Contacts of the strand formed by residues 590 - 593 (chain A) in PDB entry 3BRF
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 LEU 590 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A PRO 5.9 0.9 - - - +
563A PRO* 4.0 26.9 - - + -
585A ASP 4.4 1.6 - - - +
586A PHE* 4.3 4.3 - - + -
587A LYS* 3.6 33.7 - - + +
588A PRO 3.3 7.5 + - - +
589A ASN* 1.3 82.5 - - - +
591A LYS* 1.3 69.5 + - - +
601A THR* 4.3 12.8 - - - +
602A THR 4.9 3.6 - - - +
609A LEU* 5.1 9.3 - - + +
642A LEU* 4.4 16.4 - - + -
643A VAL 3.6 27.6 - - - +
644A ARG* 3.7 11.2 - - + +
650A TYR* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A PRO 5.9 1.5 + - - +
589A ASN 4.9 0.2 - - - -
590A LEU* 1.3 81.9 - - - +
592A VAL* 1.3 60.4 + - - +
593A TRP* 3.0 33.7 + - - +
598A PRO* 5.5 2.5 - - + -
599A VAL 5.0 5.6 - - - +
601A THR* 3.9 13.0 - - - +
642A LEU* 3.7 4.5 - - - -
643A VAL* 3.1 27.8 + - + +
645A ASP* 3.3 31.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A LEU* 5.0 8.5 - - + -
591A LYS* 1.3 70.6 - - - +
593A TRP* 1.3 65.1 + - - +
594A PHE* 4.0 25.6 - - + -
599A VAL* 3.2 30.3 + - + +
600A GLU 4.6 2.0 - - - +
601A THR* 3.2 27.3 + - + +
609A LEU* 4.6 4.0 - - + -
611A CYS* 3.4 28.5 - - - -
640A ILE* 4.6 15.3 - - + -
641A SER 3.3 8.5 - - - +
642A LEU* 4.0 13.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 593 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU* 3.5 48.0 - - + -
200A SER* 4.1 15.9 - - - -
203A MET* 3.7 24.2 - - + -
591A LYS* 3.0 37.8 + - - +
592A VAL* 1.3 77.8 - - - +
594A PHE* 1.3 57.9 + - - +
595A GLY* 3.0 10.5 + - - +
596A ALA 2.8 32.5 - - - -
597A THR 3.6 8.7 - - - +
598A PRO* 3.4 33.3 - - + +
639A PRO 3.4 4.2 - - - +
641A SER* 2.7 37.5 + - - +
643A VAL* 2.9 24.3 - - + +
----------------------------------------------------------
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