Contacts of the helix formed by residues 761 - 781 (chain A) in PDB entry 3M62
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 THR 761 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A VAL* 4.7 5.7 - - - +
757A ALA 3.9 14.8 - - - +
758A ALA* 4.3 7.7 + - - +
759A PHE 3.7 0.4 - - - -
760A VAL* 1.3 79.5 - - + +
762A PRO* 1.4 77.4 - - + +
763A GLU* 3.0 9.0 + - - +
764A ILE* 3.0 18.5 + - - +
765A VAL* 2.9 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 762 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760A VAL 4.5 0.9 - - - +
761A THR* 1.4 88.2 - - - +
763A GLU* 1.3 61.0 + - + +
764A ILE 3.2 1.2 + - - -
765A VAL* 3.8 9.6 + - + -
766A TYR* 3.5 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 763 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A ASP* 5.7 1.2 - - - +
674A VAL* 3.2 36.4 - - + +
678A ALA* 5.2 5.4 - - - +
761A THR* 3.0 6.4 + - - +
762A PRO* 1.3 79.4 - - + +
764A ILE* 1.3 68.9 + - + +
767A ARG* 4.1 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 764 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A VAL* 4.2 21.1 - - + -
677A VAL* 3.7 29.8 - - + -
678A ALA* 4.0 21.1 - - + +
681A LEU* 4.0 17.3 - - + -
758A ALA 4.5 4.3 - - - +
759A PHE* 3.5 28.7 - - + +
761A THR* 3.0 14.3 + - - +
763A GLU* 1.3 95.3 - - + +
765A VAL* 1.3 55.4 + - - +
766A TYR 3.4 1.6 - - - -
767A ARG* 3.2 5.1 + - - +
768A LEU* 2.7 40.1 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
759A PHE 3.8 8.3 - - - +
760A VAL* 3.7 27.6 - - + +
761A THR 2.9 20.6 + - - +
762A PRO* 3.8 1.5 + - + -
764A ILE* 1.3 76.9 - - - +
766A TYR* 1.3 88.4 + - + +
768A LEU* 3.7 2.8 - - - +
769A ALA* 3.0 27.4 + - - +
818A GLU* 3.8 14.4 - - + +
819A PHE* 3.7 35.5 - - + -
822A ALA* 3.7 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 766 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A PRO* 3.5 26.7 - - + +
764A ILE 3.4 0.8 - - - -
765A VAL* 1.3 88.3 - - + +
767A ARG* 1.3 68.1 + - + +
769A ALA* 3.4 2.6 + - - +
770A SER* 3.1 24.1 + - - -
818A GLU* 5.3 3.2 + - - +
821A SER* 5.4 5.0 + - - -
822A ALA* 3.8 30.7 - - + -
825A LYS* 5.8 8.1 - - + -
826A ASP* 5.1 0.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
681A LEU* 3.7 20.5 - - + +
682A ASN* 2.6 35.9 + - - +
685A THR* 3.6 24.4 - - - +
762A PRO 5.6 0.4 + - - -
763A GLU 4.1 16.8 - - - +
764A ILE 3.2 7.2 + - - +
766A TYR* 1.3 78.1 - - + +
768A LEU* 1.3 57.9 + - - +
770A SER* 3.3 8.1 + - - -
771A MET* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 768 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A LEU* 3.6 11.6 - - + +
748A PHE* 3.7 25.4 - - + -
759A PHE* 3.6 32.5 - - + +
764A ILE* 2.7 23.3 + - + +
765A VAL 3.7 3.8 - - - +
767A ARG* 1.3 69.6 - - - +
769A ALA* 1.3 67.5 + - - +
770A SER 3.2 0.2 + - - -
771A MET* 3.2 27.6 + - + +
772A LEU* 2.8 42.8 + - + +
809A VAL* 5.3 1.1 - - + -
813A LEU* 3.6 27.4 - - + -
819A PHE* 4.5 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 769 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A VAL 3.0 17.7 + - - +
766A TYR 3.8 4.7 - - - +
768A LEU* 1.3 76.0 - - - +
770A SER* 1.3 58.9 + - - +
772A LEU* 3.3 2.4 + - - -
773A ASN* 2.9 38.7 + - - +
819A PHE* 4.6 6.6 - - + -
822A ALA* 3.9 9.4 - - + +
823A VAL* 3.8 43.5 - - + +
826A ASP* 4.8 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 770 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A TYR 3.1 15.7 + - - -
767A ARG* 3.6 10.3 - - - -
769A ALA* 1.3 81.1 - - - +
771A MET* 1.3 57.8 + - - +
773A ASN* 3.6 1.7 + - - +
774A TYR* 3.1 28.4 + - - +
826A ASP* 3.7 24.3 + - - +
828A ARG* 3.4 24.0 + - - -
829A SER* 4.6 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 771 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A LEU* 4.0 17.7 - - + +
684A LEU* 3.8 33.7 - - + -
685A THR* 3.9 15.7 - - + +
745A MET* 4.6 2.9 - - + -
748A PHE* 3.9 23.3 - - + -
767A ARG 2.9 18.1 + - - +
768A LEU* 3.7 28.3 - - + +
770A SER* 1.3 75.2 - - - +
772A LEU* 1.3 79.0 + - + +
774A TYR* 3.8 3.9 - - - +
775A ASN* 3.1 50.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 772 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745A MET* 4.3 7.4 - - - -
