Contacts of the strand formed by residues 176 - 187 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172F ALA* 3.6 4.5 - - - -
173F GLU 2.9 34.4 + - - -
175F ASP* 1.3 80.5 + - - +
177F TRP* 1.3 66.1 + - - +
178F VAL* 4.9 0.9 - - - -
247F ARG* 3.8 29.8 + - - +
248F ILE 3.2 18.1 + - - -
249F PRO* 4.5 1.2 - - - +
250F LYS* 3.8 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 177 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170F ALA* 4.3 6.3 - - + -
171F ARG 3.5 5.4 - - - -
172F ALA* 3.6 40.6 - - + -
176F SER* 1.3 73.8 - - - +
178F VAL* 1.3 61.4 + - - +
179F LEU* 4.0 11.0 - - + -
201F THR* 4.0 20.9 - - + -
213F PHE* 3.6 29.4 - + + -
246F CYS 3.4 1.9 - - - +
247F ARG* 3.3 5.2 - - - -
248F ILE* 2.8 42.7 + - + +
249F PRO 3.5 9.0 - - - -
250F LYS* 3.1 57.5 + - + +
253F ILE* 3.7 27.4 - - + +
257F PRO* 4.7 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F THR* 3.6 2.6 + - - +
170F ALA* 3.4 2.4 - - - -
171F ARG* 2.7 67.2 + - - +
173F GLU* 4.1 12.8 - - + -
176F SER* 4.9 1.1 - - - -
177F TRP* 1.3 77.4 - - - +
179F LEU* 1.3 63.1 + - - +
180F ASN* 3.9 9.5 + - - +
245F ASP* 3.6 38.1 - - + +
246F CYS 3.4 2.7 - - - +
247F ARG* 3.6 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 179 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F THR* 5.2 2.7 - - + -
169F THR 3.3 7.4 - - - +
170F ALA* 3.7 22.2 - - + -
177F TRP* 4.0 19.1 - - + +
178F VAL* 1.3 79.6 - - - +
180F ASN* 1.3 66.5 + - - +
197F VAL* 4.6 10.1 - - + -
199F ALA* 4.8 7.2 - - + -
213F PHE* 5.0 5.8 - - + -
215F VAL* 4.2 9.4 - - + -
243F PHE* 3.6 43.7 - - + +
245F ASP 3.4 2.1 + - - -
246F CYS* 2.7 36.6 + - - +
248F ILE* 4.1 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 180 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F SER 4.3 1.6 - - - +
168F THR* 3.4 5.7 - - - -
169F THR* 3.0 44.0 + - - +
171F ARG* 4.2 11.1 - - - +
178F VAL* 3.9 10.3 + - - +
179F LEU* 1.3 82.0 + - - +
181F GLY* 1.3 58.5 + - - +
243F PHE* 3.4 3.3 - - - +
244F GLU* 3.5 9.9 - - - +
245F ASP* 2.8 43.6 + - - +
505F EDO 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 181 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F THR* 3.8 8.5 - - - -
180F ASN* 1.3 74.9 - - - +
182F THR* 1.3 64.6 + - - -
183F LYS 4.2 0.2 - - - -
242F ILE* 5.2 0.7 - - - -
243F PHE* 2.8 45.0 + - - +
505F EDO 3.6 19.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 182 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156F GLU* 3.6 3.1 - - - +
157F PRO* 3.4 19.1 - - + +
168F THR* 3.5 4.6 + - - -
181F GLY* 1.3 75.3 + - - -
183F LYS* 1.3 71.6 + - - +
240F ASN* 3.5 29.2 - - + +
241F LEU 3.4 4.9 - - - +
242F ILE* 3.9 20.3 - - + +
505F EDO 2.6 42.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 183 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F ALA* 3.3 28.5 - - + -
154F LEU 3.1 27.3 + - - -
155F SER 3.3 9.2 - - - +
156F GLU* 2.8 22.7 + - - +
166F ALA* 4.2 5.1 - - - +
168F THR* 3.2 24.2 + - + +
182F THR* 1.3 76.4 - - - +
184F ALA* 1.3 61.6 + - - +
186F ILE* 4.0 14.4 - - + -
197F VAL* 4.4 2.7 - - + -
198F PHE* 2.7 26.5 + - - +
240F ASN* 3.2 9.7 - - - +
241F LEU* 2.9 35.4 + - + +
243F PHE* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155F SER* 2.9 18.4 + - - +
156F GLU* 3.5 5.1 - - - +
157F PRO* 3.4 33.9 - - + -
183F LYS* 1.3 74.3 - - - +
185F TRP* 1.3 88.8 + - + +
186F ILE* 3.3 12.6 - - - +
240F ASN* 3.3 14.1 - - - +
501F FAD 4.1 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 185 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369E GLY* 3.4 34.1 - - - -
370E MET* 3.6 27.4 - - + -
373E VAL* 3.7 26.9 - - + -
155F SER* 4.1 7.0 - - - -
156F GLU 4.6 5.8 + - - -
157F PRO* 5.3 2.6 + - - +
160F GLY* 6.0 0.4 - - - -
184F ALA* 1.3 98.6 - - + +
186F ILE* 1.3 61.8 + - - +
187F THR 3.3 0.2 + - - -
228F GLU* 3.9 22.8 + - + -
238F THR* 3.5 21.8 - - + +
239F ALA* 3.8 6.1 + - - +
240F ASN* 3.9 3.6 + - - -
501F FAD 2.9 89.2 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 186 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F CYS* 3.7 29.6 - - + -
152F PHE 3.7 13.5 - - - +
153F ALA* 3.5 32.5 - - + -
154F LEU 4.4 0.4 - - - +
155F SER 4.5 0.2 - - - +
183F LYS* 4.0 12.8 - - + -
184F ALA 3.3 20.2 - - - +
185F TRP* 1.3 74.7 - - - +
187F THR* 1.3 67.0 + - - +
189F ALA* 3.2 11.3 + - + +
238F THR* 3.3 4.5 - - - -
239F ALA 3.0 33.8 + - - +
241F LEU* 3.8 24.9 - - + +
501F FAD 3.8 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 187 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F VAL* 4.4 15.5 - - + +
118F VAL* 3.7 27.5 - - + +
151F CYS* 3.2 20.4 - - - +
185F TRP 3.3 0.8 + - - -
186F ILE* 1.3 71.5 - - - +
188F ASN* 1.3 82.4 + - - +
189F ALA 3.5 0.2 + - - -
233F ILE* 5.7 1.0 - - - +
236F SER* 4.3 17.0 + - - +
237F SER 3.2 9.8 + - - +
238F THR* 4.6 2.2 + - - +
391F TYR* 5.0 0.2 - - - -
501F FAD 3.0 45.2 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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