Contacts of the helix formed by residues 758 - 772 (chain A) in PDB entry 4IQJ
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 SER 758 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A TYR* 5.7 1.0 + - - -
456A PRO* 5.5 2.8 - - - +
457A GLU* 3.2 24.9 + - - -
752A SER* 3.9 0.2 - - - -
756A GLY 3.8 1.2 + - - -
757A TYR* 1.3 78.1 - - - +
759A LEU* 1.3 62.0 + - - +
760A GLY* 3.3 7.8 + - - -
761A GLU* 3.2 22.0 + - - +
762A ALA* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 759 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A LEU* 3.8 43.1 - - + -
451A GLU* 3.2 39.1 - - + +
748A MET* 3.6 31.9 - - + +
749A GLN* 4.4 7.2 - - + -
752A SER* 3.7 28.1 + - - +
758A SER* 1.3 75.5 + - - +
760A GLY* 1.3 61.8 + - - +
762A ALA* 3.6 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 760 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A GLU* 3.6 18.5 - - - +
455A ASN* 2.7 44.4 + - - -
456A PRO* 4.1 5.8 - - - +
457A GLU* 4.9 2.2 - - - -
758A SER* 3.2 7.6 + - - -
759A LEU* 1.3 77.5 - - - +
761A GLU* 1.3 62.8 + - - +
763A ASP* 3.2 8.0 - - - +
764A LEU* 3.6 1.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 761 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A GLU* 3.1 33.9 - - - +
757A TYR* 3.6 27.3 - - + -
758A SER* 3.2 26.5 + - - +
760A GLY* 1.3 74.2 - - - +
762A ALA* 1.3 60.3 + - - +
764A LEU* 3.0 33.3 + - + +
765A LEU* 3.0 11.4 + - - +
780A HIS* 6.0 0.3 - - - -
783A ARG* 3.6 27.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 762 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A MET* 3.4 44.8 - - + +
751A ALA* 4.3 11.6 - - + +
752A SER* 4.5 3.4 - - - +
757A TYR* 4.0 5.8 - - + -
758A SER 3.0 14.3 + - - +
759A LEU* 3.8 9.0 - - - +
760A GLY 3.3 0.4 - - - -
761A GLU* 1.3 77.0 - - - +
763A ASP* 1.3 61.2 + - - +
765A LEU* 3.3 10.9 + - - +
766A ARG* 3.2 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 763 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A GLU 3.9 15.6 - - - +
452A ARG* 3.5 23.1 + - - +
455A ASN* 3.4 18.7 + - - +
458A ARG* 4.6 9.7 + - - -
748A MET* 3.9 13.2 - - + +
759A LEU 3.6 2.6 + - - -
760A GLY 3.2 15.8 + - - +
761A GLU 3.1 0.4 - - - -
762A ALA* 1.3 75.9 - - - +
764A LEU* 1.3 61.2 + - - +
766A ARG* 2.7 43.9 + - - +
767A ARG* 3.5 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 764 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A ASN* 3.9 17.5 - - - +
457A GLU* 5.1 11.7 - - + +
458A ARG* 4.0 37.2 - - + +
760A GLY 3.6 1.8 + - - +
761A GLU* 3.0 26.4 + - + +
763A ASP* 1.3 77.8 - - - +
765A LEU* 1.3 56.4 + - - +
767A ARG* 3.2 8.0 + - + +
768A ALA* 3.0 30.0 + - - +
780A HIS* 5.5 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 765 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A ILE* 6.6 0.4 - - + -
751A ALA* 3.7 28.3 - - + -
757A TYR* 4.5 20.0 - - + +
761A GLU 3.0 11.2 + - - +
762A ALA* 3.3 11.2 + - - +
764A LEU* 1.3 77.5 - - - +
766A ARG* 1.3 58.8 + - - +
768A ALA* 4.0 5.4 - - + +
769A MET* 3.4 30.8 + - + +
777A MET* 6.4 1.1 - - + -
780A HIS* 3.6 43.0 - - + +
784A PHE* 4.7 6.7 - - + -
802A PHE* 4.2 24.2 - - + -
805A LEU* 5.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 766 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A ARG* 3.4 32.0 - - - +
744A GLN* 3.1 50.6 + - - +
747A ILE* 5.8 8.5 - - + -
748A MET* 3.9 7.2 - - + -
762A ALA 3.2 11.6 + - - +
763A ASP* 2.7 40.1 + - - +
764A LEU 3.2 0.2 - - - -
765A LEU* 1.3 76.3 - - - +
767A ARG* 1.3 70.4 + - - +
769A MET* 3.3 7.2 + - - +
770A GLY* 3.0 23.2 + - - -
809A ALA* 5.2 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 767 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A ARG* 4.0 31.8 - - - +
763A ASP 3.5 9.2 + - - +
764A LEU* 3.2 10.8 + - + +
766A ARG* 1.3 86.8 - - - +
768A ALA* 1.3 59.3 + - - +
770A GLY* 4.3 1.3 - - - +
771A LYS* 2.9 62.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 768 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764A LEU 3.0 16.0 + - - +
765A LEU* 4.1 6.3 - - + +
767A ARG* 1.3 76.4 - - - +
769A MET* 1.3 59.6 + - - +
771A LYS* 4.2 6.6 - - - +
772A LYS* 3.3 15.2 + - - -
773A ARG* 3.9 5.2 + - - +
776A GLU* 3.6 23.6 - - - +
777A MET* 3.9 16.8 - - + +
780A HIS* 4.1 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 769 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A ILE* 5.7 3.8 - - + -
765A LEU* 3.4 25.8 + - + +
766A ARG* 3.3 12.5 + - - +
767A ARG 3.2 0.2 - - - -
768A ALA* 1.3 79.8 - - - +
770A GLY* 1.3 61.5 + - - +
772A LYS* 3.4 19.2 + - - +
777A MET* 3.5 25.0 - - + +
802A PHE* 4.1 24.5 - - + -
805A LEU* 4.1 13.7 - - + +
806A GLU* 3.4 45.1 - - + +
809A ALA* 3.7 24.5 - - + -
810A ASN* 4.5 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 770 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A ARG 3.0 14.3 + - - -
767A ARG* 3.2 3.3 + - - -
769A MET* 1.3 75.8 - - - +
771A LYS* 1.3 62.1 + - - +
772A LYS* 3.3 13.7 - - - +
809A ALA 5.7 4.7 + - - -
810A ASN* 5.4 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 771 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A ARG* 2.9 51.9 + - + +
768A ALA* 4.3 6.5 - - - +
770A GLY* 1.3 73.2 - - - +
772A LYS* 1.3 70.6 + - - +
773A ARG* 3.5 21.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 772 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768A ALA 3.3 10.1 + - - -
769A MET 3.4 15.2 + - - +
770A GLY* 3.3 9.8 - - - +
771A LYS* 1.3 83.3 - - - +
773A ARG* 1.3 65.6 + - - +
774A VAL* 3.5 7.8 + - - +
777A MET* 4.5 8.3 - - - -
810A ASN* 3.6 28.4 + - - +
----------------------------------------------------------
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