Contacts of the strand formed by residues 374 - 379 (chain A) in PDB entry 1OZ2
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 374 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ILE* 5.0 1.4 - - - +
288A PRO* 3.8 38.4 + - - +
289A ASP* 2.6 33.6 + - - +
342A PRO* 4.2 1.3 - - - -
370A VAL* 3.5 7.1 - - - +
371A VAL* 2.9 34.2 + - - +
372A ASP 3.3 0.2 - - - -
373A SER* 1.3 91.5 - - - +
375A PHE* 1.3 64.6 + - - +
389A TRP* 3.6 48.1 + - + +
390A CYS* 3.2 18.6 - - - +
391A ASP* 4.8 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A PRO* 3.9 8.3 - - + -
345A PHE* 3.3 53.8 - + + -
351A LEU* 4.9 1.6 - - + -
367A VAL* 4.1 15.7 - - + -
369A ASP 3.3 12.8 - - - +
370A VAL* 4.0 13.0 - - + -
374A ARG* 1.3 78.5 - - - +
376A LEU* 1.3 60.0 + - - +
377A VAL* 3.8 17.3 - - + -
389A TRP* 3.4 7.8 - - - -
390A CYS* 2.8 54.3 + - + +
391A ASP* 3.5 27.1 - - - -
392A PRO* 3.6 5.2 - - + -
397A ILE* 3.6 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A PRO* 4.3 3.8 - - + +
253A SER* 3.7 29.2 - - - -
367A VAL* 3.3 7.3 - - - -
368A THR* 3.0 43.7 + - - +
369A ASP* 2.9 35.9 + - + +
375A PHE* 1.3 72.3 - - - +
377A VAL* 1.3 59.5 + - - +
387A ASP* 3.8 24.9 - - + +
388A TYR* 3.6 23.3 - - - +
389A TRP* 3.6 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 4.7 7.9 - - + -
353A ALA* 3.7 26.9 - - + -
365A ALA* 4.0 13.0 - - + -
366A SER 3.6 3.6 - - - +
375A PHE* 3.8 27.4 - - + -
376A LEU* 1.3 72.7 - - - +
378A HIS* 1.3 60.6 + - - +
379A PHE* 4.4 7.9 - - + -
386A TYR 4.7 0.5 - - - +
387A ASP* 3.1 10.2 - - - +
388A TYR* 2.9 45.9 + - + +
390A CYS* 3.9 18.2 - - + -
397A ILE* 4.1 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ALA* 3.2 5.1 - - - -
366A SER* 2.8 31.9 + - - +
368A THR* 3.5 39.7 - - + +
377A VAL* 1.3 75.7 - - - +
379A PHE* 1.3 74.5 + - - +
380A ASP* 3.6 5.7 + - - +
382A TRP 3.3 21.3 - - - -
383A ASP 4.5 0.7 - - - -
384A ASP* 3.1 25.4 + - - -
387A ASP* 2.6 26.7 + - - +
603A SO4 2.6 37.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ALA* 3.4 34.8 - - + -
354A VAL 3.4 24.0 - - - -
355A ASP* 3.9 11.2 - - + -
363A CYS* 3.6 26.7 - - + -
364A VAL 3.8 7.6 - - - +
365A ALA* 4.2 4.3 - - + -
377A VAL* 4.4 6.7 - - + -
378A HIS* 1.3 84.2 + - - +
380A ASP* 1.3 67.6 + - - +
381A ASN 3.3 0.5 + - - -
382A TRP* 3.0 39.5 + - + +
383A ASP 5.6 0.6 + - - +
386A TYR* 3.4 40.8 - - + -
387A ASP* 4.1 0.8 + - - -
388A TYR* 3.9 15.3 - + - -
----------------------------------------------------------
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