Contacts of the strand formed by residues 258 - 263 (chain I) in PDB entry 2OHI
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 ARG 258 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256I ASP* 3.0 28.8 + - - +
257I GLU* 1.3 75.2 - - - +
259I VAL* 1.3 68.5 + - - +
260I THR* 4.6 0.7 - - - +
286I VAL* 3.8 0.4 - - - -
287I ASP* 2.9 42.8 + - - +
289I ARG* 4.3 28.0 - - + +
304I ASP* 4.5 5.8 + - - -
307I GLU* 3.3 45.6 + - - +
308I SER* 3.5 18.7 - - - +
309I GLY* 3.0 25.5 + - - +
310I ALA 3.4 5.2 + - - -
402I ILE* 3.8 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 259 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258I ARG* 1.3 79.5 - - - +
260I THR* 1.3 71.1 + - - +
261I VAL* 4.3 12.1 - - + -
277I ILE* 5.9 0.2 - - + -
281I ALA* 4.1 14.1 - - + -
286I VAL* 4.0 4.0 - - + -
287I ASP 2.9 9.6 + - - +
288I VAL* 3.5 5.4 - - + +
289I ARG 3.1 24.3 + - - +
310I ALA* 3.2 17.3 - - + +
311I ILE* 4.7 0.7 - - - -
398I LEU* 3.8 24.2 - - + -
399I ALA* 4.0 26.0 - - + +
402I ILE* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 260 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259I VAL* 1.3 72.6 + - - +
261I VAL* 1.3 61.9 + - - +
262I ILE* 3.8 25.4 + - + +
289I ARG* 3.8 9.7 - - + +
291I TYR* 4.1 22.7 - - + -
301I ILE 4.8 1.3 - - - +
304I ASP* 3.3 17.2 + - + +
305I ILE* 4.6 9.0 - - + -
308I SER* 2.5 28.2 + - - -
310I ALA 2.8 9.5 + - - -
311I ILE* 3.0 14.8 - - - +
312I ALA 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 261 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259I VAL* 4.3 12.8 - - + -
260I THR* 1.3 74.1 - - - +
262I ILE* 1.3 59.4 + - - +
274I ALA* 3.9 33.4 - - + +
277I ILE* 4.5 6.7 - - + -
278I ALA* 4.3 16.8 - - + -
281I ALA* 6.0 0.2 - - + -
288I VAL* 4.4 4.0 - - + -
289I ARG 2.7 20.0 + - - +
290I VAL* 3.2 17.2 + - + -
291I TYR* 2.6 34.6 + - - +
312I ALA* 3.6 20.9 - - + +
349I PHE* 4.3 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 262 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260I THR* 3.8 25.1 - - + +
261I VAL* 1.3 79.6 - - - +
263I TYR* 1.3 63.8 + - - +
291I TYR* 3.5 11.2 - - + +
293I LEU* 3.8 27.1 - - + -
301I ILE* 3.8 28.5 - - + -
305I ILE* 4.4 8.3 - - + -
311I ILE* 4.2 26.2 - - + -
312I ALA 2.8 12.3 + - - +
313I LEU* 3.3 11.4 - - + +
314I GLY 2.9 21.5 + - - -
329I LEU* 3.9 20.9 - - + -
349I PHE* 4.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 263 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ASP* 2.2 40.2 + - - +
261I VAL* 5.0 0.2 - - + -
262I ILE* 1.3 77.9 - - - +
264I ASP* 1.3 72.9 + - - +
265I THR* 3.9 12.8 - - + -
270I THR* 4.6 0.2 - - + -
271I ARG* 3.4 42.5 + - + -
274I ALA* 3.6 18.4 - - + -
275I HIS* 5.2 1.1 - + - -
290I VAL* 3.9 14.6 - - + -
291I TYR 3.1 31.6 + - - -
292I CYS* 3.5 21.2 - - + +
293I LEU* 2.9 31.6 + - - +
314I GLY* 3.2 12.8 - - - +
349I PHE* 4.0 20.2 - - + -
----------------------------------------------------------
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