Contacts of the helix formed by residues 737 - 746 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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735D GLU* 3.2 12.2 + - - +
736D ALA* 1.3 82.5 - - + +
738D PHE* 1.3 64.4 + - - +
739D VAL* 3.4 2.7 - - - -
740D GLU* 2.7 35.8 + - + +
741D TYR* 3.0 21.0 + - - +
852D GLU* 4.8 13.6 + - - -
853D LEU* 3.9 24.9 - - + +
856D PHE* 5.6 1.7 - - - -
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Residues in contact with PHE 738 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731D VAL* 3.5 38.1 - - + +
732D VAL* 3.7 28.7 - - + +
735D GLU* 3.2 25.1 + - + +
736D ALA 3.3 0.8 - - - -
737D ARG* 1.3 76.9 - - - +
739D VAL* 1.3 63.5 + - + +
741D TYR* 3.0 10.5 + + - +
742D PHE* 2.8 32.0 + - + +
769D ILE* 4.1 8.7 - - + -
777D TRP* 3.8 34.8 - + - -
781D TRP* 4.2 22.4 - + - -
788D LEU* 4.5 10.3 - - + -
856D PHE* 4.0 16.2 - + - -
860D LEU* 4.8 2.9 - - + -
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Residues in contact with VAL 739 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736D ALA 4.2 14.4 - - - +
737D ARG* 4.8 0.4 - - - -
738D PHE* 1.3 79.9 - - + +
740D GLU* 1.3 61.7 + - + +
742D PHE* 3.1 7.9 + - + +
743D ARG* 2.9 60.1 + - + +
768D GLY* 5.3 13.7 - - - -
769D ILE* 4.9 15.3 - - + -
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Residues in contact with GLU 740 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737D ARG* 2.7 46.9 + - + +
738D PHE 3.1 0.6 - - - -
739D VAL* 1.3 85.3 - - + +
741D TYR* 1.3 53.5 + - - +
743D ARG* 3.6 5.7 + - - +
744D SER* 2.4 36.8 + - - +
850D ALA* 4.9 2.3 - - - +
852D GLU* 4.0 11.1 - - - +
853D LEU* 3.3 26.6 - - + +
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Residues in contact with TYR 741 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737D ARG 3.0 11.3 + - - +
738D PHE* 3.0 11.9 + + - +
740D GLU* 1.3 76.9 - - - +
742D PHE* 1.3 60.4 + - - +
744D SER* 3.1 5.2 + - - -
745D ALA* 2.9 33.5 + - + +
781D TRP* 3.8 24.0 - + - -
786D PHE* 5.2 5.6 - + - -
845D ASP* 2.7 43.0 + - - -
849D VAL* 4.0 19.7 - - + -
853D LEU* 4.3 25.2 - - + +
856D PHE* 4.0 24.9 - + + -
857D GLY* 3.4 21.4 + - - -
860D LEU* 3.7 20.2 - - + +
861D ARG* 4.1 3.8 + - - -
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Residues in contact with PHE 742 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738D PHE* 2.8 22.2 + - + +
739D VAL* 3.5 9.6 - - - +
741D TYR* 1.3 75.7 - - - +
743D ARG* 1.3 70.6 + - - +
744D SER 3.2 1.0 + - - -
746D THR* 2.7 48.0 + - + -
748D GLU* 3.6 24.7 - - + -
769D ILE* 3.9 18.2 - - + -
772D LEU* 3.7 21.5 - - + -
776D PRO 4.7 0.4 - - - -
777D TRP* 4.0 13.9 - + - -
780D SER* 3.5 22.2 - - - -
781D TRP* 3.2 49.8 - + + -
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Residues in contact with ARG 743 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739D VAL* 2.9 37.0 + - + +
740D GLU* 4.2 6.1 - - - +
742D PHE* 1.3 83.7 - - + +
744D SER* 1.3 57.4 + - - +
746D THR* 3.6 5.2 - - - +
748D GLU* 3.3 38.2 + - - +
749D THR* 3.4 38.8 + - + +
762D LYS* 3.6 36.2 - - - +
768D GLY 5.5 0.4 + - - -
769D ILE* 5.6 2.8 - - - +
772D LEU* 5.1 5.8 - - - +
913D ARG* 3.4 21.5 + - - -
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Residues in contact with SER 744 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740D GLU* 2.4 32.6 + - - +
741D TYR* 3.1 5.0 + - - -
742D PHE 3.1 0.8 - - - -
743D ARG* 1.3 77.7 - - - +
745D ALA* 1.3 63.2 + - - +
746D THR 3.3 2.9 + - - -
848D LEU* 3.3 23.3 - - - +
849D VAL* 3.6 22.9 - - - -
850D ALA 5.2 0.8 + - - -
853D LEU* 5.1 3.3 - - - +
913D ARG* 2.8 26.5 + - - +
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Residues in contact with ALA 745 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741D TYR* 2.9 29.9 + - + +
744D SER* 1.3 75.1 - - - +
746D THR* 1.3 63.5 + - + +
781D TRP* 4.8 4.0 - - + -
784D THR* 3.3 18.2 - - - +
841D ALA 5.8 0.2 - - - +
844D TYR* 3.8 18.2 - - - +
845D ASP* 3.5 24.9 - - - +
848D LEU* 4.9 3.6 - - - -
849D VAL* 3.7 11.2 - - + -
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Residues in contact with THR 746 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742D PHE* 2.7 33.1 + - + +
743D ARG 3.6 6.4 - - - +
744D SER 3.3 0.2 - - - -
745D ALA* 1.3 82.5 - - - +
747D PRO* 1.3 69.3 - - - +
748D GLU* 3.1 22.2 + - - +
780D SER* 3.7 15.5 - - - +
781D TRP* 3.6 37.0 - - + -
784D THR* 3.8 2.7 - - + -
844D TYR* 5.4 0.4 - - - -
848D LEU* 5.8 0.9 - - - -
909D LEU* 5.2 2.2 - - - -
913D ARG* 3.0 20.3 + - - -
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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