Contacts of the strand formed by residues 592 - 595 (chain B) in PDB entry 2A2N
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 PHE 592 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B ILE* 4.1 19.5 - - + -
519B PHE* 3.7 23.8 - + - -
528B TYR* 3.6 28.3 - + - -
533B PHE* 5.5 1.1 - + - -
543B GLN* 3.5 4.0 - - - +
544B THR* 3.0 56.1 + - + +
545B GLY* 4.4 1.1 - - - -
578B LEU* 3.2 28.9 - - + -
579B SER 3.4 13.5 - - - +
580B MET* 4.3 3.1 - - - -
581B ALA* 4.1 3.4 - - - +
590B SER 3.4 15.0 - - - +
591B GLN* 1.3 76.5 - - - +
593B PHE* 1.3 66.4 + - - +
594B ILE* 4.8 5.2 - - + -
609B PHE* 4.1 14.8 - + + -
640B ILE* 4.5 8.5 - - + -
643B ILE* 4.7 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 593 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B PHE* 5.9 0.2 - + - -
541B MET* 3.7 35.9 - - + -
542B ILE 3.2 12.1 - - - +
543B GLN* 4.0 5.4 - - + -
572B HIS* 4.0 1.6 - + - -
577B THR 3.6 0.7 - - - +
578B LEU* 3.5 4.3 - - - +
579B SER* 2.9 60.8 + - - +
580B MET 3.3 22.4 - - - -
581B ALA* 3.8 16.6 - - + -
592B PHE* 1.3 77.7 - - - +
594B ILE* 1.3 62.7 + - - +
595B THR* 3.8 16.8 - - + -
602B LEU* 3.7 31.9 - - + -
606B HIS* 3.7 18.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 594 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B ILE* 4.2 24.7 - - + -
503B ILE* 4.2 26.7 - - + -
505B THR* 4.8 2.2 - - + -
533B PHE* 5.3 4.3 - - + -
541B MET* 3.3 1.9 - - - -
542B ILE* 2.8 48.8 + - + +
576B TYR* 3.7 17.0 - - - -
577B THR 3.0 11.0 - - - +
578B LEU* 3.8 17.0 - - + -
592B PHE* 4.8 6.1 - - + -
593B PHE* 1.3 78.3 - - - +
595B THR* 1.3 75.4 + - - +
596B VAL* 4.8 0.2 - - - +
612B VAL* 4.0 9.0 - - + -
619B VAL* 3.9 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 595 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B PHE 3.4 10.1 - - - +
541B MET* 4.0 2.0 - - + -
572B HIS* 4.3 6.8 - - + +
574B ARG 4.0 1.9 + - - -
576B TYR* 2.8 31.7 + - - -
577B THR* 3.0 30.2 + - - +
593B PHE* 3.8 25.8 - - + -
594B ILE* 1.3 78.9 - - - +
596B VAL* 1.3 58.6 + - - +
597B VAL 3.4 16.8 + - - -
599B THR* 3.4 28.9 - - + +
602B LEU* 4.8 0.4 - - + -
----------------------------------------------------------
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