Contacts of the helix formed by residues 846 - 857 (chain A) in PDB entry 2VWV
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 PRO 846 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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714A VAL* 3.6 23.6 - - + -
814A MET* 4.0 7.4 - - + -
844A ASP 3.6 7.8 - - - +
845A CYS* 1.4 94.3 - - - +
847A THR* 1.3 66.0 + - - +
848A SER* 4.1 7.9 - - - +
849A LEU* 3.1 24.8 + - + -
850A HIS* 3.3 9.0 + - - +
883A SER 3.7 20.0 - - - +
884A LEU* 3.8 17.9 - - - +
885A LYS 4.7 9.6 - - - +
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Residues in contact with THR 847 (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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841A PRO* 6.4 0.7 - - - -
845A CYS 3.4 3.3 + - - -
846A PRO* 1.3 71.0 - - - +
848A SER* 1.3 64.0 + - - +
850A HIS* 3.3 8.1 + - + +
851A GLN* 3.0 28.3 + - + +
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Residues in contact with SER 848 (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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846A PRO* 4.1 4.6 - - - +
847A THR* 1.3 79.3 - - - +
849A LEU* 1.3 63.7 + - - +
851A GLN* 3.6 6.0 + - - +
852A LEU* 3.3 16.5 + - - +
877A MET* 3.5 37.3 - - - +
883A SER* 3.4 27.0 + - - -
884A LEU* 4.2 1.4 - - - +
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Residues in contact with LEU 849 (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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714A VAL* 4.2 0.4 - - + -
718A VAL* 3.7 23.6 - - + -
721A LEU* 5.0 4.0 - - + -
810A MET* 3.5 20.4 - - + +
814A MET* 3.7 31.6 - - + -
845A CYS* 3.9 8.5 - - - -
846A PRO* 3.1 24.7 + - + +
848A SER* 1.3 81.8 + - - +
850A HIS* 1.3 63.8 + - - +
852A LEU* 3.3 2.1 + - - -
853A MET* 3.1 26.9 + - + +
874A LEU* 3.7 20.6 - - + -
877A MET* 3.4 27.8 - - + -
884A LEU* 4.0 2.2 - - + -
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Residues in contact with HIS 850 (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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839A LEU 2.9 25.4 + - - -
840A PRO* 3.5 4.5 - - + -
841A PRO* 3.6 48.9 - - + +
845A CYS* 4.2 5.1 - - - -
846A PRO 3.3 7.7 + - - +
847A THR* 3.3 11.7 + - + +
849A LEU* 1.3 78.5 - - - +
851A GLN* 1.3 58.6 + - - +
853A MET* 3.1 29.0 + - + +
854A LEU* 3.0 55.0 + - + +
857A TRP* 4.3 0.9 - + - -
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Residues in contact with GLN 851 (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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847A THR* 3.0 23.2 + - + +
848A SER* 3.8 6.7 - - - +
850A HIS* 1.3 78.6 + - - +
852A LEU* 1.3 55.9 + - - +
854A LEU* 3.2 28.1 + - - +
855A ASP* 2.9 58.8 + - - +
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Residues in contact with LEU 852 (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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810A MET* 4.0 22.9 - - + -
848A SER 3.3 11.2 + - - +
849A LEU 3.3 10.1 + - - +
851A GLN* 1.3 73.9 - - - +
853A MET* 1.3 66.5 + - - +
855A ASP* 3.3 13.8 + - - +
856A CYS* 3.0 27.0 + - - -
865A PRO* 4.2 23.8 - - + -
870A VAL* 4.3 15.0 - - + -
873A ALA* 4.2 20.2 - - + -
874A LEU* 4.1 25.6 - - + -
877A MET* 4.2 11.4 - - + -
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Residues in contact with MET 853 (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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807A GLY* 4.0 3.6 - - - +
810A MET* 3.8 46.0 - - + +
811A TRP* 3.8 29.6 - - - +
814A MET* 3.9 17.7 - - + -
842A PRO* 4.3 3.8 - - + -
845A CYS* 4.0 15.7 - - - -
849A LEU 3.1 17.5 + - - +
850A HIS* 3.1 25.1 + - - +
852A LEU* 1.3 77.3 - - - +
854A LEU* 1.3 62.6 + - - +
856A CYS* 3.0 8.7 + - - +
857A TRP* 3.0 45.0 + - + -
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Residues in contact with LEU 854 (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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838A ARG* 3.8 22.2 - - + -
850A HIS* 3.0 46.0 + - + +
851A GLN* 3.2 32.1 + - - +
853A MET* 1.3 76.6 - - - +
855A ASP* 1.3 63.0 + - - +
857A TRP* 3.1 33.7 + - + +
858A GLN* 3.3 14.8 + - - +
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Residues in contact with ASP 855 (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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851A GLN* 2.9 43.4 + - - +
852A LEU* 3.5 19.3 - - + +
854A LEU* 1.3 77.0 - - - +
856A CYS* 1.3 61.1 + - - +
857A TRP 3.3 0.7 + - - -
858A GLN* 2.8 39.1 + - - +
864A ARG* 3.6 3.8 - - - -
865A PRO* 3.5 20.9 - - + +
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Residues in contact with CYS 856 (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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803A ALA* 3.4 25.6 - - - +
804A TRP* 3.4 12.8 - - - -
806A TYR* 4.4 13.2 - - - -
807A GLY* 3.8 18.6 - - - -
810A MET* 4.7 2.7 - - - -
852A LEU* 3.0 21.9 + - - -
853A MET 3.0 8.0 + - - +
855A ASP* 1.3 75.2 - - - +
857A TRP* 1.3 57.4 + - - +
858A GLN 3.3 0.9 - - - -
864A ARG* 3.2 25.1 + - - -
865A PRO* 4.1 20.6 - - - -
870A VAL* 4.5 8.7 - - - -
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Residues in contact with TRP 857 (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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804A TRP* 3.2 42.3 + + + -
807A GLY* 3.4 24.6 - - - -
808A ILE* 3.4 38.7 - - + +
811A TRP* 4.2 6.7 - + + -
821A TYR* 5.5 1.6 - - - -
838A ARG* 2.9 48.4 + - - +
839A LEU* 3.6 42.6 - - + -
850A HIS* 4.3 1.1 - - - -
853A MET* 3.0 41.5 + - + +
854A LEU* 3.4 27.8 - - + +
855A ASP 3.1 1.0 - - - -
856A CYS* 1.3 79.9 - - - +
858A GLN* 1.3 59.4 + - - -
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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
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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