Contacts of the helix formed by residues 765 - 782 (chain C) in PDB entry 2VF7
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C THR* 5.6 0.2 - - - -
43C GLY* 3.1 28.7 + - - +
44C VAL* 3.6 16.6 + - + -
439C HIS* 3.6 12.4 + - + -
441C LEU* 5.8 0.6 - - + +
480C GLN* 3.4 21.7 + - + +
481C THR* 2.9 38.1 - - + -
484C TYR* 4.4 2.8 - + - +
764C LEU* 1.3 73.5 - - - +
766C PRO* 1.3 77.5 - - + +
767C ALA* 3.0 34.3 - - + +
768C ASP* 2.7 44.3 + - - +
769C VAL* 2.9 11.5 + - - +
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Residues in contact with PRO 766 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C HIS* 3.7 24.5 - - + +
441C LEU* 4.0 26.5 - - + -
484C TYR* 3.5 33.7 + - + -
764C LEU 4.3 2.9 - - - +
765C HIS* 1.3 94.9 - - + +
767C ALA* 1.3 58.4 + - - +
769C VAL* 3.5 1.1 + - + -
770C GLU 3.3 10.6 + - - -
794C GLN* 2.9 39.5 + - - +
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Residues in contact with ALA 767 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C VAL* 4.7 2.7 - - + -
480C GLN* 3.4 28.9 - - + +
484C TYR* 3.6 10.7 - - + -
489C ARG* 3.5 18.6 + - - +
765C HIS* 3.0 20.2 - - + +
766C PRO* 1.3 73.8 - - - +
768C ASP* 1.3 64.6 + - - +
770C GLU* 3.4 17.2 - - - +
771C ARG* 3.5 7.8 + - - +
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Residues in contact with ASP 768 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C VAL* 3.4 18.9 - - - +
45C SER* 2.9 39.2 + - - -
738C ARG* 5.1 7.8 + - - +
764C LEU* 3.5 20.3 - - + +
765C HIS* 2.7 36.1 + - - +
767C ALA* 1.3 72.5 - - - +
769C VAL* 1.3 62.8 + - - +
771C ARG* 3.4 12.0 + - - +
772C LEU* 3.2 20.4 + - - +
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Residues in contact with VAL 769 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761C THR* 3.6 25.6 - - - +
764C LEU* 3.8 20.9 - - + +
765C HIS 2.9 16.1 + - - +
767C ALA 3.4 0.2 - - - -
768C ASP* 1.3 74.5 - - - +
770C GLU* 1.3 59.2 + - - +
772C LEU* 3.8 10.6 - - + +
773C GLN* 3.0 42.9 + - + +
794C GLN* 3.1 42.4 - - + +
795C VAL* 4.2 12.8 - - + -
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Residues in contact with GLU 770 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C TYR* 3.6 17.5 + - - +
489C ARG* 3.0 27.8 + - - +
490C HIS 4.2 14.4 - - - +
491C THR* 4.5 16.1 - - + +
766C PRO 3.3 13.1 + - - +
767C ALA 3.4 10.5 - - - +
769C VAL* 1.3 78.7 - - - +
771C ARG* 1.3 60.3 + - - +
773C GLN* 3.7 13.6 + - - +
774C ARG* 3.5 42.1 + - - +
794C GLN* 4.9 2.0 - - - +
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Residues in contact with ARG 771 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715C ARG 3.4 9.5 + - - -
716C GLU* 2.9 33.2 + - - +
717C VAL* 3.7 8.3 - - - -
718C GLY* 3.4 27.9 + - - -
738C ARG* 5.3 2.2 - - - +
767C ALA 3.5 7.6 + - - +
768C ASP* 3.4 14.2 + - - +
769C VAL 3.3 0.4 - - - -
770C GLU* 1.3 76.7 - - - +
772C LEU* 1.3 67.4 + - - +
774C ARG* 3.0 39.4 + - - +
775C GLN* 3.6 8.4 + - + +
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Residues in contact with LEU 772 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717C VAL* 5.9 0.9 - - + -
738C ARG* 5.5 11.7 - - + -
741C LEU* 3.6 31.9 - - + -
757C LEU* 5.9 0.9 - - + -
760C PRO* 4.2 28.5 - - + +
764C LEU* 4.6 12.6 - - + -
768C ASP 3.2 13.7 + - - +
769C VAL* 3.8 11.9 - - + +
770C GLU 3.5 0.2 - - - -
771C ARG* 1.3 79.8 - - - +
773C GLN* 1.3 57.9 + - + +
775C GLN* 2.7 30.9 + - + +
776C LEU* 3.1 37.1 + - + +
795C VAL* 6.0 4.0 - - + -
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Residues in contact with GLN 773 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C THR* 5.5 8.5 - - - +
525C MET* 6.4 1.1 - - + -
769C VAL* 3.0 34.1 + - + +
770C GLU* 3.9 14.5 - - - +
772C LEU* 1.3 80.9 - - + +
774C ARG* 1.3 55.4 + - - +
775C GLN 3.1 0.7 - - - -
776C LEU* 3.9 14.9 - - + +
777C VAL* 3.0 36.7 + - + +
794C GLN* 3.5 13.6 + - - +
795C VAL* 3.2 37.3 + - + +
