Contacts of the strand formed by residues 328 - 333 (chain B) in PDB entry 1HQR
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 GLU 328 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ILE* 1.3 80.4 - - - +
329B VAL* 1.3 66.6 + - - +
374B GLN 4.2 0.7 - - - +
375B VAL* 3.8 1.7 - - - +
376B GLU* 3.2 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B CYS* 4.1 0.9 - - - -
319B VAL* 3.5 28.5 - - + -
327B ILE* 4.8 8.5 - - + +
328B GLU* 1.3 78.3 - - - +
330B ARG* 1.3 66.9 + - - +
331B TRP* 6.3 0.2 - - - -
357B THR* 4.8 9.0 - - + -
359B VAL* 3.5 38.0 - - + +
373B CYS* 3.5 28.3 - - - -
374B GLN 3.7 2.9 - - - +
375B VAL* 4.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B VAL* 1.3 78.0 - - - +
331B TRP* 1.3 63.8 + - - +
332B PHE* 3.6 25.6 - - + -
337B GLU* 5.6 0.7 - - + -
372B THR 3.7 0.3 - - - +
373B CYS* 3.4 7.6 - - - -
374B GLN* 2.8 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B VAL* 4.3 22.2 - - + -
315B LEU* 4.0 20.4 - - + -
316B VAL 4.1 0.9 - - - -
317B CYS* 3.6 31.2 - - + -
330B ARG* 1.3 74.6 - - - +
332B PHE* 1.3 66.5 + - - +
337B GLU* 3.6 1.1 - - - +
338B GLU* 3.0 34.2 + - + +
342B VAL* 3.4 25.6 - - + -
359B VAL* 3.4 30.4 + - + +
361B LEU* 3.3 42.1 - - + +
371B TYR* 4.3 15.3 - + + -
372B THR* 3.2 46.0 - - - -
373B CYS* 3.8 4.3 - - + -
388B TRP* 5.9 1.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ARG* 3.6 24.0 - - + -
331B TRP* 1.3 85.4 - - - +
333B ARG* 1.3 62.2 + - - +
334B ASN 4.1 1.6 - - - +
335B SER* 5.3 4.3 - - - +
336B GLN* 3.2 12.6 - - - +
337B GLU* 3.1 34.3 - - + -
338B GLU* 4.3 0.9 - - - -
371B TYR* 3.2 7.7 - - - +
372B THR* 3.0 38.8 + - - +
374B GLN* 4.8 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B PHE* 1.3 73.4 - - - +
334B ASN* 1.3 80.1 + - - +
335B SER 2.4 19.7 + - - -
336B GLN* 3.0 16.0 + - - +
338B GLU* 2.9 40.4 + - + +
363B THR* 3.7 24.2 - - - +
369B GLU* 4.8 10.1 - - - +
370B VAL 4.9 0.2 - - - +
371B TYR* 3.7 35.3 - - + +
----------------------------------------------------------
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