Contacts of the helix formed by residues 771 - 779 (chain A) in PDB entry 1OH7
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 TYR 771 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A GLY* 4.9 1.3 - - - -
615A PRO* 3.7 43.1 - - + +
746A HIS* 6.5 0.9 - + - -
747A LEU 5.1 1.1 - - - -
749A ALA* 3.2 39.2 + - + -
750A LEU* 5.2 0.7 - - - -
751A GLU* 3.3 41.5 + - + +
756A ILE* 4.0 11.4 - - + -
767A ALA* 5.3 5.6 - - + -
768A SER* 5.4 4.9 + - - -
769A LYS* 3.6 38.3 + - + +
770A SER* 1.3 78.5 - - - +
772A GLY* 1.3 60.5 + - - +
773A LEU 3.4 2.5 - - - -
774A ALA* 3.2 7.9 + - + +
775A VAL* 3.1 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 772 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771A TYR* 1.3 70.7 - - - +
773A LEU* 1.3 65.4 + - - +
775A VAL* 3.4 5.3 + - - +
776A ALA* 3.1 24.1 + - - +
670B PHE* 3.9 13.3 - - - -
699B THR* 3.4 21.7 + - - -
703B ASP* 2.6 21.5 + - - -
707B LEU* 4.3 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 773 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771A TYR 5.1 0.2 - - - -
772A GLY* 1.3 75.9 - - - +
774A ALA* 1.3 57.0 + - - +
776A ALA* 3.2 6.1 + - - +
777A ALA* 3.0 26.8 + - - +
786A ILE* 3.9 9.7 - - + +
789A ALA* 3.8 13.5 - - + +
790A ARG* 3.6 60.3 - - + +
793A LEU* 3.9 24.0 - - + -
703B ASP* 3.4 34.0 + - + +
706B SER* 4.4 1.6 - - - -
707B LEU* 3.5 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 774 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751A GLU* 3.5 27.4 - - + +
754A ASP 5.6 3.8 - - - +
755A THR 6.2 0.4 - - - -
756A ILE* 4.1 27.3 - - + +
771A TYR* 3.2 14.1 + - - +
773A LEU* 1.3 79.8 - - - +
775A VAL* 1.3 56.7 + - - +
777A ALA* 3.3 9.0 + - - +
778A LEU* 3.1 24.9 + - - +
790A ARG* 4.6 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 775 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A PRO* 4.7 6.3 - - + -
616A ASN* 4.0 34.3 - - + +
617A MET* 5.4 1.1 - - - -
756A ILE* 5.4 2.9 - - + -
758A PHE* 4.7 8.3 - - + -
771A TYR* 3.1 19.5 + - + +
772A GLY* 3.8 7.2 - - - +
774A ALA* 1.3 73.6 - - + +
776A ALA* 1.3 66.2 + - - +
778A LEU* 3.2 13.0 + - + +
779A ALA* 3.1 19.9 + - - +
670B PHE* 3.6 26.5 - - + -
671B MET* 3.7 28.5 - - + +
674B MET* 5.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 776 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A GLY 3.1 13.9 + - - +
773A LEU 3.3 9.9 - - - +
775A VAL* 1.3 74.5 - - - +
777A ALA* 1.3 64.6 + - - +
779A ALA* 3.1 10.9 + - - -
780A GLY 3.4 0.2 + - - -
781A VAL* 3.3 24.9 + - + +
786A ILE* 3.9 13.9 - - + -
674B MET* 3.9 27.8 - - + -
707B LEU* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 777 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754A ASP* 5.2 14.6 - - - +
773A LEU 3.0 13.3 + - - +
774A ALA* 3.5 12.8 - - - +
775A VAL 3.3 0.2 - - - -
776A ALA* 1.3 75.1 - - - +
778A LEU* 1.3 62.4 + - - +
780A GLY* 3.2 13.9 + - - -
781A VAL 4.3 4.6 + - - +
783A LYS* 6.0 7.1 - - - -
786A ILE* 3.9 26.4 - - + +
790A ARG* 6.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 778 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A MET* 4.8 12.6 - - + -
755A THR* 4.4 17.0 - - - +
756A ILE* 4.1 24.5 - - + +
758A PHE* 4.3 14.4 - - + -
774A ALA 3.1 12.9 + - - +
775A VAL* 3.2 14.6 - - + +
777A ALA* 1.3 78.6 - - - +
779A ALA* 1.3 55.2 + - - +
780A GLY* 3.2 4.1 + - - -
671B MET* 5.2 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 779 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775A VAL 3.1 10.2 + - - +
776A ALA 3.1 10.5 + - - +
778A LEU* 1.3 73.9 - - - +
780A GLY* 1.3 60.1 + - - +
781A VAL 3.4 1.3 - - - -
671B MET* 3.9 18.6 - - - -
674B MET* 3.9 17.0 - - + -
675B THR* 3.2 33.4 + - - +
678B ALA* 3.5 11.8 - - - +
----------------------------------------------------------
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