Contacts of the strand formed by residues 176 - 187 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172G ALA* 3.6 0.2 - - - -
173G GLU* 2.8 31.2 + - - -
174G GLY 3.1 2.8 + - - -
175G ASP* 1.3 83.4 + - - +
177G TRP* 1.3 62.0 - - - +
247G ARG* 3.4 40.6 + - - +
248G ILE 3.3 16.2 + - - -
249G PRO* 4.3 0.9 - - - +
250G LYS* 3.3 15.0 - - - +
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Residues in contact with TRP 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170G ALA 4.4 1.1 - - - -
171G ARG 3.4 12.6 - - - -
172G ALA* 3.5 39.5 - - + -
176G SER* 1.3 74.0 - - - +
178G VAL* 1.3 61.7 + - - +
179G LEU* 3.9 9.9 - - + -
201G THR* 4.0 23.8 - - + -
213G PHE* 3.6 28.6 - + + -
246G CYS 3.4 1.6 - - - +
247G ARG* 3.4 5.0 - - - -
248G ILE* 2.7 43.0 + - + +
249G PRO 3.6 6.5 - - - -
250G LYS* 3.0 62.2 + - + +
252G SER* 4.9 0.7 - - - -
253G ILE* 3.9 28.0 - - + +
257G PRO* 4.9 10.1 - - + -
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Residues in contact with VAL 178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169G THR* 3.7 1.4 + - - +
170G ALA* 3.3 2.9 - - - -
171G ARG* 2.7 54.8 + - - +
173G GLU* 3.6 20.9 - - + -
176G SER 4.8 0.4 - - - +
177G TRP* 1.3 77.8 - - - +
179G LEU* 1.3 63.9 + - - +
180G ASN* 4.0 16.2 + - - +
245G ASP* 3.4 35.9 - - - +
246G CYS 3.5 2.5 - - - +
247G ARG* 3.4 34.1 - - + +
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Residues in contact with LEU 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168G THR* 5.2 1.8 - - + -
169G THR 3.3 7.9 - - - +
170G ALA* 4.0 14.6 - - + -
177G TRP* 3.9 10.1 - - + +
178G VAL* 1.3 88.2 - - - +
180G ASN* 1.3 65.2 + - - +
197G VAL* 4.8 11.4 - - + -
199G ALA* 4.9 5.2 - - + -
213G PHE* 4.7 9.6 - - + -
215G VAL* 3.9 16.8 - - + -
243G PHE* 3.8 26.2 - - + +
245G ASP 3.4 2.3 + - - -
246G CYS* 2.9 38.8 + - + +
248G ILE* 3.6 35.2 - - + -
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Residues in contact with ASN 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B MET* 6.0 4.0 - - + +
167G SER 4.3 1.7 - - - +
168G THR* 3.4 4.8 - - - -
169G THR* 2.8 48.0 + - - +
171G ARG* 5.0 7.3 - - - +
178G VAL* 4.0 20.4 + - - +
179G LEU* 1.3 79.5 + - - +
181G GLY* 1.3 57.6 + - - +
243G PHE* 3.5 4.2 - - - +
244G GLU* 3.8 6.4 - - - +
245G ASP* 2.8 26.8 + - - +
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Residues in contact with GLY 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167G SER 5.2 1.1 - - - -
168G THR* 3.6 17.5 - - - -
180G ASN* 1.3 74.3 - - - +
182G THR* 1.3 61.4 + - - -
183G LYS 4.2 0.2 - - - -
242G ILE* 4.6 0.8 - - - +
243G PHE* 2.7 47.9 + - - +
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Residues in contact with THR 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156G GLU* 3.6 8.5 - - - +
157G PRO* 3.4 30.4 - - + +
168G THR* 3.5 11.6 + - - -
181G GLY* 1.3 75.5 + - - -
183G LYS* 1.3 75.5 + - - +
240G ASN* 3.7 26.9 - - + +
241G LEU 3.4 4.7 - - - +
242G ILE* 4.0 21.4 - - + +
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Residues in contact with LYS 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153G ALA* 3.2 40.4 - - + -
154G LEU 3.0 25.1 + - - -
155G SER 3.3 7.0 - - - +
156G GLU* 3.0 20.4 + - - +
166G ALA* 4.3 3.8 - - - +
168G THR* 3.2 25.1 - - + +
182G THR* 1.3 80.1 - - - +
184G ALA* 1.3 60.2 + - - +
186G ILE* 4.2 4.5 - - + -
197G VAL* 4.1 2.5 - - + -
198G PHE* 2.6 26.5 + - - +
240G ASN* 3.1 5.2 - - - -
241G LEU* 2.9 36.4 + - + +
243G PHE* 3.9 22.9 - - + -
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Residues in contact with ALA 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155G SER* 2.8 16.1 + - - -
156G GLU* 3.4 28.7 - - - +
157G PRO* 3.4 12.8 - - + -
183G LYS* 1.3 74.6 - - - +
185G TRP* 1.3 87.7 + - + +
186G ILE* 3.2 14.8 - - - +
240G ASN* 3.2 13.2 - - - +
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Residues in contact with TRP 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155G SER* 4.1 7.4 - - - -
156G GLU 4.4 7.1 + - - -
157G PRO* 5.3 2.8 + - - +
184G ALA* 1.3 96.4 - - + +
186G ILE* 1.3 59.5 + - - +
187G THR 3.2 1.9 + - - -
228G GLU* 3.8 21.7 + - + -
238G THR* 3.4 18.0 - - + +
239G ALA 3.9 2.3 + - - +
240G ASN* 3.6 8.1 + - - -
501G FAD 2.9 89.7 + + + +
297H ARG* 6.1 0.2 - - - +
369H GLY* 3.6 32.1 - - - -
370H MET* 3.8 27.6 - - + -
373H VAL* 3.8 28.5 - - + -
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Residues in contact with ILE 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151G CYS* 3.8 27.6 - - + -
152G PHE 3.5 13.9 - - - +
153G ALA* 3.6 17.3 - - + -
154G LEU 4.3 0.7 - - - +
155G SER 4.6 0.2 - - - +
183G LYS* 4.2 18.8 - - + -
184G ALA 3.2 24.2 - - - +
185G TRP* 1.3 74.2 - - - +
187G THR* 1.3 71.2 + - - +
189G ALA* 3.2 19.1 + - + +
238G THR* 3.3 2.5 - - - -
239G ALA 2.9 36.7 + - - +
241G LEU* 4.3 11.7 - - + -
501G FAD 3.5 20.6 - - + +
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Residues in contact with THR 187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G VAL* 4.3 13.1 - - + +
118G VAL* 3.8 26.2 - - + +
151G CYS* 3.5 16.1 - - - +
185G TRP 3.2 1.6 + - - -
186G ILE* 1.3 72.4 - - - +
188G ASN* 1.3 81.4 + - - +
233G ILE* 5.6 0.9 - - - +
236G SER* 4.2 18.2 + - - +
237G SER 3.1 10.1 - - - +
238G THR* 4.4 3.0 + - - +
391G TYR* 4.8 3.8 - - - -
501G FAD 3.0 44.9 + - - +
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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