Contacts of the strand formed by residues 525 - 528 (chain B) in PDB entry 2P2B
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 HIS 525 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B PHE* 4.7 3.0 - - - -
309B TRP* 3.5 44.4 + + + -
520B LEU 3.4 3.6 - - - +
521B ASN* 3.5 2.8 - - - -
522B VAL* 2.7 51.0 + - - +
523B SER* 3.7 13.2 + - - -
524B GLY* 1.3 76.3 - - - +
526B ARG* 1.3 63.4 + - - +
527B LEU* 3.6 18.0 + - + +
590B LEU* 3.3 49.8 + - + +
991B COA 3.7 14.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 526 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B THR* 3.2 18.0 - - - +
265B SER* 2.8 37.1 + - - +
266B GLY* 4.5 4.0 - - - -
309B TRP* 6.0 3.8 - - - -
415B GLN* 4.4 1.8 - - - +
417B GLU* 2.8 43.0 + - - -
488B TYR* 4.2 5.9 + - - -
515B ARG* 3.8 30.7 - - - +
519B VAL* 3.6 21.0 - - + +
520B LEU 3.4 5.6 - - - -
521B ASN* 5.0 2.7 - - - +
524B GLY 4.0 2.0 + - - -
525B HIS* 1.3 71.5 - - - +
527B LEU* 1.3 67.2 + - - +
998B PRX 2.9 50.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PHE* 5.6 9.9 - - + -
265B SER* 3.7 11.9 - - - +
519B VAL* 3.4 5.6 - - - -
520B LEU* 2.7 45.7 + - + +
522B VAL* 4.0 22.2 - - + -
525B HIS* 4.1 13.7 - - + +
526B ARG* 1.3 84.0 - - - +
528B GLY* 1.3 61.1 + - - +
531B GLU* 4.6 7.4 - - - +
532B ILE* 4.3 12.6 - - + -
559B ILE* 4.1 3.8 - - + -
587B ILE* 5.1 5.6 - - + -
590B LEU* 3.4 28.5 - - + +
591B ALA* 3.9 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B SER* 3.4 2.4 - - - -
266B GLY 3.4 25.1 - - - -
518B ASP 4.1 2.0 - - - -
520B LEU* 5.3 0.2 - - - -
527B LEU* 1.3 70.9 - - - +
529B THR* 1.3 66.3 + - - -
530B ALA 3.3 2.5 - - - -
531B GLU* 2.9 40.2 + - - +
532B ILE* 3.3 14.9 + - - +
----------------------------------------------------------
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