Contacts of the strand formed by residues 353 - 358 (chain A) in PDB entry 2VZ3
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 353 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A PRO* 3.7 19.5 - - + +
347A GLN* 3.5 6.1 + - - -
351A SER* 2.7 31.3 + - - +
352A THR* 1.3 79.7 - - - +
354A MET* 1.3 59.4 + - - +
355A ASN* 3.5 7.2 + - - +
367A SER* 6.6 0.4 - - - -
369A GLY 3.9 5.8 - - - +
370A LYS* 4.5 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A PHE* 3.9 13.5 - - + -
347A GLN* 3.3 11.0 - - - +
348A ALA 3.5 18.4 - - - +
352A THR 4.0 2.0 - - - +
353A ALA* 1.3 73.8 - - - +
355A ASN* 1.3 70.8 + - - +
367A SER* 3.8 1.6 - - - -
368A ALA* 2.9 41.8 + - + +
369A GLY 2.8 17.5 + - - +
370A LYS 4.0 3.6 - - - +
371A ARG* 3.9 24.2 - - + +
417A ILE* 3.7 30.3 - - - -
426A PRO* 3.9 12.3 - - + +
428A THR* 3.7 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A PRO* 3.2 46.7 + - - +
320A MET* 3.9 1.0 - - - +
346A PHE* 3.7 3.5 - - - -
347A GLN* 2.8 62.7 + - - +
353A ALA* 3.5 8.3 + - - +
354A MET* 1.3 84.7 + - - +
356A TRP* 1.3 62.4 + - - +
357A TYR* 4.0 7.8 + - + -
365A VAL* 4.0 15.7 - - + +
366A LYS 3.5 5.0 - - - +
367A SER* 3.6 18.7 + - - -
368A ALA* 3.9 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A TRP* 3.5 35.7 - + - -
344A SER* 3.8 13.2 - - - -
345A VAL 3.9 2.7 - - - -
346A PHE* 3.7 42.2 - + + -
355A ASN* 1.3 72.1 - - - +
357A TYR* 1.3 61.3 + - - +
358A TYR* 3.6 22.2 - - + +
365A VAL* 3.2 8.5 - - - +
366A LYS* 2.8 39.6 + - + +
367A SER 4.6 1.6 - - - -
368A ALA* 3.6 23.3 - - + +
419A LEU* 4.1 15.0 - - + -
420A GLY 4.3 3.8 - - - -
421A GLU 3.7 13.7 - - - -
422A PRO* 3.8 15.0 - - + -
423A GLY* 3.2 26.7 - - - +
424A THR* 2.8 24.8 + - - -
426A PRO* 4.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PHE* 3.9 30.3 - + + -
286A ILE* 3.5 17.6 - - + +
315A ALA* 3.9 15.5 - - + -
316A LYS 2.8 29.5 + - - -
317A VAL* 3.8 0.2 - - - -
320A MET* 3.3 34.2 + - - +
337A LEU* 5.1 2.9 - - + -
343A GLY 4.5 0.2 - - - +
344A SER* 3.3 8.5 - - - -
345A VAL* 2.9 42.1 + - + +
347A GLN* 3.9 29.6 - - + -
355A ASN* 4.0 9.5 - - + +
356A TRP* 1.3 75.1 - - - +
358A TYR* 1.3 61.8 + - - +
359A THR* 5.2 0.9 - - - -
364A ASP 3.5 11.7 - - - -
365A VAL* 3.4 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PHE* 5.1 0.2 - - - -
312A LEU* 4.5 0.2 - - - +
315A ALA* 4.3 5.4 - - - +
342A LYS 6.0 1.6 - - - -
344A SER* 4.7 9.9 - - - +
356A TRP* 3.6 24.2 - - + +
357A TYR* 1.3 78.5 - - - +
359A THR* 1.3 64.4 + - - +
360A SER* 3.6 10.3 - - - +
363A GLY* 3.3 5.8 - - - -
364A ASP* 2.9 54.2 + - + +
365A VAL 4.5 0.4 - - - -
366A LYS* 3.6 24.0 - - + +
422A PRO* 4.2 19.7 - - + -
423A GLY* 2.8 34.2 + - - -
----------------------------------------------------------
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