Contacts of the helix formed by residues 765 - 782 (chain A) in PDB entry 2VF8
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 HIS 765 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A THR* 5.7 0.4 - - - -
43A GLY* 3.1 34.3 - - - -
44A VAL* 3.2 14.5 + - + -
45A SER 4.0 0.9 - - - +
439A HIS* 3.4 22.0 + + + -
480A GLN* 4.1 11.7 - - + +
481A THR* 3.1 47.8 + - - +
484A TYR* 4.2 1.6 - + - -
763A GLY 3.8 0.2 + - - -
764A LEU* 1.3 76.2 - - - +
766A PRO* 1.3 101.4 - - + +
767A ALA* 3.2 14.1 + - + +
768A ASP* 2.8 31.1 + - - +
769A VAL* 3.1 6.8 + - - +
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Residues in contact with PRO 766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A HIS* 4.0 26.0 - - + +
441A LEU* 4.3 17.5 - - + -
484A TYR* 3.5 38.8 - - + -
764A LEU 3.6 1.1 - - - +
765A HIS* 1.3 96.2 - - + +
767A ALA* 1.3 62.5 + - - +
768A ASP 2.9 1.6 + - - -
769A VAL* 2.9 25.9 + - + +
770A GLU* 3.2 12.6 + - - +
792A LYS* 5.1 4.3 - - + +
794A GLN* 4.1 8.0 + - - +
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Residues in contact with ALA 767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 4.5 6.7 - - + -
480A GLN* 3.2 31.4 - - - +
484A TYR* 3.3 26.2 + - + +
765A HIS* 3.2 12.6 + - + +
766A PRO* 1.3 77.2 - - - +
768A ASP* 1.3 62.2 + - - +
770A GLU* 3.5 14.6 - - - +
771A ARG* 3.5 9.4 + - - +
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Residues in contact with ASP 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 4.1 13.8 - - - +
45A SER* 3.1 37.8 + - - -
738A ARG* 4.0 12.1 + - - +
764A LEU* 3.1 27.7 - - + +
765A HIS* 2.8 23.9 + - - +
767A ALA* 1.3 78.9 - - - +
769A VAL* 1.3 64.4 + - - +
770A GLU 3.1 1.8 - - - -
771A ARG* 3.0 15.3 + - - +
772A LEU* 2.9 20.1 + - - +
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Residues in contact with VAL 769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761A THR* 3.8 29.4 - - + -
764A LEU* 3.6 20.4 - - + +
765A HIS 3.1 14.6 + - - +
766A PRO* 2.9 6.7 + - + +
768A ASP* 1.3 75.3 - - - +
770A GLU* 1.3 54.4 + - - +
772A LEU* 3.2 9.8 - - + +
773A GLN* 2.7 41.5 + - + +
792A LYS* 5.2 3.6 - - + +
794A GLN* 2.8 49.6 - - + +
795A VAL* 5.1 4.0 - - + -
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Residues in contact with GLU 770 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A TYR* 3.0 35.5 + - + +
766A PRO 3.2 5.3 + - - +
767A ALA 3.5 11.9 - - - +
768A ASP 3.1 0.8 - - - -
769A VAL* 1.3 82.0 - - - +
771A ARG* 1.3 57.0 + - - +
773A GLN* 3.6 8.0 + - - +
774A ARG* 3.0 55.3 + - - +
794A GLN* 4.1 14.7 + - - +
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Residues in contact with ARG 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715A ARG 3.5 11.9 + - - -
716A GLU* 2.6 37.0 + - - +
717A VAL* 3.8 3.6 - - - +
718A GLY* 3.1 14.7 - - - -
738A ARG* 3.5 26.9 - - - +
764A LEU* 5.9 0.2 - - + -
767A ALA 3.5 8.1 + - - +
768A ASP* 3.0 16.4 + - - +
770A GLU* 1.3 75.1 - - - +
772A LEU* 1.3 70.5 + - + +
774A ARG* 3.5 17.0 - - - +
775A GLN* 3.2 27.7 + - + +
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Residues in contact with LEU 772 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737A GLN* 4.9 5.8 - - - +
738A ARG* 6.4 1.8 - - + -
741A LEU* 4.1 22.2 - - + -
760A PRO* 3.7 42.4 - - + +
761A THR* 5.4 4.5 - - + -
764A LEU* 5.1 10.3 - - + -
768A ASP 2.9 12.5 + - - +
769A VAL* 3.2 15.5 - - + +
771A ARG* 1.3 75.6 - - - +
773A GLN* 1.3 71.1 + - + +
775A GLN* 2.6 20.3 + - + -
776A LEU* 3.2 33.2 + - + -
790A GLU* 6.0 0.4 - - - +
795A VAL* 6.5 0.9 - - + -
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Residues in contact with GLN 773 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A MET* 6.3 2.2 - - - -
769A VAL* 2.7 22.0 + - + +
770A GLU* 3.8 8.2 - - - +
772A LEU* 1.3 73.7 - - + +
774A ARG* 1.3 53.3 + - - +
776A LEU* 2.9 16.5 + - + +
777A VAL* 2.8 37.1 + - - +
794A GLN* 3.9 16.8 + - - +
795A VAL* 3.4 40.0 + - + +
798A ALA* 3.1 30.8 - - - +
