Contacts of the strand formed by residues 587 - 593 (chain A) in PDB entry 2DB3
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 GLY 587 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ASP 3.2 5.5 + - - +
465A VAL* 3.2 4.4 - - - -
466A LYS* 2.6 35.6 + - - +
559A LYS* 4.6 3.1 - - - -
580A THR* 3.1 21.8 - - - -
581A GLY* 4.0 2.2 - - - -
586A ASN* 1.3 78.7 - - - +
588A ARG* 1.3 57.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A VAL* 5.3 1.1 - - - -
466A LYS* 3.2 15.3 - - + +
484A ILE* 4.6 7.1 - - - +
487A GLU* 4.4 16.1 + - - -
488A GLN* 4.2 25.6 + - - +
559A LYS 3.6 15.7 + - - +
560A HIS* 3.0 62.9 + - + +
561A VAL* 3.1 10.6 + - - +
580A THR* 3.7 8.4 - - - +
587A GLY* 1.3 75.7 - - - +
589A ALA* 1.3 62.7 + - - +
590A THR* 4.1 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A VAL* 5.0 3.4 - - + -
466A LYS 2.8 9.9 + - - +
467A GLN* 3.3 11.9 - - + +
468A THR* 2.8 27.9 + - - +
561A VAL* 3.2 13.0 - - + +
563A ASN* 5.5 0.2 - - - +
573A TYR* 5.3 0.4 - - - +
577A ILE* 3.8 38.4 - - + +
588A ARG* 1.3 76.2 - - - +
590A THR* 1.3 64.0 + - - +
591A SER* 4.2 2.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A THR* 3.4 12.0 - - - +
470A TYR* 3.8 34.8 - - + -
484A ILE* 3.9 17.0 - - + +
560A HIS* 2.6 32.8 + - - -
561A VAL 2.8 6.1 + - - +
562A ILE* 3.1 10.1 - - - +
563A ASN* 2.8 24.1 + - - -
588A ARG* 4.1 7.4 + - - +
589A ALA* 1.3 73.0 + - - +
591A SER* 1.3 65.3 + - - +
592A PHE* 3.9 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A THR 2.9 6.9 + - - -
469A ILE* 3.5 22.5 - - - +
470A TYR* 2.9 27.0 + - - +
563A ASN* 2.9 29.1 + - - -
566A MET* 3.6 20.9 - - - -
573A TYR* 3.5 11.1 + - - -
577A ILE* 5.0 0.5 - - - +
589A ALA 4.9 1.7 - - - -
590A THR* 1.3 76.7 + - - +
592A PHE* 1.3 67.2 + - - +
593A PHE 3.6 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A TYR* 3.7 11.0 - + - -
472A VAL* 4.2 16.2 - - + -
477A LYS* 3.5 50.2 - - + -
480A LYS* 4.0 13.5 - - + -
481A LEU* 4.0 13.9 - - + -
484A ILE* 3.6 33.4 - - + -
562A ILE* 4.1 14.4 - - + -
563A ASN 2.9 18.0 + - - +
564A TYR* 3.6 28.4 - + - +
566A MET* 3.4 17.4 + - - +
590A THR* 3.9 11.7 - - + -
591A SER* 1.3 77.0 - - - +
593A PHE* 1.3 62.0 + - - +
594A ASP 3.8 1.7 + - - -
598A ASP* 4.1 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 593 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A ILE* 3.7 16.2 - - + -
470A TYR 2.7 15.1 + - - +
471A GLU* 3.3 5.1 - - - -
472A VAL 2.8 25.8 + - - +
566A MET* 4.3 8.5 - - + -
591A SER 3.6 1.0 + - - -
592A PHE* 1.3 72.4 - - - +
594A ASP* 1.3 68.1 + - - +
595A PRO* 3.4 17.6 - - + +
598A ASP* 3.1 40.2 - - + -
599A ARG* 4.2 4.9 - - + -
601A ILE* 4.2 4.7 - - + -
602A ALA* 3.9 20.4 - - + -
605A LEU* 4.3 10.8 - - + -
619A PHE* 3.7 25.8 - + + -
620A LEU* 3.5 27.8 - - + -
----------------------------------------------------------
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