Contacts of the strand formed by residues 176 - 187 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173D GLU* 2.9 28.7 + - - +
174D GLY 3.2 1.2 - - - -
175D ASP* 1.3 83.0 + - - +
177D TRP* 1.3 67.2 + - - +
178D VAL* 4.9 0.2 - - - -
247D ARG* 3.7 41.1 + - - +
248D ILE 3.1 19.5 + - - -
249D PRO* 4.3 1.0 - - - +
250D LYS* 3.5 13.3 - - - +
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Residues in contact with TRP 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D ALA 4.3 2.2 - - - -
171D ARG 3.6 10.1 - - - -
172D ALA* 3.6 38.8 - - + -
176D SER* 1.3 71.9 - - - +
178D VAL* 1.3 60.1 + - - +
179D LEU* 4.1 10.1 - - + -
201D THR* 3.9 25.4 - - + -
213D PHE* 3.6 29.9 - + + -
246D CYS 3.5 1.2 - - - +
247D ARG* 3.3 4.0 - - - -
248D ILE* 2.8 43.7 + - + +
249D PRO 3.6 21.1 - - - -
250D LYS* 3.1 43.7 + - + +
252D SER* 4.8 1.1 - - - -
253D ILE* 4.1 23.9 - - + +
257D PRO* 5.0 10.5 - - + -
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Residues in contact with VAL 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D THR* 3.5 2.1 + - - +
170D ALA* 3.3 3.3 - - - -
171D ARG* 2.8 62.4 + - + +
173D GLU* 3.7 28.7 - - + +
176D SER 4.7 0.9 - - - +
177D TRP* 1.3 76.8 - - - +
179D LEU* 1.3 63.7 + - - +
180D ASN* 3.8 12.6 + - - +
245D ASP* 3.7 33.7 - - + +
246D CYS 3.4 2.7 - - - +
247D ARG* 3.9 22.0 - - + +
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Residues in contact with LEU 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D THR* 5.2 2.7 - - + -
169D THR 3.3 6.3 - - - +
170D ALA* 3.9 19.3 - - + -
177D TRP* 4.1 10.3 - - + -
178D VAL* 1.3 79.1 - - - +
180D ASN* 1.3 61.4 + - - +
197D VAL* 4.5 12.1 - - + -
199D ALA* 4.9 7.0 - - + -
213D PHE* 4.9 6.7 - - + -
215D VAL* 4.1 17.3 - - + -
243D PHE* 3.6 35.8 - - + +
245D ASP 3.3 6.2 + - - -
246D CYS* 2.7 36.5 + - - +
248D ILE* 3.9 36.3 - - + -
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Residues in contact with ASN 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D SER 4.3 1.4 - - - +
168D THR* 3.3 5.3 - - - +
169D THR* 2.8 49.5 + - - +
171D ARG* 5.4 4.2 - - - +
178D VAL* 3.8 18.0 + - - +
179D LEU* 1.3 84.1 + - - +
181D GLY* 1.3 58.3 + - - +
243D PHE* 3.6 4.0 - - - +
244D GLU* 3.8 8.8 - - - +
245D ASP* 3.1 23.6 + - - +
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Residues in contact with GLY 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D SER 5.2 1.6 - - - -
168D THR* 3.8 15.7 - - - -
180D ASN* 1.3 73.7 - - - +
182D THR* 1.3 63.0 + - - -
242D ILE* 5.3 0.2 - - - -
243D PHE* 2.8 41.5 + - - +
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Residues in contact with THR 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D GLU* 3.6 9.0 - - - +
157D PRO* 3.5 28.7 - - + +
168D THR* 3.5 9.7 + - - -
181D GLY* 1.3 74.5 + - - -
183D LYS* 1.3 75.7 + - - +
240D ASN* 3.7 28.9 - - + +
241D LEU 3.3 5.4 - - - +
242D ILE* 3.8 22.1 - - + +
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Residues in contact with LYS 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ALA* 3.2 45.3 + - + -
154D LEU* 3.0 24.4 + - - +
155D SER 3.3 6.3 - - - +
156D GLU* 2.9 20.0 + - - +
166D ALA* 4.3 4.8 - - - +
168D THR* 3.3 24.2 - - + +
182D THR* 1.3 76.8 - - - +
184D ALA* 1.3 61.2 + - - +
186D ILE* 4.1 5.4 - - + -
197D VAL* 4.3 2.2 - - + -
198D PHE* 2.8 25.7 + - - +
240D ASN* 3.1 8.7 - - - +
241D LEU* 2.8 37.1 + - + +
243D PHE* 4.0 20.4 - - + -
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Residues in contact with ALA 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D SER* 2.9 17.3 + - - +
156D GLU* 3.6 5.8 - - - +
157D PRO* 3.4 32.5 - - + -
183D LYS* 1.3 73.9 - - - +
185D TRP* 1.3 88.3 + - + +
186D ILE* 3.2 13.3 - - - +
240D ASN* 3.3 14.6 - - - +
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Residues in contact with TRP 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C ARG* 6.1 0.4 - - - +
369C GLY* 3.5 35.9 - - - -
370C MET* 3.8 27.6 - - + -
373C VAL* 3.7 28.3 - - + -
155D SER* 4.1 7.2 - - - -
156D GLU 4.7 6.3 + - - -
157D PRO* 5.3 3.0 + - - +
160D GLY* 6.0 0.2 - - - -
184D ALA* 1.3 95.5 - - + +
186D ILE* 1.3 62.2 + - - +
187D THR 3.2 0.2 + - - -
228D GLU* 3.9 20.5 + - + -
238D THR* 3.5 23.1 - - + -
239D ALA 3.9 4.1 + - - +
240D ASN* 3.9 5.3 + - - -
501D FAD 2.8 89.5 + + + +
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Residues in contact with ILE 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D CYS* 3.7 23.3 - - + -
152D PHE 3.5 17.3 - - - +
153D ALA* 3.5 33.0 - - + -
155D SER 4.6 0.2 - - - +
183D LYS* 4.1 12.8 - - + -
184D ALA 3.2 23.6 - - - +
185D TRP* 1.3 76.3 - - - +
187D THR* 1.3 73.2 + - - +
189D ALA* 3.4 9.5 - - + +
238D THR* 3.2 3.9 - - - -
239D ALA 3.1 36.8 + - - +
241D LEU* 4.0 19.7 - - + -
501D FAD 3.6 9.9 - - - +
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Residues in contact with THR 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D VAL* 4.0 20.2 - - + +
118D VAL* 3.7 28.4 - - + +
151D CYS* 3.4 19.6 - - - +
185D TRP 3.2 1.2 + - - -
186D ILE* 1.3 71.5 - - - +
188D ASN* 1.3 79.0 + - - +
233D ILE* 5.5 0.6 - - + +
236D SER* 4.2 15.7 + - - +
237D SER 3.1 10.1 - - - +
238D THR* 4.4 2.9 + - - +
391D TYR* 4.8 0.3 - - - -
501D FAD 3.0 45.0 + - - +
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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