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Residues in contact with ARG 774 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770A GLU* 3.0 52.1 + - - +
771A ARG* 3.5 17.7 - - - +
772A LEU 2.7 4.0 + - - -
773A GLN* 1.3 72.0 - - - +
775A GLN* 1.3 71.1 + - - +
777A VAL* 3.1 16.2 - - + +
778A LYS* 3.1 23.5 + - - +
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Residues in contact with GLN 775 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716A GLU* 2.8 43.2 + - - +
717A VAL* 4.8 4.5 - - + +
741A LEU* 4.9 9.0 - - + -
745A LEU* 3.3 36.8 - - + +
771A ARG* 3.2 18.4 + - - +
772A LEU* 2.6 14.8 + - + +
774A ARG* 1.3 85.4 - - - +
776A LEU* 1.3 59.0 + - - +
778A LYS* 2.7 37.6 + - - +
779A LEU* 3.3 21.9 + - - +
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Residues in contact with LEU 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A MET* 4.7 23.3 - - + -
741A LEU* 4.9 13.5 - - + -
757A LEU* 4.7 25.1 - - + -
760A PRO* 5.6 4.7 - - + -
772A LEU* 3.2 37.0 + - + -
773A GLN* 2.9 24.2 + - + +
775A GLN* 1.3 75.4 - - - +
777A VAL* 1.3 66.4 + - - +
778A LYS 3.0 1.8 - - - -
779A LEU* 2.8 35.9 + - + +
780A VAL* 2.9 19.6 + - + +
786A VAL* 4.8 8.5 - - + -
795A VAL* 5.9 4.5 - - + -
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Residues in contact with VAL 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494A HIS* 5.1 15.0 - - + -
497A ARG* 5.5 3.3 + - - +
525A MET* 5.8 1.9 - - - -
773A GLN* 2.8 17.9 + - + +
774A ARG* 3.1 20.4 - - + +
776A LEU* 1.3 70.7 - - - +
778A LYS* 1.3 65.7 - - + +
780A VAL* 3.6 8.8 - - - +
781A ASP* 2.9 35.7 + - - +
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Residues in contact with LYS 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716A GLU* 2.9 18.6 + - - -
745A LEU* 4.0 15.6 - - + +
774A ARG 3.1 6.5 + - - +
775A GLN* 2.7 49.1 + - - +
776A LEU 3.0 0.6 - - - -
777A VAL* 1.3 84.1 - - + +
779A LEU* 1.3 55.9 + - - +
780A VAL 3.0 0.2 - - - -
781A ASP* 2.7 38.4 + - - +
782A ALA* 3.5 5.5 + - - +
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Residues in contact with LEU 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741A LEU* 5.1 9.4 - - + -
744A GLU* 5.2 0.9 - - + +
745A LEU* 4.7 24.9 - - + -
748A SER* 5.2 10.2 - - - +
755A TYR* 3.4 45.3 - - + +
775A GLN 3.3 7.7 + - - +
776A LEU* 2.8 57.7 + - + +
778A LYS* 1.3 74.5 - - + +
780A VAL* 1.3 56.7 + - - +
781A ASP 3.5 0.2 - - - -
782A ALA* 4.5 9.2 + - - +
784A ASN* 2.9 29.3 + - - +
786A VAL* 4.0 13.5 - - + -
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Residues in contact with VAL 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497A ARG* 3.5 29.5 + - - +
523A GLY 4.1 4.3 - - - +
524A VAL* 4.0 19.7 - - - +
525A MET* 4.1 10.8 - - + +
776A LEU 2.9 22.3 + - - +
777A VAL* 3.6 10.3 - - - +
779A LEU* 1.3 79.8 - - - +
781A ASP* 1.3 63.1 + - - +
782A ALA 3.4 0.4 - - - -
783A GLY* 3.1 12.1 + - - -
784A ASN 3.2 20.7 + - - +
786A VAL* 3.9 27.4 - - + -
800A ASP* 4.7 0.2 - - - +
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Residues in contact with ASP 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497A ARG* 2.7 36.6 + - - +
777A VAL* 2.9 29.9 - - - +
778A LYS* 2.7 22.2 + - - +
780A VAL* 1.3 67.5 - - - +
782A ALA* 1.3 51.6 + - - +
783A GLY* 2.7 16.3 + - - -
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Residues in contact with ALA 782 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748A SER* 5.1 14.8 - - - +
750A ARG* 4.0 6.9 + - - +
751A GLY* 3.0 32.0 + - - +
778A LYS 3.5 7.1 + - - +
779A LEU* 4.9 8.1 - - - +
780A VAL 3.4 0.4 - - - -
781A ASP* 1.3 75.1 - - - +
783A GLY* 1.3 56.6 + - - +
784A ASN* 3.6 1.8 - - - +
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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
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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) + - + + + + + -
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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