Contacts of the strand formed by residues 176 - 187 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172C ALA* 3.4 3.8 - - - -
173C GLU 2.7 41.3 + - - -
174C GLY 3.2 3.0 + - - -
175C ASP* 1.3 80.5 + - - +
177C TRP* 1.3 63.3 + - - +
178C VAL* 4.9 0.4 - - - -
247C ARG* 4.0 27.6 + - - +
248C ILE 3.2 17.4 + - - -
249C PRO* 4.3 1.0 - - - +
250C LYS* 3.6 11.0 - - - +
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Residues in contact with TRP 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C ALA* 4.2 5.4 - - + -
171C ARG 3.4 8.5 - - - -
172C ALA* 3.6 30.7 - - + -
176C SER* 1.3 72.4 - - - +
178C VAL* 1.3 61.6 + - - +
179C LEU* 4.0 10.5 - - + -
201C THR* 3.8 23.8 - - + -
213C PHE* 3.5 26.2 - + + -
246C CYS 3.6 1.2 - - - +
247C ARG* 3.4 3.5 - - - -
248C ILE* 2.9 42.0 + - + +
249C PRO 3.5 7.2 - - - -
250C LYS* 2.9 68.9 + - + +
253C ILE* 4.0 28.4 - - + +
257C PRO* 4.7 12.6 - - + -
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Residues in contact with VAL 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C THR* 3.4 5.0 + - - +
171C ARG* 2.7 54.8 + - - +
173C GLU* 4.1 10.3 - - + -
176C SER* 4.8 0.9 - - - +
177C TRP* 1.3 77.6 - - - +
179C LEU* 1.3 62.0 + - - +
180C ASN* 3.9 10.0 + - - +
245C ASP* 3.8 44.2 - - - +
246C CYS 3.3 2.7 - - - +
247C ARG* 3.2 42.6 - - + +
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Residues in contact with LEU 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C THR* 5.3 2.5 - - + -
169C THR 3.2 7.2 - - - +
170C ALA* 3.7 22.4 - - + -
177C TRP* 4.0 9.9 - - + -
178C VAL* 1.3 78.3 - - - +
180C ASN* 1.3 65.7 + - - +
197C VAL* 4.5 13.7 - - + -
199C ALA* 4.7 5.8 - - + -
213C PHE* 4.7 8.5 - - + -
215C VAL* 4.0 17.3 - - + -
243C PHE* 3.4 34.2 - - + +
245C ASP 3.4 0.9 + - - -
246C CYS* 2.7 37.2 + - + +
248C ILE* 3.8 34.8 - - + -
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Residues in contact with ASN 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C SER 4.3 1.7 - - - +
168C THR* 3.3 5.9 - - - -
169C THR* 2.8 50.1 + - - +
171C ARG* 4.2 11.9 - - - +
178C VAL* 3.9 13.5 + - - +
179C LEU* 1.3 79.7 + - - +
181C GLY* 1.3 58.0 + - - +
243C PHE 3.5 2.2 - - - +
244C GLU* 3.6 7.1 - - - +
245C ASP* 2.7 41.8 + - - +
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Residues in contact with GLY 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C SER 5.4 0.4 - - - -
168C THR* 3.6 14.6 - - - -
180C ASN* 1.3 74.7 - - - +
182C THR* 1.3 62.3 + - - -
183C LYS 4.2 0.2 - - - -
242C ILE* 5.2 0.7 - - - -
243C PHE* 2.8 43.1 + - - +
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Residues in contact with THR 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C GLU* 3.6 7.6 - - - +
157C PRO* 3.4 29.1 - - + +
168C THR* 3.4 12.4 + - - -
181C GLY* 1.3 73.5 + - - -
183C LYS* 1.3 73.3 + - - +
240C ASN* 3.6 26.5 - - + +
241C LEU 3.2 7.2 - - - +
242C ILE* 3.7 22.3 - - + +
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Residues in contact with LYS 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ALA* 3.3 44.1 + - + -
154C LEU* 3.2 23.5 + - - +
155C SER 3.3 8.1 - - - +
156C GLU* 2.8 22.0 + - - +
166C ALA* 4.2 4.4 - - - +
168C THR* 3.4 25.7 - - + +
182C THR* 1.3 74.8 - - - +
184C ALA* 1.3 59.8 + - - +
186C ILE* 4.0 4.9 - - + -
197C VAL* 4.2 2.7 - - + -
198C PHE* 2.6 27.3 + - - +
240C ASN* 3.1 9.7 - - - +
241C LEU* 2.8 35.5 + - + +
243C PHE* 4.0 20.6 - - + -
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Residues in contact with ALA 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C SER* 2.8 19.3 + - - +
156C GLU* 3.5 5.8 - - - +
157C PRO* 3.4 33.7 - - + -
183C LYS* 1.3 73.9 - - - +
185C TRP* 1.3 81.7 + - + +
186C ILE* 2.9 19.5 - - - +
240C ASN* 3.4 13.7 - - - +
501C FAD 4.1 0.2 + - - -
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Residues in contact with TRP 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C SER* 4.1 6.7 - - - -
156C GLU 4.8 5.1 + - - -
157C PRO* 5.4 4.0 + - + +
160C GLY* 6.0 0.2 - - - -
184C ALA* 1.3 90.5 - - + +
186C ILE* 1.3 61.4 + - - +
187C THR 3.3 0.2 + - - -
228C GLU* 4.0 24.8 + - + -
238C THR* 3.3 15.5 - - + -
239C ALA 4.1 2.7 + - - +
240C ASN* 3.9 7.1 + - - -
501C FAD 2.8 91.6 + + + +
297D ARG* 6.1 0.2 - - - +
369D GLY* 3.5 22.9 - - - -
370D MET* 3.6 42.4 - - + -
373D VAL* 3.7 27.6 - - + -
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Residues in contact with ILE 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C CYS* 3.7 31.6 - - + -
152C PHE 3.6 17.7 - - - +
153C ALA* 3.6 29.6 - - + -
155C SER 4.4 0.7 - - - +
183C LYS* 4.0 9.9 - - + -
184C ALA 2.9 33.7 - - - +
185C TRP* 1.3 74.3 - - - +
187C THR* 1.3 62.2 + - - +
189C ALA* 3.2 19.3 + - + +
238C THR* 3.4 4.7 - - - +
239C ALA 3.1 27.2 + - - +
241C LEU* 4.0 20.9 - - + -
501C FAD 3.9 10.1 - - - +
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Residues in contact with THR 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C VAL* 4.2 18.9 - - + +
118C VAL* 3.7 27.2 - - + +
151C CYS* 3.3 21.0 - - - +
185C TRP 3.3 1.0 + - - -
186C ILE* 1.3 69.9 - - - +
188C ASN* 1.3 80.2 + - - +
189C ALA 3.3 0.4 - - - -
233C ILE* 5.6 1.4 - - + +
236C SER* 4.4 13.0 - - - +
237C SER 3.2 11.0 - - - +
238C THR* 4.4 2.4 + - - +
391C TYR* 4.9 0.7 - - - -
501C FAD 3.0 44.0 + - - +
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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