Contacts of the strand formed by residues 589 - 598 (chain B) in PDB entry 5TKD
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 ILE 589 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B VAL* 3.8 11.0 - - + -
585B ASP 4.3 1.1 - - - +
586B GLN* 3.3 29.2 - - + +
587B LYS 3.4 3.4 - - - +
588B GLU* 1.3 86.1 - - - +
590B THR* 1.3 63.3 + - - +
591B GLN* 4.3 0.4 - - + -
607B ARG 3.3 7.4 - - - +
608B LEU* 3.7 21.5 - - + -
641B LEU* 4.2 35.7 - - + -
677B CYS* 4.0 26.5 - - + -
679B ARG* 4.6 7.2 - - - +
684B ILE* 4.0 19.7 - - + -
686B VAL* 4.3 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 590 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A HIS* 6.0 1.1 - - + -
589B ILE* 1.3 75.2 + - - +
591B GLN* 1.3 63.8 + - - +
592B LEU* 3.9 23.0 - - + +
606B GLY* 3.1 8.1 - - - -
607B ARG* 3.0 49.8 + - - +
636B GLU* 5.1 4.0 + - - -
641B LEU* 3.9 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 591 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B ILE* 5.7 0.4 - - - +
590B THR* 1.3 75.8 - - - +
592B LEU* 1.3 70.1 + - - +
604B TYR* 3.4 54.7 + - + -
641B LEU* 3.7 15.2 - - + +
643B VAL* 4.1 5.0 - - - +
679B ARG* 2.9 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 592 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A GLU* 5.1 0.9 - - - +
590B THR* 3.9 20.4 - - + +
591B GLN* 1.3 83.1 + - - +
593B SER* 1.3 68.3 + - - +
604B TYR* 3.6 13.9 - - - -
605B GLU* 2.8 22.4 + - + +
606B GLY* 4.0 11.7 - - - +
607B ARG* 3.8 38.6 - - + +
638B ARG* 3.7 33.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 593 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A ARG* 6.0 2.3 - - - -
592B LEU* 1.3 79.0 - - - +
594B HIS* 1.3 67.2 + - - +
595B LEU* 3.5 3.5 + - - +
604B TYR* 3.3 1.0 - - - -
605B GLU* 2.9 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 594 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592B LEU 3.8 1.6 + - - -
593B SER* 1.3 78.0 - - - +
595B LEU* 1.3 61.3 + - - +
596B GLY* 3.3 31.8 + - - -
597B GLN* 4.0 8.1 - - + -
602B ASN* 2.9 24.9 + - + -
603B VAL 3.7 8.3 - - - -
604B TYR* 3.6 38.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 595 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B SER* 4.0 4.7 - - - +
594B HIS* 1.3 79.5 - - - +
596B GLY* 1.3 56.0 + - - +
603B VAL* 2.7 18.4 + - + +
604B TYR 3.7 2.7 - - - -
605B GLU* 3.6 40.6 - - + +
640B VAL* 3.6 27.1 - - + -
901B 7GL 3.5 68.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 596 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B HIS* 3.3 17.9 + - - -
595B LEU* 1.3 83.5 - - - +
597B GLN* 1.3 63.9 + - - -
603B VAL* 2.8 24.8 + - - -
901B 7GL 3.7 20.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 597 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B HIS* 4.0 8.5 - - + -
596B GLY* 1.3 76.8 - - - -
598B GLY* 1.3 62.3 + - - +
601B THR 3.4 9.3 + - - +
602B ASN* 3.0 33.2 + - - +
738B ARG* 4.3 13.5 + - - +
901B 7GL 3.9 13.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 598 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B GLN* 1.3 77.5 - - - +
599B THR* 1.3 65.1 + - - -
600B ARG 3.2 4.0 + - - -
601B THR* 3.1 27.8 + - - +
603B VAL* 4.7 2.1 - - - +
901B 7GL 4.5 5.6 - - - +
----------------------------------------------------------
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