Contacts of the strand formed by residues 595 - 599 (chain B) in PDB entry 6IWQ
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 595 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B ILE* 5.9 1.1 - - + -
556B PHE* 3.5 9.7 - - - +
557B VAL* 3.5 38.5 + - + +
579B LEU* 6.1 0.7 - - + -
586B LEU* 3.6 30.3 - - + -
587B THR 4.1 5.2 - - - +
588B LYS* 5.1 0.9 - - - +
593B SER 4.1 0.2 + - - -
594B LYS* 1.3 76.0 - - - +
596B MET* 1.3 61.5 + - - +
608B TRP* 4.5 16.2 - - + -
626B LEU* 4.7 15.7 - - + -
635B VAL* 3.7 34.4 + - + +
636B PHE* 4.5 9.0 - - - -
637B ILE* 4.8 2.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 596 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B GLY 3.9 6.3 - - - +
555B GLY 3.0 20.2 - - - +
556B PHE* 3.5 19.3 - - + +
557B VAL* 5.4 1.6 - - - -
585B CYS 3.7 0.2 - - - +
586B LEU* 2.9 9.3 - - - -
587B THR* 2.9 57.5 + - - +
588B LYS 4.9 0.2 - - - +
589B GLY* 4.6 15.7 - - - +
594B LYS 4.5 2.0 - - - +
595B VAL* 1.3 75.4 - - - +
597B ILE* 1.3 59.6 + - - +
598B THR* 2.9 44.6 - - + +
605B PHE* 4.9 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 597 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B SER* 3.8 19.1 - - - +
551B LYS* 3.4 26.2 - - + +
552B THR* 3.8 6.1 - - - -
553B ASN 3.2 0.8 + - - -
554B GLY* 2.2 39.8 - - - -
555B GLY* 2.9 20.2 + - - -
556B PHE* 4.6 3.3 - - - +
557B VAL* 5.3 8.0 - - + +
571B PHE* 5.0 2.5 - - + -
581B GLN* 4.1 20.4 - - + +
584B GLN* 3.8 24.2 - - + +
585B CYS 3.5 9.4 - - - +
586B LEU* 3.5 22.2 - - + +
596B MET* 1.3 73.8 - - - +
598B THR* 1.3 57.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 598 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B ASN* 3.6 13.2 - - - +
554B GLY* 2.9 27.1 - - - +
584B GLN* 4.0 5.4 - - - -
585B CYS* 3.0 28.4 + - - +
596B MET* 2.9 37.6 - - + +
597B ILE* 1.3 85.3 - - - +
599B HIS* 1.3 73.2 + - - +
605B PHE* 3.7 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 599 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B ASN* 3.9 20.0 + - - +
583B ASP* 3.6 41.0 + - + +
584B GLN* 3.9 12.1 - - + +
598B THR* 1.3 82.6 + - - +
600B CYS* 1.3 77.6 + - - +
601B ASN* 4.5 10.4 + - - -
604B GLU* 5.7 1.2 - - - +
605B PHE* 4.0 8.1 - - - -
----------------------------------------------------------
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