Contacts of the strand formed by residues 210 - 216 (chain B) 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 ILE 210 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU* 5.7 2.7 - - + -
163B ALA 4.2 5.4 - - - +
164B GLY* 3.7 37.9 - - - +
166B ALA* 4.4 11.7 - - + +
198B PHE* 4.1 18.2 - - + -
199B ALA 3.5 8.7 - - - +
200B SER* 4.6 8.1 - - - -
209B SER* 1.3 84.7 + - - +
211B SER* 1.3 66.1 + - - +
258B GLY 3.1 13.2 + - - +
260B GLY* 2.7 39.7 + - - -
261B PHE* 3.8 27.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B VAL 3.6 0.9 - - - +
198B PHE* 3.3 4.9 - - - -
199B ALA 2.8 35.6 + - - -
201B THR* 2.9 26.9 + - - +
210B ILE* 1.3 72.5 - - - +
212B ALA* 1.3 60.6 + - - +
213B PHE* 3.7 23.5 - - - -
253B ILE* 4.0 11.9 - - - -
256B GLU 5.0 1.1 - - - -
257B PRO* 3.4 6.6 - - - +
258B GLY 2.9 19.8 + - - -
260B GLY* 3.7 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B VAL* 4.5 2.7 - - + -
197B VAL 3.5 4.9 - - - +
198B PHE* 3.8 26.0 - - + -
211B SER* 1.3 71.1 - - - +
213B PHE* 1.3 58.6 + - - +
253B ILE* 3.4 10.7 - - - +
254B LEU* 2.7 56.4 + - + +
256B GLU 5.8 0.4 + - - -
260B GLY* 3.9 3.9 - - - +
263B ILE* 4.3 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ALA* 3.5 30.5 - - + -
177B TRP* 3.5 36.6 - + + -
179B LEU* 4.8 6.3 - - + -
195B ALA 3.4 3.6 - - - +
196B VAL* 3.4 2.3 - - - +
197B VAL* 2.8 46.4 + - - +
199B ALA* 3.9 12.1 - - + -
201B THR* 3.9 6.1 - - + -
211B SER* 3.7 35.0 - - - -
212B ALA* 1.3 78.4 - - - +
214B LEU* 1.3 65.6 + - - +
215B VAL* 3.6 7.2 + - + -
248B ILE* 4.0 26.7 - - + -
252B SER 3.5 2.9 - - - -
253B ILE* 3.8 20.4 - - + -
254B LEU* 4.4 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B TYR* 5.3 0.4 - - + -
127B ILE* 3.9 31.2 - - + -
135B GLN* 4.1 26.9 - - + +
139B TRP* 3.5 61.3 - - + +
195B ALA 3.6 3.8 - - - +
196B VAL* 4.2 11.4 - - + -
213B PHE* 1.3 74.1 - - - +
215B VAL* 1.3 59.5 + - - +
216B PRO* 4.2 2.1 - - - +
248B ILE* 3.9 2.9 - - - +
252B SER* 2.9 38.7 + - - +
254B LEU* 4.2 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TRP* 4.0 3.3 - - - -
179B LEU* 3.9 19.3 - - + -
194B ALA* 3.2 4.0 - - - +
195B ALA* 2.9 36.1 + - + +
197B VAL* 3.2 36.1 - - + -
213B PHE 4.0 2.7 - - - +
214B LEU* 1.3 77.4 - - - +
216B PRO* 1.4 78.9 - - + +
217B MET* 4.1 1.6 - - + +
219B THR* 4.3 10.1 - - + -
222B LEU* 4.5 4.9 - - + -
243B PHE* 3.8 21.8 - - + -
246B CYS* 4.7 0.2 - - - -
248B ILE* 4.3 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TRP* 3.9 20.2 - - + -
193B SER 3.7 8.5 - - - +
214B LEU 4.2 2.2 - - - +
215B VAL* 1.4 97.1 - - + +
217B MET* 1.3 60.9 + - - +
218B PRO 3.8 5.6 - - - +
219B THR* 3.3 32.4 - - - +
222B LEU* 4.0 0.2 - - - +
248B ILE* 4.4 12.3 - - + -
249B PRO* 6.1 2.9 - - + -
252B SER* 5.9 0.2 - - - +
----------------------------------------------------------
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