748A PHE* 5.8 1.1 - - + -
768A LEU* 2.8 35.8 + - + +
769A ALA* 3.9 2.5 - - - +
771A MET* 1.3 91.3 - - + +
773A ASN* 1.3 53.8 + - - +
775A ASN* 3.7 0.6 - - - -
776A LEU* 2.8 35.0 + - - +
806A LEU* 3.2 28.1 - - + +
809A VAL* 4.0 25.4 - - + -
810A TYR* 3.1 21.7 + - + +
819A PHE* 3.8 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 773 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769A ALA* 2.9 23.5 + - - +
770A SER 4.0 0.9 - - - +
772A LEU* 1.3 76.8 - - - +
774A TYR* 1.3 56.1 + - - +
776A LEU* 3.2 7.7 + - - +
777A GLU* 2.9 28.1 + - - +
810A TYR* 2.5 38.4 + - - -
823A VAL* 4.0 14.5 + - - +
826A ASP* 3.3 30.6 + - - +
829A SER* 3.2 24.4 - - - -
830A PHE* 3.7 21.8 - - - +
834A LEU* 4.2 3.2 - - + +
835A PHE* 4.9 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 774 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A THR* 3.6 23.3 - - - -
689A ASP* 2.6 35.4 + - - -
770A SER 3.1 19.5 + - - +
771A MET* 3.8 5.8 - - - +
773A ASN* 1.3 73.6 - - - +
775A ASN* 1.3 75.3 + - - +
777A GLU* 3.1 21.8 + - + +
778A SER* 3.2 15.2 + - - -
783A LYS* 3.1 23.5 + - - -
828A ARG* 4.0 31.0 - - - +
829A SER* 3.7 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 775 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A LEU* 2.8 32.6 + - - +
685A THR* 4.7 1.8 - - - +
688A LEU* 3.6 28.8 - - - +
741A ALA* 5.9 0.3 - - - +
745A MET* 4.3 17.1 - - + +
771A MET* 3.1 33.6 + - - +
772A LEU 3.8 3.4 - - - +
774A TYR* 1.3 85.0 - - - +
776A LEU* 1.3 62.5 + - - +
778A SER* 3.2 8.7 + - - -
779A LEU* 3.2 29.9 + - + +
802A LEU* 5.3 1.9 - - - +
806A LEU* 4.1 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 776 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A LEU 2.8 18.9 + - - +
773A ASN* 3.4 7.6 - - + +
774A TYR 3.1 0.2 - - - -
775A ASN* 1.3 76.2 - - - +
777A GLU* 1.3 61.5 + - - +
779A LEU* 3.3 2.5 + - - +
780A VAL* 3.1 36.7 + - + +
803A LEU* 3.8 26.5 - - + -
806A LEU* 3.5 13.8 - - + +
807A THR* 4.4 7.2 - - + -
810A TYR* 3.9 9.2 - - + +
834A LEU* 3.7 31.0 - - + +
835A PHE* 3.7 36.6 - - + -
838A ALA* 4.2 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 777 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A ASN 2.9 9.5 + - - +
774A TYR* 3.1 17.4 + - + +
776A LEU* 1.3 76.2 - - - +
778A SER* 1.3 61.6 + - - +
780A VAL* 4.0 6.8 - - - +
781A GLY* 3.1 21.8 + - - -
782A PRO* 5.2 0.7 - - - +
783A LYS* 5.2 5.5 + - + +
828A ARG 3.7 5.7 - - - +
829A SER* 3.0 39.3 + - - +
834A LEU* 3.7 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 778 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A LEU* 3.9 23.5 - - - +
689A ASP* 4.4 2.6 + - - -
692A LEU* 4.6 0.7 - - - -
774A TYR* 3.2 10.6 + - - -
775A ASN* 3.2 8.5 + - - -
777A GLU* 1.3 78.1 - - - +
779A LEU* 1.3 62.5 + - - +
781A GLY 3.3 8.3 - - - +
783A LYS* 3.2 46.0 + - - +
784A CYS* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 779 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A LEU* 4.0 7.9 - - + -
745A MET* 5.7 0.2 - - + -
775A ASN* 3.2 21.8 + - + +
776A LEU 3.3 3.6 + - - +
778A SER* 1.3 79.4 - - - +
780A VAL* 1.3 61.8 + - - +
781A GLY 3.7 1.0 + - - +
784A CYS* 3.7 28.4 - - - +
785A GLY 5.1 0.9 + - - -
799A PRO* 3.5 32.9 - - + +
802A LEU* 4.0 33.2 - - + -
803A LEU* 4.1 28.6 - - + +
806A LEU* 4.0 20.9 - - + -
841A ILE* 3.9 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 780 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776A LEU* 3.1 27.9 + - + +
777A GLU 4.3 2.5 - - - +
779A LEU* 1.3 79.4 - - - +
781A GLY* 1.3 60.7 + - - +
803A LEU* 4.1 6.3 - - + -
834A LEU* 3.8 37.5 - - + +
837A ARG* 2.8 48.3 + - + -
838A ALA* 3.7 34.5 - - + +
841A ILE* 3.8 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 781 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777A GLU 3.1 15.1 + - - -
778A SER 3.3 4.3 + - - +
779A LEU 4.4 0.7 - - - +
780A VAL* 1.3 82.5 - - - +
782A PRO* 1.3 71.4 - - - +
783A LYS 3.2 4.0 + - - -
784A CYS* 4.4 0.2 - - - +
785A GLY* 2.9 24.2 + - - -
837A ARG* 4.9 4.7 - - - -
----------------------------------------------------------
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