Contacts of the strand formed by residues 363 - 366 (chain A) in PDB entry 4WII
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 363 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A PHE* 3.7 18.2 - - + +
301A VAL* 3.3 4.0 - - - -
302A GLY* 2.8 41.7 + - - +
303A ASN* 4.4 13.7 - - - +
353A ASP* 3.4 3.8 - - - -
361A GLN 3.7 0.6 + - - -
362A LEU* 1.3 72.5 - - - +
364A VAL* 1.3 61.0 + - - +
365A ARG* 4.0 32.6 - - + +
454A ASP* 5.4 1.4 + - - -
457A ASP* 3.1 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 4.0 21.5 - - + -
300A PHE 3.3 12.6 - - - +
301A VAL* 4.1 22.4 - - + -
317A PHE* 4.8 4.7 - - + -
348A ALA 4.9 0.9 - - - +
349A LYS* 3.4 34.1 - - + +
352A LEU* 3.9 16.2 - - + +
353A ASP* 2.8 39.0 + - + +
362A LEU* 4.3 5.2 - - + -
363A ARG* 1.3 76.8 - - - +
365A ARG* 1.4 77.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 3.4 9.5 - - - +
300A PHE* 2.6 47.3 + - + +
349A LYS* 4.3 4.9 - - - +
353A ASP* 2.9 30.1 + - - -
363A ARG* 4.0 34.6 + - + +
364A VAL* 1.4 91.9 + - - +
366A PHE* 1.3 65.4 + - - +
456A GLU* 3.5 32.0 + - - +
457A ASP* 2.7 41.1 + - - +
605A EDO 4.2 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLN 5.5 0.2 - - - -
296A ARG* 3.3 22.4 - - - -
298A ARG 3.6 12.1 - - - -
299A LEU* 3.8 7.2 - - + -
342A ARG* 3.3 33.2 - - - +
345A ALA* 3.6 31.4 - - + -
346A GLU* 3.6 35.4 - - + -
349A LYS* 4.3 19.6 - - + +
365A ARG* 1.3 73.2 - - - +
367A ALA* 1.3 67.7 + - - +
368A THR* 5.1 0.7 - - - +
456A GLU* 5.5 1.4 + - - -
605A EDO 3.2 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