Contacts of the helix formed by residues 765 - 781 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B THR* 5.5 0.2 - - - -
43B GLY* 3.0 34.1 - - - -
44B VAL* 3.3 15.6 + - + +
438B GLU 5.8 0.2 - - - -
439B HIS* 3.5 19.9 + + + -
441B LEU* 6.5 0.2 - - + -
480B GLN* 3.9 9.9 - - + -
481B THR* 3.0 50.4 + - - +
484B TYR* 4.2 7.4 - + + -
764B LEU* 1.3 71.3 - - - +
766B PRO* 1.3 87.8 - - + +
767B ALA* 2.7 22.4 + - - +
768B ASP* 2.9 30.8 + - - +
769B VAL* 3.0 11.1 + - - +
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Residues in contact with PRO 766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B HIS* 3.8 20.4 - - + +
441B LEU* 4.0 26.0 - - + -
484B TYR* 3.5 32.0 + - + -
764B LEU 3.7 0.2 - - - -
765B HIS* 1.3 96.8 - - + +
767B ALA* 1.3 59.5 + - - +
769B VAL* 3.8 11.0 - - + -
770B GLU* 3.4 20.1 + - - +
792B LYS* 4.0 10.5 - - - +
794B GLN* 3.4 21.3 + - - +
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Residues in contact with ALA 767 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B VAL* 4.2 7.0 - - + -
480B GLN* 3.5 28.5 - - + +
484B TYR* 3.5 24.7 - - + +
765B HIS* 2.7 18.2 + - - +
766B PRO* 1.3 73.6 - - - +
768B ASP* 1.3 63.1 + - - +
770B GLU* 3.5 7.1 + - - +
771B ARG* 3.4 20.2 + - - +
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Residues in contact with ASP 768 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B VAL* 2.8 29.6 - - - +
45B SER* 3.1 28.5 + - - -
738B ARG* 4.6 10.4 + - - +
764B LEU* 3.7 18.2 - - + +
765B HIS* 2.9 27.1 + - - +
767B ALA* 1.3 74.6 - - - +
769B VAL* 1.4 58.8 + - - +
771B ARG* 3.1 20.3 + - - +
772B LEU* 2.8 27.8 + - - +
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Residues in contact with VAL 769 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761B THR* 4.4 20.6 - - + -
764B LEU* 3.7 26.2 - - + +
765B HIS 3.0 16.0 + - - +
766B PRO* 3.6 7.6 - - + +
768B ASP* 1.4 75.1 - - - +
770B GLU* 1.3 60.3 + - - +
772B LEU* 2.9 11.3 + - + +
773B GLN* 2.8 45.5 + - + +
792B LYS* 4.5 4.3 - - + +
794B GLN* 3.3 40.6 - - + +
795B VAL* 5.1 4.7 - - + -
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Residues in contact with GLU 770 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484B TYR* 3.7 17.3 - - + +
766B PRO 3.4 16.3 + - - +
767B ALA 3.5 8.1 - - - +
768B ASP 3.2 0.2 - - - -
769B VAL* 1.3 84.3 - - + +
771B ARG* 1.3 62.4 + - - +
773B GLN* 3.9 7.1 + - - +
774B ARG* 2.6 57.1 + - - +
794B GLN* 4.7 4.3 - - - +
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Residues in contact with ARG 771 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715B ARG 3.2 10.9 + - - -
716B GLU* 2.8 36.7 + - - +
717B VAL 4.9 2.5 - - - +
718B GLY* 3.1 30.7 - - - +
738B ARG* 6.0 0.2 - - - +
767B ALA 3.4 6.8 + - - +
768B ASP* 3.1 28.3 + - - +
769B VAL 3.1 0.4 - - - -
770B GLU* 1.3 81.9 + - - +
772B LEU* 1.3 64.2 + - - +
774B ARG* 3.5 23.6 - - - +
775B GLN* 3.1 26.2 + - - +
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Residues in contact with LEU 772 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717B VAL* 4.8 6.3 - - + +
737B GLN* 5.2 3.4 - - - +
738B ARG* 4.4 21.3 - - + -
741B LEU* 3.5 30.7 - - + -
757B LEU* 5.3 0.2 - - + -
760B PRO* 4.6 22.0 - - + +
761B THR* 5.6 4.0 - - + -
764B LEU* 4.2 15.9 - - + -
768B ASP 2.8 13.4 + - - +
769B VAL* 2.9 13.6 + - + +
771B ARG* 1.3 78.5 - - - +
773B GLN* 1.3 58.0 + - + +
775B GLN* 2.8 31.5 + - + +
776B LEU* 3.0 32.8 + - + +
795B VAL* 6.3 2.0 - - + -
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Residues in contact with GLN 773 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525B MET* 4.3 15.2 - - - -
769B VAL* 2.8 28.2 + - + +
770B GLU* 4.0 8.2 - - - +