798C ALA* 4.3 13.6 - - + +
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Residues in contact with ARG 774 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770C GLU* 3.5 31.7 + - - +
771C ARG* 3.0 37.0 + - - +
773C GLN* 1.3 75.2 - - - +
775C GLN* 1.3 71.1 + - - +
777C VAL* 4.5 8.1 - - + -
778C LYS* 3.7 24.7 - - - +
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Residues in contact with GLN 775 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716C GLU* 3.3 51.1 + - - +
717C VAL* 4.8 13.2 - - + -
741C LEU* 4.6 15.5 - - + -
745C LEU* 3.9 24.7 - - + +
771C ARG* 3.9 13.6 - - + +
772C LEU* 2.7 18.4 + - + +
774C ARG* 1.3 90.1 + - - +
776C LEU* 1.3 61.5 + - - +
777C VAL 3.3 1.6 - - - -
778C LYS* 3.4 19.0 + - - +
779C LEU* 3.1 29.6 + - - +
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Residues in contact with LEU 776 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525C MET* 3.9 32.5 - - + -
741C LEU* 4.8 8.3 - - + -
757C LEU* 3.8 28.9 - - + -
760C PRO* 5.7 2.2 - - + -
772C LEU* 3.1 42.1 + - + +
773C GLN* 3.6 14.1 + - + +
775C GLN* 1.3 78.1 - - - +
777C VAL* 1.3 58.6 + - + +
779C LEU* 3.0 27.5 - - + +
780C VAL* 3.0 32.4 + - - +
786C VAL* 4.5 8.7 - - + -
795C VAL* 6.4 0.9 - - + -
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Residues in contact with VAL 777 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C HIS* 3.5 45.3 - - + +
497C ARG* 3.8 10.3 + - - +
773C GLN* 3.0 24.6 + - + +
774C ARG* 4.6 7.2 - - + -
776C LEU* 1.3 75.2 - - + +
778C LYS* 1.3 69.0 + - + +
780C VAL* 3.3 3.6 + - - -
781C ASP* 3.1 29.4 + - - +
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Residues in contact with LYS 778 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716C GLU* 2.8 30.1 + - - +
745C LEU* 6.6 0.2 - - + -
774C ARG* 3.7 23.3 + - - +
775C GLN* 3.4 19.8 + - - +
776C LEU 3.3 0.4 - - - -
777C VAL* 1.3 82.2 - - + +
779C LEU* 1.3 62.6 + - - +
781C ASP* 3.3 25.1 + - - +
782C ALA* 3.4 8.3 + - - +
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Residues in contact with LEU 779 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741C LEU* 4.3 24.0 - - + -
745C LEU* 5.2 8.7 - - + -
748C SER* 4.2 14.4 - - - +
755C TYR* 4.0 32.1 - - + -
775C GLN 3.1 17.5 + - - +
776C LEU* 3.0 34.5 + - + +
777C VAL 3.2 0.2 - - - -
778C LYS* 1.3 79.3 - - - +
780C VAL* 1.3 61.5 + - + +
782C ALA* 3.4 8.1 + - - -
784C ASN* 2.7 39.1 + - + +
786C VAL* 3.4 26.0 - - + -
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Residues in contact with VAL 780 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497C ARG* 3.6 30.7 + - - +
523C GLY 3.6 24.3 - - - +
524C VAL* 3.7 9.4 - - - -
525C MET* 4.3 13.9 - - + +
776C LEU 3.0 21.7 + - - +
777C VAL* 3.3 4.7 + - - +
779C LEU* 1.3 74.8 - - + +
781C ASP* 1.3 63.7 + - - +
783C GLY* 3.4 12.9 + - - -
784C ASN 3.8 13.0 + - - +
786C VAL* 3.4 27.8 - - + -
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Residues in contact with ASP 781 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C HIS* 4.1 6.9 + - - -
497C ARG* 2.8 28.0 + - - +
777C VAL* 3.1 26.2 + - - +
778C LYS* 3.4 14.1 - - - +
779C LEU 3.3 0.4 - - - -
780C VAL* 1.3 72.3 - - - +
782C ALA* 1.3 57.2 + - - +
783C GLY* 3.0 10.2 + - - -
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Residues in contact with ALA 782 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748C SER* 3.5 12.6 - - - +
749C GLY* 4.2 16.5 - - - +
750C ARG 4.4 0.3 - - - -
751C GLY* 3.2 21.3 + - - -
778C LYS 3.4 8.1 + - - +
779C LEU* 3.4 4.9 + - - +
780C VAL 3.3 1.0 - - - -
781C ASP* 1.3 76.6 - - - +
783C GLY* 1.3 57.0 + - - +
784C ASN* 3.4 22.4 - - - +
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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
------------------------------------------------------------
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