Contacts of the helix formed by residues 833 - 840 (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 THR 833 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413A HIS* 2.9 35.0 - - + -
529A THR* 3.4 8.5 + - - +
530A GLY* 3.8 11.9 - - - +
531A VAL 4.6 0.7 - - - +
793A MET* 3.4 21.8 - - - +
804A ASP* 2.6 37.0 + - - +
825A VAL* 4.5 6.8 - - - +
831A SER* 3.2 1.5 + - - -
832A VAL* 1.3 82.6 - - + +
834A ALA* 1.3 65.6 + - - +
835A PRO* 3.4 0.7 - - - -
836A TYR* 3.2 6.4 + - - +
837A LEU* 3.2 16.6 + - - +
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Residues in contact with ALA 834 (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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825A VAL* 3.1 29.2 - - + +
826A ALA* 3.7 8.5 - - - +
828A ALA 3.8 17.3 - - - +
831A SER* 2.7 20.6 + - - +
833A THR* 1.3 79.1 - - - +
835A PRO* 1.3 64.6 - - + +
837A LEU* 3.1 6.8 + - - +
838A ARG* 2.8 32.7 + - - +
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Residues in contact with PRO 835 (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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831A SER 4.1 5.6 - - - +
832A VAL* 3.5 18.6 - - - +
833A THR 3.5 0.2 - - - -
834A ALA* 1.3 95.6 - - + +
836A TYR* 1.3 65.2 + - + +
838A ARG* 3.6 28.6 - - - +
839A ALA* 2.8 25.5 + - - +
842A ARG* 5.4 1.0 + - - -
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Residues in contact with TYR 836 (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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413A HIS* 4.6 2.5 - - - -
414A PRO* 3.5 34.1 + - + -
415A ALA* 3.2 41.3 + - + +
442A ASP* 6.1 0.2 - - - -
793A MET* 3.9 20.0 - - + +
832A VAL 3.8 18.8 - - - -
833A THR 3.2 7.4 + - - +
835A PRO* 1.3 85.0 - - + +
837A LEU* 1.3 59.3 + - - +
839A ALA* 3.2 11.3 - - + +
840A ALA* 3.1 25.1 + - - +
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Residues in contact with LEU 837 (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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793A MET* 3.6 19.0 - - + +
796A VAL* 4.2 13.7 - - + -
797A ALA* 4.3 10.1 - - + +
802A VAL* 4.9 1.8 - - + -
822A PRO* 3.5 28.5 - - + +
825A VAL* 3.5 33.0 - - + -
826A ALA* 3.8 3.6 - - + +
833A THR* 3.2 11.3 + - - +
834A ALA 3.4 8.1 - - - +
836A TYR* 1.3 74.8 - - - +
838A ARG* 1.3 57.4 + - - +
839A ALA 3.1 0.9 - - - -
840A ALA* 2.7 22.3 + - + +
841A LEU* 3.1 40.5 + - + +
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Residues in contact with ARG 838 (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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826A ALA* 2.9 34.5 + - + +
827A GLN* 4.5 5.5 - - - +
828A ALA 4.3 14.8 + - - -
834A ALA* 2.8 12.9 + - - +
835A PRO* 3.6 33.3 - - - +
837A LEU* 1.3 74.7 - - - +
839A ALA* 1.3 64.7 + - - +
840A ALA 3.1 0.5 + - - -
841A LEU* 3.2 12.7 + - - +
842A ARG* 3.3 42.5 + - + +
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Residues in contact with ALA 839 (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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835A PRO 2.8 16.8 + - - +
836A TYR* 3.2 19.5 - - + +
837A LEU 3.1 0.2 - - - -
838A ARG* 1.3 78.2 - - - +
840A ALA* 1.3 57.4 + - + +
841A LEU 3.2 3.1 + - - -
842A ARG* 3.9 30.1 + - - +
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Residues in contact with ALA 840 (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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793A MET* 4.0 19.5 - - + -
794A GLN* 4.7 6.7 - - - +
797A ALA* 3.8 15.1 - - + +
836A TYR 3.1 15.4 + - - +
837A LEU* 2.7 13.4 + - - +
839A ALA* 1.3 71.8 - - + +
841A LEU* 1.3 64.1 + - - +
842A ARG 4.9 1.6 - - - -
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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