP 185 (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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297A ARG* 6.0 0.6 - - - +
369A GLY* 3.5 33.4 - - - -
370A MET* 3.8 28.0 - - + -
373A VAL* 3.9 18.6 - - + -
155B SER* 4.0 8.3 - - - -
156B GLU 4.5 6.9 + - - -
157B PRO* 5.3 3.2 + - + +
184B ALA* 1.3 96.2 - - + +
186B ILE* 1.3 56.6 + - - +
187B THR 3.3 0.2 + - - -
228B GLU* 3.8 35.2 + - + -
230B LYS* 6.5 0.2 - - + -
238B THR* 3.3 15.3 - - + -
239B ALA* 3.9 3.7 + - - +
240B ASN* 3.8 6.1 + - - -
501B FAD 2.7 94.6 + + + +
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Residues in contact with ILE 186 (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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151B CYS* 3.7 31.6 - - + -
152B PHE 3.7 17.3 - - - +
153B ALA* 3.4 31.4 - - + -
154B LEU 4.4 0.2 - - - +
183B LYS* 4.0 10.5 - - + -
184B ALA 3.3 23.3 - - - +
185B TRP* 1.3 74.6 - - - +
187B THR* 1.3 63.0 + - - +
189B ALA* 3.3 23.3 + - + +
238B THR* 3.3 5.0 - - - +
239B ALA 3.0 28.0 + - - +
241B LEU* 3.9 21.3 - - + -
501B FAD 3.8 8.3 - - - +
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Residues in contact with THR 187 (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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114B VAL* 4.2 15.2 - - + +
118B VAL* 3.7 28.9 - - + +
151B CYS* 3.3 18.9 - - - +
185B TRP 3.3 0.8 + - - -
186B ILE* 1.3 71.5 - - - +
188B ASN* 1.3 80.5 + - - +
233B ILE* 5.6 1.1 - - + +
236B SER* 4.2 16.6 + - - +
237B SER 3.2 10.0 + - - +
238B THR* 4.5 2.5 + - - +
391B TYR* 4.9 0.9 - - - -
501B FAD 2.9 45.2 + - - +
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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
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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