Contacts of the strand formed by residues 597 - 602 (chain B) in PDB entry 2QKT
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 597 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595B LEU* 3.3 12.9 - - + +
596B GLY* 1.3 80.0 - - - +
598B SER* 1.3 62.8 + - - +
599B LEU* 4.1 11.2 + - + +
608B ILE* 4.2 15.5 - - + -
610B ASP 3.6 1.3 - - - +
611B LEU* 3.5 39.3 - - + -
619B ILE* 4.2 19.3 - - + -
623B LEU* 4.2 19.5 - - + -
629B ILE* 4.8 1.3 - - + -
649B PHE* 3.7 40.5 - - + -
658B MET* 4.6 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 598 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B GLY 5.3 1.2 + - - -
597B LEU* 1.3 73.2 + - - +
599B LEU* 1.3 56.8 + - - +
608B ILE* 3.6 2.3 - - - -
609B ALA* 2.8 34.8 + - - -
610B ASP* 2.9 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 599 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B LEU* 4.2 15.0 + - + +
598B SER* 1.3 82.3 - - - +
600B SER* 1.3 62.4 + - - +
606B CYS* 3.9 15.7 - - + +
607B THR 3.1 14.6 - - - +
608B ILE* 3.9 20.9 - - + -
609B ALA* 4.7 2.6 - - - +
629B ILE* 3.9 10.1 - - + -
645B CYS* 3.5 25.9 + - - +
646B TYR* 3.7 21.2 - - - -
648B LEU* 3.4 37.0 - - + -
649B PHE* 4.0 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 600 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B LEU* 1.3 75.7 - - - +
601B PRO* 1.3 76.5 + - - +
606B CYS* 3.6 3.1 - - - -
607B THR* 2.9 42.6 + - - +
609B ALA* 4.1 15.3 - - - +
645B CYS* 4.2 5.2 - - - -
646B TYR* 4.5 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 601 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B SER* 1.3 93.7 + - - +
602B ASN* 1.3 60.7 + - - +
607B THR* 4.6 0.9 + - - -
642B PHE* 3.7 38.8 - - + +
645B CYS* 4.0 10.3 - - + -
646B TYR* 3.3 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 602 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B PRO* 1.3 73.7 + - - +
603B GLU* 1.3 78.7 + - - +
604B ILE* 3.0 28.0 + - - +
605B GLY 3.0 30.1 + - - +
607B THR* 3.1 30.4 + - - +
628B ILE* 3.5 18.8 - - + +
638B GLU* 5.7 0.2 - - - -
639B GLY 5.8 0.7 + - - -
----------------------------------------------------------
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