Contacts of the strand formed by residues 310 - 314 (chain E) 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 ALA 310 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258E ARG 3.5 4.2 + - - -
259E VAL* 3.4 14.5 - - + -
260E THR 3.1 21.1 + - - -
308E SER* 3.3 7.9 - - - -
309E GLY* 1.3 81.1 - - - +
311E ILE* 1.3 63.8 + - - +
344E ARG* 4.7 0.9 - - - -
345E LYS* 3.2 13.7 - - + +
398E LEU* 3.5 28.0 - - + +
402E ILE* 3.7 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 311 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E THR* 3.2 16.8 - - - +
262E ILE* 4.2 16.6 - - + -
305E ILE* 4.0 37.0 - - + -
308E SER* 4.7 4.5 - - - -
310E ALA* 1.3 79.7 - - - +
312E ALA* 1.3 60.0 + - - +
313E LEU* 5.0 6.5 - - + -
333E LEU* 5.0 3.6 - - + -
344E ARG* 5.3 2.4 - - + +
345E LYS 2.9 6.9 + - - +
346E ALA* 3.2 19.3 - - + -
347E LEU 2.9 22.3 + - - -
366E LEU* 4.0 22.0 - - + -
371E PHE* 3.7 30.5 - - + -
398E LEU* 3.8 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 312 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E THR 2.8 7.8 + - - +
261E VAL* 4.2 20.2 - - + -
262E ILE* 2.8 32.1 + - - +
277E ILE* 4.2 11.2 - - + -
311E ILE* 1.3 76.4 - - - +
313E LEU* 1.3 59.4 + - - +
347E LEU* 3.0 20.6 - - + +
349E PHE* 3.9 16.8 - - + -
398E LEU* 4.6 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 313 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262E ILE* 3.4 29.4 - - + +
293E LEU* 4.5 2.2 - - + -
311E ILE* 4.3 7.7 - - + +
312E ALA* 1.3 73.3 - - - +
314E GLY* 1.3 69.1 + - - +
326E VAL* 3.9 25.4 - - + -
329E LEU* 4.5 12.1 - - + -
330E LEU* 3.8 30.5 - - + -
333E LEU* 5.8 0.7 - - + -
347E LEU 2.6 11.1 + - - +
348E VAL* 3.3 5.0 - - + -
349E PHE* 3.0 26.0 + - - +
362E MET* 3.8 18.7 - - + +
366E LEU* 4.2 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 314 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262E ILE 2.8 12.1 + - - -
263E TYR* 3.1 5.0 - - - -
264E ASP 2.9 20.8 + - - -
270E THR* 3.9 3.8 - - - -
313E LEU* 1.3 76.6 - - - +
315E ALA* 1.3 63.8 + - - +
326E VAL* 4.1 5.0 - - - +
349E PHE* 3.2 30.7 - - - -
362E MET* 4.3 2.0 - - - -
----------------------------------------------------------
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