Contacts of the strand formed by residues 586 - 590 (chain A) in PDB entry 5M64
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 VAL 586 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A ARG 4.6 1.3 - - - +
585A ASP* 1.3 79.3 - - - +
587A VAL* 1.3 70.7 + - - +
603A HIS 3.3 19.5 - - - +
604A LYS* 4.6 2.5 - - + +
637A PHE* 4.2 5.2 - - - -
638A PRO* 3.3 22.7 - - + +
644A ARG* 3.4 45.5 - - + +
647A ALA* 3.6 36.1 - - + +
648A LEU* 3.9 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A ILE* 4.7 7.9 - - + +
581A ILE* 4.9 0.7 - - + -
585A ASP* 4.3 1.1 + - - +
586A VAL* 1.3 81.2 - - - +
588A LEU* 1.3 71.0 + - - +
589A MET* 5.6 0.4 - - + -
602A GLY* 3.5 1.7 - - - -
603A HIS 2.8 33.7 + - - +
605A VAL* 3.6 40.6 - - + -
635A MET* 3.9 29.8 - - + -
636A HIS 3.4 12.8 - - - +
637A PHE* 3.6 24.9 - - + -
638A PRO* 4.1 3.1 - - - -
647A ALA* 6.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A VAL* 1.3 79.3 - - - +
589A MET* 1.3 84.7 + - - +
600A MET* 3.6 36.3 - - + -
601A MET* 3.5 20.4 - - - +
602A GLY* 3.9 5.4 - - - +
635A MET 3.8 0.2 - - - -
636A HIS* 2.8 68.4 + - + +
638A PRO* 4.2 10.0 - - + +
647A ALA* 5.8 6.1 - - + -
651A ALA* 5.6 4.9 - - + -
1087B LEU* 5.0 16.4 - - + -
1091B ARG* 4.5 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A ILE* 3.6 47.1 - - + -
587A VAL* 4.1 0.9 + - + -
588A LEU* 1.3 86.2 - - - +
590A ASN* 1.3 61.5 + - - +
600A MET* 3.8 1.0 - - - +
601A MET 2.8 37.5 + - - +
603A HIS* 4.8 1.6 - - + -
614A LEU* 4.1 16.4 - - + -
616A LEU* 3.9 29.8 - - + -
620A ASN* 4.8 4.0 - - - -
624A TYR* 3.6 10.7 + - + +
633A MET* 3.6 24.2 - - + +
634A ASN 3.3 19.3 - - - +
635A MET* 4.5 8.1 - - + -
636A HIS 4.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A MET* 1.3 76.6 - - - +
591A ARG* 1.3 79.3 + - - +
592A GLN* 4.3 6.6 - - - +
594A THR* 3.7 10.9 - - - +
599A SER 2.9 18.6 - - - +
600A MET* 3.9 9.2 - - - +
624A TYR* 4.9 3.4 - - - -
633A MET* 3.3 3.5 - - - +
634A ASN* 2.8 46.6 + - - +
636A HIS* 4.0 19.5 + - + +
1075B GLU* 2.4 41.8 + - - +
1091B ARG* 5.0 0.2 - - - +
----------------------------------------------------------
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