Contacts of the strand formed by residues 361 - 366 (chain D) in PDB entry 1OEY
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 THR 361 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D LYS* 3.9 21.8 - - + -
356D VAL 3.3 7.6 - - - +
357D HIS* 2.7 41.4 + - + +
360D TYR* 1.3 75.3 - - - +
362D VAL* 1.3 69.0 + - - +
293M ASP* 5.2 1.3 - - + -
294M LEU 3.4 23.3 + - - +
295M VAL* 4.3 6.3 - - + -
296M ARG* 2.9 28.2 + - - +
335M TYR* 3.6 9.2 - - - +
336M ASN 4.3 1.2 + - - -
337M THR* 3.8 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 362 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354D LEU 3.8 0.3 - - - +
355D LYS* 3.4 4.9 - - - +
356D VAL* 2.9 46.3 + - + +
360D TYR* 3.5 30.1 - - + -
361D THR* 1.3 78.2 - - - +
363D VAL* 1.3 66.5 + - - +
364D MSE 3.8 25.4 - - + -
382D LYS* 4.0 15.5 - - + -
383D LEU* 4.0 11.7 - - + -
295M VAL* 4.2 3.8 - - - -
296M ARG 4.4 8.7 - - - +
298M LEU* 3.9 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 363 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D THR* 3.9 24.5 - - + +
354D LEU 3.3 4.3 - - - +
355D LYS* 3.9 20.6 - - + -
362D VAL* 1.3 82.6 - - - +
364D MSE 1.3 64.2 + - - +
382D LYS* 4.1 3.5 - - - +
421D CYS* 6.0 0.9 - - - -
287M TYR* 4.0 12.6 - - - +
289M ASP* 4.8 3.6 - - + +
295M VAL* 3.9 30.8 - - + +
296M ARG 5.2 0.6 + - - -
302M ASP* 3.8 20.7 + - - +
305M LEU* 3.7 27.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 364 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D THR* 3.2 8.6 - - - -
354D LEU* 2.9 46.6 + - + +
356D VAL* 3.8 21.8 - - + -
362D VAL* 3.8 28.7 - - + -
363D VAL* 1.3 75.6 - - - +
365D LYS* 1.3 71.8 + - - +
378D MSE 4.0 31.9 - - - +
379D VAL* 3.9 17.9 - - + -
382D LYS* 3.9 28.0 - - + +
301M GLU* 5.8 0.4 - - - -
302M ASP* 5.5 0.4 - - - -
305M LEU* 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 365 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351D ALA* 6.3 4.9 - - + -
352D TYR 3.7 8.5 - - - +
353D THR* 4.4 6.5 - - + -
364D MSE 1.3 85.4 - - - +
366D THR* 1.3 61.8 + - - +
378D MSE 4.4 8.5 - - - +
301M GLU* 3.1 38.3 + - + +
305M LEU* 6.1 7.6 - - + +
308M ARG* 4.8 18.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 366 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352D TYR* 3.0 32.5 + - + +
353D THR 3.8 24.5 - - - +
354D LEU* 3.9 14.4 - - + +
364D MSE 4.3 3.1 - - - -
365D LYS* 1.3 78.2 - - - +
367D GLN* 1.3 75.7 + - - +
368D PRO* 4.1 0.2 - - - +
370D LEU* 4.1 4.2 - - - +
375D VAL* 5.3 0.5 - - - +
378D MSE 3.7 20.7 - - - -
414D TRP* 3.6 30.2 - - + -
----------------------------------------------------------
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