Contacts of the helix formed by residues 683 - 687 (chain B) in PDB entry 5IJ7
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 LYS 683 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TRP* 4.4 7.3 - - + -
613B HIS* 3.5 5.1 - - - -
614B LEU* 2.8 42.3 + - + +
615B LEU* 4.7 0.9 - - - +
616B LEU 5.2 1.1 - - - +
626B ILE* 3.5 23.3 - - + +
682B ASN* 1.3 72.4 - - - +
684B ILE* 1.3 54.7 + - - +
685B ARG 3.0 6.8 + - - -
686B PHE* 3.1 32.1 + - + +
568T SER* 3.9 26.7 - - - +
582T ASP* 2.9 42.6 + - - +
585T ASP* 3.3 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 684 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B LEU* 3.8 21.6 - - + +
626B ILE* 4.3 6.5 - - + -
638B ILE* 4.1 10.8 - - + -
639B SER* 4.0 12.7 + - - +
640B GLU 3.2 17.7 - - - +
641B TYR* 3.7 24.8 - - + -
682B ASN* 3.1 23.5 + - - +
683B LYS* 1.3 71.0 - - - +
685B ARG* 1.3 59.4 + - - +
686B PHE 3.0 5.8 - - - -
687B ALA* 3.1 24.3 + - + +
710B ILE* 3.9 31.9 - - + -
722B LEU* 3.9 22.7 - - + -
724B PHE* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 685 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B MET* 4.2 1.2 - - - -
111B TYR 3.9 8.1 + - - -
113B TRP* 3.1 57.0 - - - +
641B TYR* 3.8 16.5 + - + +
642B CYS 5.5 0.2 - - - +
665B PHE* 4.6 1.6 - - - -
677B ALA* 2.6 53.2 + - + -
678B THR* 3.0 19.0 + - - +
681B GLY* 4.4 4.3 - - - -
682B ASN* 2.9 25.5 + - - +
683B LYS 3.0 0.6 + - - -
684B ILE* 1.3 76.8 - - - +
686B PHE* 1.4 79.1 + - + +
687B ALA 3.4 5.1 + - - +
726B TYR* 4.2 4.7 + - - -
9001B 6BN 3.4 58.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 686 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B MET* 3.6 41.7 - - + -
113B TRP* 3.6 26.9 - + - -
616B LEU* 3.8 17.9 - - + -
624B TRP* 3.7 20.6 - - + -
625B GLY* 3.2 18.3 - - - -
626B ILE* 3.3 17.0 + - + -
683B LYS* 3.1 25.2 + - + +
684B ILE 3.0 0.8 - - - -
685B ARG* 1.4 93.7 - - + +
687B ALA* 1.3 61.9 + - - +
688B ASN* 3.2 18.4 + - - -
9001B 6BN 3.5 32.7 - + + +
568T SER* 5.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 687 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626B ILE* 3.6 17.2 - - + +
684B ILE* 3.1 23.3 + - + +
685B ARG 4.0 1.4 - - - +
686B PHE* 1.3 75.0 - - - +
688B ASN* 1.3 55.5 + - - +
695B CYS* 6.4 0.2 - - + -
710B ILE* 5.9 0.9 - - + -
722B LEU* 3.5 22.4 - - + +
723B PHE 4.6 0.4 - - - +
724B PHE* 4.0 20.9 - - + -
726B TYR* 2.6 30.7 + - - -
9001B 6BN 4.0 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