Contacts of the helix formed by residues 737 - 746 (chain B) in PDB entry 6V3O
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 ARG 737 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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735B GLU* 2.9 44.1 + - - +
736B ALA* 1.3 80.1 - - + +
738B PHE* 1.3 64.2 + - - +
739B VAL 3.5 0.7 - - - -
740B GLU* 3.4 12.6 + - + +
741B TYR* 3.1 20.8 + - - +
852B GLU 4.3 12.1 + - - -
853B LEU* 3.6 37.9 - - + +
855B PRO* 6.3 0.2 - - - +
856B PHE* 4.3 21.3 - - + +
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Residues in contact with PHE 738 (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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731B VAL* 3.3 39.0 - - + +
732B VAL* 3.7 25.4 - - + +
735B GLU* 3.1 24.4 + - + +
736B ALA 3.2 0.8 - - - -
737B ARG* 1.3 76.2 - - - +
739B VAL* 1.3 62.6 + - + +
741B TYR* 2.9 10.3 + + - +
742B PHE* 2.8 31.1 + - + +
769B ILE* 3.9 18.4 - - + -
777B TRP* 3.8 33.0 - + - -
781B TRP* 4.2 17.7 - + - -
788B LEU* 4.5 14.8 - - + -
856B PHE* 4.1 13.2 - + - -
860B LEU* 4.7 4.5 - - + -
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Residues in contact with VAL 739 (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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732B VAL 5.7 1.1 - - - +
735B GLU 5.8 0.2 - - - +
736B ALA 4.0 14.8 - - - +
738B PHE* 1.3 78.9 - - + +
740B GLU* 1.3 64.5 + - + +
742B PHE* 3.1 8.7 + - + +
743B ARG* 3.1 37.0 + - - +
768B GLY* 4.0 22.2 - - - -
769B ILE* 4.0 28.9 - - + +
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Residues in contact with GLU 740 (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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736B ALA 5.7 0.2 - - - +
737B ARG* 3.4 14.3 + - - +
738B PHE 3.2 0.6 - - - -
739B VAL* 1.3 83.5 - - + +
741B TYR* 1.3 56.4 + - - +
743B ARG* 3.7 3.6 + - - +
744B SER* 2.5 38.4 + - - +
850B ALA* 5.8 0.7 - - - +
852B GLU* 4.9 6.9 - - - +
853B LEU* 3.4 22.6 - - + +
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Residues in contact with TYR 741 (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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737B ARG 3.1 12.1 + - - +
738B PHE* 2.9 13.5 + + - +
740B GLU* 1.3 76.9 - - - +
742B PHE* 1.3 64.5 + - - +
744B SER* 3.2 4.6 + - - -
745B ALA* 3.0 30.0 + - + +
781B TRP* 3.9 23.6 - + - -
786B PHE* 5.0 6.5 - + - -
845B ASP* 2.8 37.2 + - - -
849B VAL* 3.8 29.8 - - + -
853B LEU* 4.3 17.0 - - + +
856B PHE* 4.0 24.9 - + + -
857B GLY* 3.4 20.9 + - - -
860B LEU* 3.7 21.7 - - + +
861B ARG* 4.0 3.8 + - - -
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Residues in contact with PHE 742 (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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738B PHE* 2.8 18.5 + - + +
739B VAL* 3.1 11.4 + - + +
741B TYR* 1.3 76.9 - - - +
743B ARG* 1.3 71.8 + - + +
746B THR* 2.7 49.1 + - - +
748B GLU* 3.8 31.2 - - + -
769B ILE* 3.9 28.0 - - + -
772B LEU* 4.8 7.9 - - + -
776B PRO 4.7 2.5 - - - -
777B TRP* 4.0 16.2 - + - -
780B SER* 3.8 15.5 - - - -
781B TRP* 3.3 49.1 - + + -
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Residues in contact with ARG 743 (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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739B VAL* 3.1 23.3 + - - +
740B GLU* 4.5 3.6 - - - +
742B PHE* 1.3 90.7 - - + +
744B SER* 1.3 57.8 + - - +
746B THR* 3.7 6.3 - - - +
748B GLU* 3.6 32.9 + - + +
749B THR* 3.5 31.3 + - - +
762B LYS* 3.6 36.6 - - - +
766B GLY 5.9 0.4 - - - +
769B ILE* 6.0 2.4 - - - +
772B LEU* 5.1 3.6 - - - +
913B ARG* 3.3 20.6 + - - -
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Residues in contact with SER 744 (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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740B GLU* 2.5 30.7 + - - +
741B TYR* 3.2 5.8 + - - -
743B ARG* 1.3 77.8 - - - +
745B ALA* 1.3 61.7 + - - +
746B THR 3.3 2.4 + - - -
848B LEU* 3.2 33.1 - - - +
849B VAL* 4.0 13.5 - - - -
850B ALA 5.3 1.6 + - - -
853B LEU* 5.8 0.9 - - - +
913B ARG* 2.7 25.0 + - - +
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Residues in contact with ALA 745 (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 TYR* 3.0 30.0 + - + +
744B SER* 1.3 75.8 - - - +
746B THR* 1.3 63.8 + - + +
781B TRP* 4.8 4.8 - - + -
784B THR* 3.3 18.4 - - - +
844B TYR* 3.7 22.1 - - - +
845B ASP* 3.5 24.0 - - - +
849B VAL* 3.8 10.8 - - + -
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Residues in contact with THR 746 (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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742B PHE* 2.7 28.8 + - + +
743B ARG 3.7 6.1 - - - +
744B SER 4.7 0.2 - - - -
745B ALA* 1.3 82.4 - - - +
747B PRO* 1.3 71.6 - - - +
748B GLU* 3.2 21.7 + - - +
780B SER* 3.5 16.4 - - - +
781B TRP* 3.6 39.3 - - + -
784B THR* 3.8 2.7 - - + -
844B TYR* 5.2 0.2 - - - -
909B LEU* 4.9 3.4 - - - -
913B ARG* 3.0 20.1 + - - -
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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