Contacts of the helix formed by residues 763 - 770 (chain E) in PDB entry 3V53
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 ASP 763 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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760E SER 5.0 4.9 - - - +
761E ILE 2.9 12.6 + - - +
762E VAL* 1.3 74.3 - - - +
764E SER* 1.3 60.6 + - - +
765E ILE* 3.0 30.3 + - + +
766E LEU* 3.2 15.9 + - + +
767E MET* 3.3 10.1 + - - +
771E ILE* 5.2 1.2 - - - +
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Residues in contact with SER 764 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763E ASP* 1.3 72.8 - - - +
765E ILE* 1.3 58.6 + - - +
767E MET* 3.5 15.4 - - - +
768E GLU* 3.2 31.6 + - - +
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Residues in contact with ILE 765 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763E ASP* 3.0 17.7 - - + -
764E SER* 1.3 80.8 - - - +
766E LEU* 1.3 65.0 + - - +
767E MET 3.1 1.3 - - - -
768E GLU* 3.3 21.2 - - + +
769E ARG* 3.2 26.5 + - + +
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Residues in contact with LEU 766 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761E ILE 5.1 3.6 - - - +
762E VAL* 5.2 2.7 - - - -
763E ASP* 3.2 18.9 + - + +
765E ILE* 1.3 76.5 - - - +
767E MET* 1.3 58.9 + - - +
769E ARG* 4.9 1.6 - - - -
770E ARG* 2.9 18.0 + - + +
771E ILE* 2.9 38.4 + - + +
833E GLU* 5.4 10.8 - - + +
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Residues in contact with MET 767 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763E ASP 3.3 6.8 + - - +
764E SER* 3.5 21.1 - - - +
765E ILE 3.1 0.2 - - - -
766E LEU* 1.3 79.0 - - - +
768E GLU* 1.3 59.5 + - + +
771E ILE* 3.8 38.1 - - + +
772E ARG* 3.0 35.1 + - + +
795E CYS* 3.5 48.0 - - - +
798E VAL* 4.7 6.5 - - + -
799E MET* 4.7 13.5 - - + +
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Residues in contact with GLU 768 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764E SER* 3.2 18.6 + - - +
765E ILE* 3.3 32.1 - - + +
767E MET* 1.3 80.5 - - + +
769E ARG* 1.3 60.8 + - + +
772E ARG* 4.9 4.7 - - - +
773E PRO* 4.4 7.3 - - - +
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Residues in contact with ARG 769 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765E ILE* 3.2 19.8 + - + +
766E LEU* 4.9 1.1 - - - -
768E GLU* 1.3 82.2 - - + +
770E ARG* 1.3 62.4 + - + +
771E ILE 4.0 0.2 - - - -
773E PRO* 3.4 15.8 - - - +
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Residues in contact with ARG 770 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812A ALA 3.0 26.7 + - - -
813A MET* 3.4 25.7 + - - +
814A VAL 4.6 5.5 + - - -
816A ASP* 3.0 25.3 + - - +
766E LEU* 2.9 13.7 + - - +
769E ARG* 1.3 82.2 - - + +
771E ILE* 1.3 67.2 + - + +
772E ARG 3.8 0.4 - - - -
773E PRO* 3.8 7.1 - - - +
774E TRP* 3.7 24.6 - - - +
829E LEU* 3.8 21.6 - - + +
833E GLU* 3.3 41.8 + - + +
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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