772B LEU* 1.3 70.8 - - + +
774B ARG* 1.3 70.5 + - - +
775B GLN 2.6 2.9 + - - -
776B LEU* 2.7 20.9 + - - +
777B VAL* 2.7 25.2 + - + +
794B GLN* 4.6 3.1 - - - +
795B VAL* 3.0 49.0 + - + +
798B ALA* 3.5 25.9 - - - +
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Residues in contact with ARG 774 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770B GLU* 2.6 48.0 + - - +
771B ARG* 3.5 23.4 - - - +
773B GLN* 1.3 78.8 - - - +
775B GLN* 1.3 73.8 + - - +
777B VAL* 3.5 11.0 + - - +
778B LYS* 3.3 24.6 + - - +
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Residues in contact with GLN 775 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716B GLU* 3.2 42.2 + - - +
717B VAL* 4.4 12.8 - - + -
741B LEU* 5.1 4.7 - - + -
745B LEU* 3.3 26.5 - - + +
771B ARG 3.1 16.1 - - - +
772B LEU* 2.8 18.3 + - - +
773B GLN 2.6 4.0 + - - -
774B ARG* 1.3 88.6 - - - +
776B LEU* 1.3 58.7 + - - -
778B LYS* 2.8 41.7 + - - +
779B LEU* 2.9 22.3 - - - +
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Residues in contact with LEU 776 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525B MET* 4.4 18.4 - - + -
741B LEU* 4.0 27.4 - - + -
757B LEU* 3.8 34.1 - - + -
760B PRO* 5.6 2.5 - - + -
772B LEU* 3.0 36.0 + - + +
773B GLN* 2.7 17.0 + - - +
775B GLN* 1.3 67.9 - - - +
777B VAL* 1.3 56.2 + - + +
778B LYS 3.0 2.0 - - - -
779B LEU* 2.7 38.4 + - + +
780B VAL* 3.1 13.8 + - + +
786B VAL* 4.4 24.0 - - + -
795B VAL* 6.0 1.8 - - + -
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Residues in contact with VAL 777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B HIS* 5.5 4.7 - - + -
497B ARG* 3.7 30.1 - - - +
525B MET* 6.3 4.9 - - + -
773B GLN* 2.7 30.9 + - + +
774B ARG* 3.6 9.2 - - - +
776B LEU* 1.3 72.2 - - + +
778B LYS* 1.3 57.1 + - + +
780B VAL* 3.9 8.6 - - + +
781B ASP* 3.0 42.5 + - - +
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Residues in contact with LYS 778 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716B GLU* 2.9 16.9 + - - -
745B LEU* 4.9 4.4 - - + +
774B ARG* 3.3 12.2 + - + +
775B GLN* 2.8 48.8 + - - +
776B LEU 2.9 0.4 + - - -
777B VAL* 1.3 81.4 - - + +
779B LEU* 1.3 58.0 + - + +
781B ASP* 3.9 7.6 - - - +
782B ALA* 3.4 19.8 + - - +
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Residues in contact with LEU 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741B LEU* 4.6 15.7 - - + -
744B GLU* 5.4 2.2 - - + -
745B LEU* 3.9 24.2 - - + +
748B SER* 5.6 4.0 - - - +
755B TYR* 3.4 44.0 - - + +
775B GLN 2.9 24.7 - - - +
776B LEU* 2.7 26.2 + - + +
778B LYS* 1.3 74.4 - - + +
780B VAL* 1.3 59.1 + - - +
781B ASP 3.4 0.7 - - - -
782B ALA* 3.4 7.9 + - + -
784B ASN* 2.8 49.0 + - - +
786B VAL* 4.7 6.5 - - + -
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Residues in contact with VAL 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B ARG* 4.5 18.3 - - - +
523B GLY 3.5 12.6 - - - +
524B VAL* 3.2 39.9 - - - +
525B MET* 3.7 15.7 - - + +
776B LEU* 3.1 22.9 + - + +
777B VAL* 3.9 10.1 - - + +
779B LEU* 1.3 72.5 - - - +
781B ASP* 1.3 63.4 + - - +
782B ALA 3.0 4.5 - - - -
783B GLY* 3.2 11.1 + - - -
784B ASN 3.5 6.5 - - - +
786B VAL* 3.9 17.9 - - + +
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Residues in contact with ASP 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B ARG* 3.7 24.8 + - - +
777B VAL* 3.0 31.0 + - - +
778B LYS* 3.9 9.3 - - - +
780B VAL* 1.3 76.0 - - - +
782B ALA* 1.3 58.9 + - - +
783B GLY 3.1 2.0 + - - -
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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
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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