Contacts of the helix formed by residues 754 - 770 (chain A) in PDB entry 3MP6
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 GLY 754 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749A ILE* 5.1 2.2 - - - -
753A LYS* 1.3 72.3 - - - +
755A TYR* 1.3 58.8 + - - -
757A GLY* 3.2 3.5 + - - -
758A LEU* 2.9 27.6 + - - +
1031A VAL* 3.8 17.7 - - - +
1034A ASP* 3.1 28.7 - - - -
1035A LYS* 3.7 15.5 + - - +
1037A LEU* 6.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 755 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749A ILE* 3.6 26.9 - - + +
750A ASN 4.1 2.5 - - - -
751A GLY* 3.4 28.1 + - - -
753A LYS 2.8 28.3 + - - -
754A GLY* 1.3 71.6 - - - +
756A ASN* 1.3 92.7 + - - +
758A LEU* 3.4 5.6 + - - +
759A ALA* 3.0 27.5 + - - +
775A VAL* 3.8 13.4 - - + +
777A HIS* 3.4 52.4 - + + -
1034A ASP* 3.6 0.4 + - - -
1035A LYS* 6.5 0.7 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
755A TYR* 1.3 100.7 + - - +
757A GLY* 1.3 65.9 + - - +
759A ALA* 3.2 9.9 + - - +
760A GLU* 3.1 27.0 + - - +
1034A ASP* 3.1 16.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 757 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754A GLY 3.2 3.8 + - - -
756A ASN* 1.3 73.4 - - - +
758A LEU* 1.3 65.0 + - - +
760A GLU* 3.0 23.4 + - - +
761A VAL* 3.2 14.9 + - - +
1030A ALA* 3.4 24.1 - - - +
1031A VAL* 4.0 7.2 - - - -
1034A ASP* 2.9 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 758 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A ILE* 3.9 26.7 - - + -
749A ILE* 4.1 19.5 - - + -
754A GLY 2.9 16.7 + - - +
755A TYR* 3.6 6.5 - - - +
756A ASN 3.3 0.2 - - - -
757A GLY* 1.3 75.0 - - - +
759A ALA* 1.3 57.9 + - - +
761A VAL* 3.1 7.9 + - + +
762A GLY* 2.9 22.9 + - - -
775A VAL* 4.1 19.0 - - + +
799A PHE* 4.0 12.1 - - + -
1017A PHE* 3.9 25.8 - - + -
1022A LEU* 3.9 29.4 - - + -
1031A VAL* 3.8 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 759 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A TYR 3.0 14.5 + - - +
756A ASN* 3.5 13.0 - - - +
757A GLY 3.2 0.2 - - - -
758A LEU* 1.3 74.5 - - - +
760A GLU* 1.3 59.8 + - - +
762A GLY* 3.2 4.3 + - - +
763A LYS* 2.8 27.4 + - - +
775A VAL* 4.0 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 760 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756A ASN* 3.1 16.0 + - - +
757A GLY* 3.0 15.5 + - - +
759A ALA* 1.3 72.5 - - - +
761A VAL* 1.3 65.5 + - - +
763A LYS* 3.2 15.1 + - - +
764A LYS* 3.2 22.6 + - - +
767A LYS* 5.5 0.2 + - - -
1030A ALA* 4.0 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 761 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757A GLY 3.2 11.8 + - - +
758A LEU* 3.1 8.9 + - + +
760A GLU* 1.3 71.9 - - - +
762A GLY* 1.3 66.0 + - - +
764A LYS* 3.1 14.4 + - + +
765A PHE* 3.1 20.4 + - - +
1017A PHE* 3.7 22.0 - - + -
1021A TYR* 3.8 32.8 - - + +
1022A LEU* 3.8 6.7 - - + +
1027A GLY* 3.4 31.2 - - - +
1030A ALA* 4.0 7.6 - - + -
1031A VAL* 4.2 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 762 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758A LEU 2.9 12.9 + - - -
759A ALA* 3.2 7.2 + - - -
761A VAL* 1.3 75.4 - - - +
763A LYS* 1.3 55.8 + - - +
765A PHE* 3.2 4.2 + - - +
766A GLU* 2.8 37.8 + - - +
773A VAL* 4.0 18.1 - - - +
1017A PHE* 3.8 15.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 763 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759A ALA 2.8 15.6 + - - +
760A GLU* 3.2 11.8 + - - +
762A GLY* 1.3 72.2 - - - +
764A LYS* 1.3 56.4 + - - +
766A GLU* 3.2 19.6 + - + +
767A LYS* 2.9 59.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 764 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760A GLU* 3.2 17.8 + - - +
761A VAL* 3.1 14.0 + - + +
763A LYS* 1.3 75.3 - - - +
765A PHE* 1.3 62.8 + - - +
767A LYS* 3.3 23.6 + - - +
768A ASP* 3.2 26.5 + - - +
1021A TYR* 4.0 14.4 - - + -
1026A GLU* 3.7 39.3 + - + +
1027A GLY* 6.0 1.3 - - - -
1030A ALA* 5.4 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 765 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745A LEU* 4.0 11.0 - - + -
761A VAL 3.1 12.0 + - - +
762A GLY 3.4 7.2 - - - +
764A LYS* 1.3 75.8 - - - +
766A GLU* 1.3 54.2 + - - +
768A ASP 3.3 1.4 + - - -
769A THR* 2.8 68.9 + - + +
771A ILE* 4.0 14.4 - - + -
773A VAL* 3.4 26.0 - - + -
1013A LEU* 3.8 29.2 - - + -
1016A GLU* 4.0 9.9 - - + -
1017A PHE* 3.7 39.0 - + + -
1021A TYR* 3.7 34.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 766 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A GLY 2.8 21.2 + - - +
763A LYS* 3.3 25.8 - - + +
765A PHE* 1.3 77.1 - - - +
767A LYS* 1.3 57.1 + - + +
770A GLY* 2.9 29.9 + - - -
771A ILE 3.2 25.6 - - - +
772A LYS* 3.8 10.7 + - - +
773A VAL* 2.9 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 767 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760A GLU 5.5 0.2 + - - -
763A LYS* 2.9 58.3 + - + +
764A LYS* 3.6 24.1 - - - +
765A PHE 3.3 0.2 - - - -
766A GLU* 1.3 79.8 - - + +
768A ASP* 1.3 68.2 + - - +
770A GLY* 4.3 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 768 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764A LYS 3.2 13.1 + - - +
765A PHE 3.9 1.8 - - - +
767A LYS* 1.3 85.6 - - - +
769A THR* 1.3 61.2 + - + +
1021A TYR* 2.6 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 769 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A PHE* 2.8 55.5 + - + +
768A ASP* 1.3 84.8 - - + +
770A GLY* 1.3 60.7 + - - +
771A ILE* 3.0 36.0 + - - +
1013A LEU* 5.3 2.5 - - + -
1016A GLU* 4.1 20.0 - - - +
1021A TYR* 4.7 1.3 - - - +
----------------------------------------------------------
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 GLU* 2.9 15.5 + - - -
767A LYS 4.3 2.3 + - - -
768A ASP 3.7 1.0 - - - -
769A THR* 1.3 77.4 - - - +
771A ILE* 1.3 65.5 + - - +
772A LYS 4.2 0.3 + - - -
----------------------------------------------------------
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