Contacts of the helix formed by residues 737 - 746 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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735F GLU* 2.9 35.7 + - + +
736F ALA* 1.3 77.3 - - + +
738F PHE* 1.3 64.4 + - - +
739F VAL 3.4 0.7 - - - -
740F GLU* 3.4 18.3 + - - +
741F TYR* 3.1 20.8 + - - +
852F GLU 4.3 10.7 + - - -
853F LEU* 3.9 32.4 - - + +
856F PHE* 4.3 24.1 - - + +
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Residues in contact with PHE 738 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731F VAL* 3.5 34.1 - - + +
732F VAL* 3.7 23.8 - - + +
735F GLU* 3.2 21.4 + - + +
736F ALA 3.2 3.2 - - - -
737F ARG* 1.3 76.6 - - - +
739F VAL* 1.3 68.6 + - + +
741F TYR* 2.9 10.1 + + - +
742F PHE* 2.8 28.4 + - + -
769F ILE* 3.9 16.4 - - + -
777F TRP* 3.8 34.5 - + - -
781F TRP* 4.2 12.6 - + - -
788F LEU* 4.1 19.1 - - + -
856F PHE* 4.0 21.8 - + - -
860F LEU* 4.8 3.6 - - + -
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Residues in contact with VAL 739 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732F VAL 5.7 1.3 - - - +
735F GLU 4.9 0.2 + - - -
736F ALA 4.2 6.3 + - - +
737F ARG 3.4 0.6 - - - -
738F PHE* 1.3 80.4 - - + +
740F GLU* 1.3 64.2 + - - +
742F PHE* 3.2 6.7 + - + +
743F ARG* 3.1 42.5 + - + +
762F LYS* 5.6 3.8 - - - +
768F GLY* 3.9 28.0 - - - -
769F ILE* 4.2 21.1 - - + +
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Residues in contact with GLU 740 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736F ALA 5.1 0.8 + - - +
737F ARG* 3.4 21.6 + - - +
738F PHE 3.2 0.6 - - - -
739F VAL* 1.3 80.9 - - - +
741F TYR* 1.3 61.3 + - - +
743F ARG* 3.5 4.3 + - - +
744F SER* 3.0 29.9 + - - +
850F ALA* 5.2 5.7 - - - +
853F LEU* 3.4 24.1 - - + +
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Residues in contact with TYR 741 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737F ARG 3.1 10.9 + - - +
738F PHE* 2.9 12.2 + + - +
740F GLU* 1.3 76.6 - - - +
742F PHE* 1.3 59.5 + - - +
744F SER* 3.1 3.8 + - - -
745F ALA* 2.9 34.7 + - + +
781F TRP* 3.8 24.0 - + - -
786F PHE* 5.1 6.6 - - - -
845F ASP* 2.8 43.1 + - - -
849F VAL* 3.8 24.5 - - + -
853F LEU* 4.1 22.3 - - + +
856F PHE* 3.9 25.6 - + + -
857F GLY* 3.5 19.6 + - - -
860F LEU* 3.7 20.5 - - + +
861F ARG* 4.2 3.1 + - - -
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Residues in contact with PHE 742 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738F PHE* 2.8 21.2 + - + +
739F VAL* 3.2 9.6 + - + +
741F TYR* 1.3 76.9 - - - +
743F ARG* 1.3 68.1 + - + +
746F THR* 2.6 50.8 + - + -
748F GLU* 3.6 31.0 - - + -
769F ILE* 3.9 17.7 - - + -
772F LEU* 3.8 30.1 - - + -
776F PRO 4.7 1.6 - - - -
777F TRP* 4.1 7.9 - + - -
780F SER* 4.0 9.6 - - - -
781F TRP* 3.3 52.5 - + + -
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Residues in contact with ARG 743 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739F VAL* 3.1 28.4 + - + +
740F GLU* 3.5 4.9 + - - +
741F TYR 3.3 0.2 - - - -
742F PHE* 1.3 87.3 - - + +
744F SER* 1.3 58.9 + - - +
746F THR* 3.8 4.8 - - - +
748F GLU* 3.3 38.0 + - + +
749F THR* 3.6 39.3 - - + +
752F GLY* 6.3 0.4 - - - -
761F ALA* 5.6 2.2 - - - +
762F LYS* 4.3 26.3 - - - +
772F LEU* 5.0 4.4 - - - +
913F ARG* 3.5 20.6 + - - -
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Residues in contact with SER 744 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740F GLU* 3.0 21.5 + - - +
741F TYR* 3.1 6.3 + - - -
743F ARG* 1.3 80.3 - - - +
745F ALA* 1.3 61.1 + - - +
746F THR 3.4 1.4 + - - +
848F LEU* 3.1 25.7 + - - +
849F VAL* 3.8 21.5 - - - -
850F ALA 5.2 1.7 + - - -
853F LEU* 5.2 3.4 - - - +
913F ARG* 2.8 24.9 + - - +
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Residues in contact with ALA 745 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741F TYR* 2.9 34.2 + - + +
744F SER* 1.3 76.4 - - - +
746F THR* 1.3 65.0 + - + +
781F TRP* 4.6 4.8 - - + -
784F THR* 3.4 17.5 - - - +
844F TYR* 3.7 21.2 - - + +
845F ASP* 3.6 23.6 - - - +
848F LEU* 5.0 0.7 - - - -
849F VAL* 3.9 7.6 - - + -
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Residues in contact with THR 746 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742F PHE* 2.6 32.0 + - + +
743F ARG 3.8 5.7 - - - +
745F ALA* 1.3 83.5 - - - +
747F PRO* 1.3 71.4 - - - +
748F GLU* 3.1 21.9 + - - +
780F SER* 3.5 17.3 - - - +
781F TRP* 3.6 35.4 - - + -
784F THR* 3.8 2.0 - - + -
844F TYR* 5.3 0.4 - - - -
909F LEU* 5.0 3.4 - - - -
913F ARG* 2.9 21.4 + - - -
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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