Contacts of the strand formed by residues 176 - 187 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A ALA* 3.5 6.6 - - - +
173A GLU 3.0 28.0 + - - -
174A GLY 3.2 2.2 - - - +
175A ASP* 1.3 94.1 + - - +
177A TRP* 1.3 68.2 + - - +
178A VAL* 5.1 1.6 - - - -
247A ARG* 3.1 39.8 + - - +
248A ILE 3.4 15.2 + - - -
249A PRO* 4.5 4.5 - - - +
250A LYS* 4.3 2.2 - - - +
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Residues in contact with TRP 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ALA* 4.5 5.6 - - + -
171A ARG 3.4 7.2 - - - -
172A ALA* 3.8 36.6 - - + -
176A SER* 1.3 78.0 - - - +
178A VAL* 1.3 63.0 + - - +
179A LEU* 4.1 10.3 - - + -
201A THR* 4.2 19.3 - - + -
213A PHE* 3.5 29.4 - + + -
246A CYS 3.4 1.6 - - - +
247A ARG* 3.4 3.8 - - - -
248A ILE* 3.0 42.1 + - + +
249A PRO 3.8 19.3 - - - -
250A LYS* 3.2 25.7 + - + +
253A ILE* 3.9 28.8 - - + +
257A PRO* 4.7 13.7 - - + -
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A THR* 3.6 2.4 + - - +
170A ALA* 3.3 2.6 - - - -
171A ARG* 2.9 55.9 + - - +
173A GLU* 3.7 29.4 - - + -
176A SER* 5.1 0.7 - - - -
177A TRP* 1.3 78.5 - - - +
179A LEU* 1.3 64.3 + - - +
180A ASN* 4.0 12.0 + - - +
245A ASP* 3.9 32.3 - - + +
246A CYS 3.4 3.6 - - - +
247A ARG* 4.7 16.6 - - + +
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A THR* 5.2 2.2 - - + -
169A THR 3.2 8.5 - - - +
170A ALA* 3.8 21.8 - - + -
177A TRP* 4.1 9.0 - - + -
178A VAL* 1.3 80.0 - - - +
180A ASN* 1.3 66.5 + - - +
197A VAL* 4.3 14.1 - - + -
199A ALA* 4.7 4.7 - - + -
213A PHE* 4.7 8.3 - - + -
215A VAL* 4.2 9.4 - - + -
243A PHE* 3.6 42.1 - - + +
245A ASP 3.5 1.9 + - - -
246A CYS 2.9 34.0 + - - +
248A ILE* 3.9 33.4 - - + -
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Residues in contact with ASN 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A SER 4.3 1.7 - - - +
168A THR* 3.4 5.0 - - - -
169A THR* 2.9 46.1 + - - +
171A ARG* 4.3 13.5 - - - +
178A VAL* 4.0 16.0 + - - +
179A LEU* 1.3 80.1 + - - +
181A GLY* 1.3 59.1 + - - +
243A PHE* 3.5 3.7 - - - +
244A GLU* 3.5 9.4 - - - +
245A ASP* 2.9 35.9 + - - +
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Residues in contact with GLY 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A SER 5.4 0.7 - - - -
168A THR* 3.4 15.9 - - - -
180A ASN* 1.3 75.1 - - - +
182A THR* 1.3 61.6 + - - -
183A LYS 4.2 0.2 - - - -
242A ILE* 3.7 0.8 - - - -
243A PHE* 2.8 42.9 + - - +
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Residues in contact with THR 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A GLU* 3.5 14.7 - - - +
157A PRO* 3.6 22.5 - - + +
168A THR* 3.3 11.2 + - - -
181A GLY* 1.3 74.0 + - - -
183A LYS* 1.3 73.4 + - - +
240A ASN* 3.7 27.4 - - + +
241A LEU 3.4 4.7 - - - +
242A ILE* 4.0 20.6 - - + +
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Residues in contact with LYS 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ALA* 3.4 40.6 + - + -
154A LEU* 3.2 27.1 + - - +
155A SER 3.3 9.0 - - - +
156A GLU* 2.7 21.3 + - - +
166A ALA* 4.2 4.6 - - - +
168A THR* 3.4 25.5 - - + +
182A THR* 1.3 75.1 - - - +
184A ALA* 1.3 60.0 + - - +
186A ILE* 4.0 7.6 - - + -
197A VAL* 4.5 3.1 - - + -
198A PHE* 2.6 27.8 + - - +
240A ASN* 3.1 11.1 - - - +
241A LEU* 2.8 32.3 + - + +
243A PHE* 4.1 18.2 - - + -
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Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A SER* 2.9 17.5 + - - +
156A GLU* 3.6 5.3 - - - +
157A PRO* 3.5 32.8 - - + -
183A LYS* 1.3 71.5 - - - +
185A TRP* 1.3 84.3 + - + +
186A ILE* 3.2 17.8 - - - +
228A GLU* 5.9 0.4 - - - +
240A ASN* 3.3 17.3 - - - +
501A FAD 4.2 0.2 + - - -
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Residues in contact with TRP 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A SER* 4.0 8.7 - - - -
156A GLU 4.4 6.6 + - - -
157A PRO* 5.3 3.6 + - + +
184A ALA* 1.3 96.6 - - + +
186A ILE* 1.3 61.9 + - - +
187A THR 3.2 0.2 + - - -
228A GLU* 4.0 27.0 + - + -
230A LYS* 6.6 0.2 - - + -
238A THR* 3.4 16.6 - - + +
239A ALA* 3.8 6.3 + - - +
240A ASN* 3.9 3.6 + - - -
501A FAD 2.9 89.5 + + + +
297B ARG* 6.0 0.6 - - - +
369B GLY* 3.4 35.2 - - - -
370B MET* 3.7 27.1 - - + -
373B VAL* 3.8 26.0 - - + -
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Residues in contact with ILE 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A CYS* 3.6 35.7 - - + -
152A PHE 3.7 16.4 - - - +
153A ALA* 3.6 31.4 - - + -
154A LEU 4.3 0.9 - - - +
155A SER 4.5 0.2 - - - +
183A LYS* 4.0 11.7 - - + -
184A ALA 3.2 25.4 - - - +
185A TRP* 1.3 74.6 - - - +
187A THR* 1.3 63.3 + - - +
189A ALA* 3.2 17.7 + - + +
238A THR* 3.3 3.7 - - - -
239A ALA 3.0 27.1 + - - +
241A LEU* 3.9 20.4 - - + -
501A FAD 3.8 10.3 - - - +
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Residues in contact with THR 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A VAL* 4.2 17.6 - - + +
118A VAL* 3.7 25.8 - - + +
151A CYS* 3.3 19.6 - - - +
185A TRP 3.2 1.8 + - - -
186A ILE* 1.3 70.9 - - - +
188A ASN* 1.3 81.0 + - - +
189A ALA 3.2 0.4 - - - -
233A ILE* 5.6 0.9 - - - +
236A SER* 4.1 18.1 + - - +
237A SER 3.1 9.9 - - - +
238A THR* 4.5 2.9 + - - +
391A TYR* 4.9 0.5 - - - -
501A FAD 3.0 43.4 + - - +
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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
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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