Contacts of the helix formed by residues 752 - 768 (chain A) in PDB entry 2ITN
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 752 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A ALA* 3.3 11.3 + - - +
751A THR* 1.3 73.8 - - - +
753A PRO* 1.4 58.5 - - - +
754A LYS* 2.7 23.6 + - - +
755A ALA* 2.7 28.3 + - - +
756A ASN* 3.8 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 753 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751A THR 3.1 11.2 - - - +
752A SER* 1.4 80.5 - - - -
754A LYS* 1.3 61.2 + - - +
755A ALA 3.3 0.4 - - - -
756A ASN* 3.4 11.3 + - + +
757A LYS* 3.2 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 754 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A PHE* 6.2 2.5 - - + -
752A SER* 2.7 14.8 + - - +
753A PRO* 1.3 76.2 - - - +
755A ALA* 1.3 60.5 + - - +
757A LYS* 3.6 29.4 + - + +
758A GLU* 3.2 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 755 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A PHE* 4.5 7.0 - - + -
747A LEU* 3.8 28.3 - - + +
750A ALA 5.0 9.2 - - - +
752A SER* 2.7 21.8 + - - +
754A LYS* 1.3 72.3 - - - +
756A ASN* 1.3 67.3 + - - +
758A GLU* 3.0 24.6 + - - +
759A ILE* 3.3 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 756 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751A THR* 3.4 46.5 + - - +
752A SER 3.8 3.8 + - - -
753A PRO* 3.4 10.6 + - + +
755A ALA* 1.3 76.7 - - - +
757A LYS* 1.3 61.8 + - - +
759A ILE* 3.2 18.7 - - - +
760A LEU* 3.0 29.3 - - + +
784A SER 4.8 1.0 - - - +
785A THR* 4.4 5.3 + - - -
786A VAL* 3.4 26.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 757 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A PRO 3.2 15.2 + - - +
754A LYS* 3.7 32.1 - - + +
755A ALA 3.2 0.6 - - - -
756A ASN* 1.3 76.1 - - - +
758A GLU* 1.3 73.3 + - + +
759A ILE 3.5 0.2 - - - -
760A LEU* 3.7 7.3 + - - +
761A ASP* 3.2 52.4 + - - +
866A GLU* 5.8 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 758 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A PHE* 3.8 21.2 - - + -
754A LYS* 3.2 38.7 + - - +
755A ALA* 3.0 17.3 + - - +
757A LYS* 1.3 90.0 - - + +
759A ILE* 1.3 62.6 + - - +
761A ASP* 3.4 9.2 + - - +
762A GLU* 3.3 23.8 + - - +
857A GLY* 5.0 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 759 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745A LYS* 3.4 37.0 - - + +
747A LEU* 4.7 20.4 - - + -
755A ALA 3.3 10.9 + - - +
756A ASN* 3.2 22.9 - - - +
758A GLU* 1.3 75.4 - - - +
760A LEU* 1.3 61.0 + - + +
762A GLU* 3.4 9.8 + - + +
763A ALA* 3.0 25.8 + - - +
780A ILE* 6.3 0.2 - - + -
786A VAL* 3.6 35.0 - - + +
788A LEU* 4.0 23.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 760 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A LEU* 6.0 1.8 - - + -
756A ASN* 3.0 29.1 + - + +
757A LYS* 4.1 7.4 - - - +
758A GLU 3.3 0.6 - - - -
759A ILE* 1.3 78.7 - - + +
761A ASP* 1.3 62.8 + - - +
763A ALA* 3.7 7.6 - - + +
764A TYR* 2.8 30.5 + - - +
780A ILE* 4.3 24.2 - - + -
782A LEU* 5.0 3.8 - - + -
786A VAL* 4.3 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 761 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757A LYS* 3.2 40.2 + - - +
758A GLU* 3.4 11.7 - - - +
760A LEU* 1.3 78.7 - - - +
762A GLU* 1.3 61.2 - - - +
764A TYR* 3.3 7.3 + - - +
765A VAL* 3.0 30.9 + - + +
856A PHE 5.3 1.3 - - - +
857A GLY* 5.8 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 762 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745A LYS* 3.4 31.7 + - - -
758A GLU 3.3 11.2 + - - +
759A ILE* 3.4 14.3 - - - +
761A ASP* 1.3 78.3 - - - +
763A ALA* 1.3 56.4 + - - +
765A VAL* 3.1 2.6 + - - +
766A MET* 2.8 55.9 + - + +
788A LEU* 3.8 6.7 - - + +
855A ASP* 4.6 6.8 + - - -
856A PHE 3.8 14.6 + - - +
857A GLY* 3.3 34.9 - - - +
2020A MG 4.2 6.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 763 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A LEU* 4.5 8.3 - - + -
759A ILE 3.0 16.2 + - - +
760A LEU* 3.7 12.1 - - + +
761A ASP 3.4 0.2 - - - -
762A GLU* 1.3 74.5 - - - +
764A TYR* 1.3 56.4 + - - +
766A MET* 4.7 0.2 - - - -
767A ALA* 2.7 37.7 + - - +
777A LEU* 3.4 13.6 - - + +
780A ILE* 3.8 20.2 - - + -
788A LEU* 3.7 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 764 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A ASN* 3.4 31.0 + - - +
704A LEU* 5.9 1.1 - - - -
760A LEU 2.8 18.3 + - - +
761A ASP* 3.5 8.3 - - - +
763A ALA* 1.3 79.8 - - - +
765A VAL* 1.3 67.1 + - + +
767A ALA* 4.0 4.4 - - - +
768A SER* 2.6 34.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 765 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761A ASP* 3.0 17.9 + - + +
762A GLU 3.8 3.1 - - - +
764A TYR* 1.3 87.6 - - + +
766A MET* 1.3 58.1 + - - +
768A SER* 3.1 20.3 + - - -
769A VAL* 3.4 13.5 + - + +
833A LEU* 4.2 26.2 - - + -
856A PHE* 3.7 45.8 - - + +
859A ALA* 4.1 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 766 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A GLU* 2.8 37.3 + - + +
763A ALA 4.2 0.9 - - - +
765A VAL* 1.3 70.1 - - - +
767A ALA* 1.4 65.3 + - - +
769A VAL* 3.3 24.8 + - + +
775A CYS* 4.6 16.0 - - - +
776A ARG* 5.7 0.2 - - - -
777A LEU* 3.7 30.1 + - + +
788A LEU* 3.4 40.8 - - + -
790A THR* 4.1 19.3 - - + -
854A THR* 5.3 5.2 - - - -
855A ASP 6.1 0.4 - - - +
856A PHE* 3.7 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 767 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A ALA* 3.3 17.4 - - + +
703A LEU 4.3 18.6 - - - +
704A LEU* 4.4 12.6 - - + -
763A ALA 2.7 24.8 + - - +
764A TYR* 4.0 5.2 - - - +
766A MET* 1.4 72.6 - - - +
768A SER* 1.3 59.4 + - - +
769A VAL 3.4 3.3 + - - +
777A LEU* 3.7 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 768 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A ASN* 3.1 27.3 + - - -
702A ALA* 4.0 9.8 - - - +
764A TYR* 2.6 28.1 + - - -
765A VAL* 3.1 11.0 + - - -
767A ALA* 1.3 78.3 - - - +
769A VAL* 1.3 60.2 + - - +
827A TYR* 4.3 0.5 + - - -
831A ARG* 2.5 39.3 + - - +
833A LEU* 5.9 3.4 - - - -
----------------------------------------------------------
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