Contacts of the helix formed by residues 803 - 812 (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 SER 803 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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802E SER* 1.3 73.6 - - - +
804E PRO* 1.3 66.3 - - - +
805E GLN* 3.0 20.0 + - - +
806E SER* 2.5 43.5 + - - -
807E ILE* 2.9 8.7 + - - +
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Residues in contact with PRO 804 (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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753E PHE* 3.5 51.6 - - + +
802E SER 3.3 1.3 - - - +
803E SER* 1.3 85.8 - - - +
805E GLN* 1.3 57.8 + - + +
807E ILE* 4.0 3.5 - - + +
808E LEU* 3.2 23.9 + - - +
823E ILE* 3.5 10.3 - - + +
827E TRP* 3.6 50.5 - - + -
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Residues in contact with GLN 805 (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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749E LYS* 2.9 27.1 + - - +
753E PHE* 3.2 14.6 - - + -
803E SER* 3.0 10.4 + - - +
804E PRO* 1.3 80.3 - - + +
806E SER* 1.3 59.4 + - - +
807E ILE 3.3 0.2 - - - -
808E LEU* 3.2 20.3 + - - +
809E ASP* 2.9 62.9 + - - +
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Residues in contact with SER 806 (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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797E LYS* 4.5 7.1 + - - -
802E SER* 3.6 11.6 - - - -
803E SER* 2.5 42.5 + - - -
805E GLN* 1.3 78.5 - - - +
807E ILE* 1.3 59.0 + - - +
809E ASP* 3.5 6.2 + - - +
810E ASP* 3.1 31.8 + - - +
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Residues in contact with ILE 807 (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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793E PHE* 5.6 0.9 - - + -
794E VAL* 4.5 12.3 - - + -
797E LYS* 4.2 28.3 - - + +
798E VAL* 3.9 21.1 - - + -
802E SER* 4.1 11.0 - - - +
803E SER 2.9 12.7 + - - +
804E PRO* 4.0 4.7 - - + +
806E SER* 1.3 77.0 - - - +
808E LEU* 1.3 56.3 + - - +
810E ASP* 2.9 8.8 + - + +
811E VAL* 2.8 42.4 + - + +
823E ILE* 3.7 24.0 - - + -
826E MET* 5.8 0.2 - - - -
827E TRP* 3.9 28.7 - - + -
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Residues in contact with LEU 808 (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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749E LYS* 4.1 3.6 - - - +
753E PHE* 3.7 27.4 - - + -
804E PRO 3.2 10.5 + - - +
805E GLN* 3.2 31.1 + - - +
807E ILE* 1.3 79.6 - - - +
809E ASP* 1.3 65.9 + - - +
811E VAL* 4.3 1.0 - - - +
812E ALA* 3.1 33.0 + - + +
819E ALA* 4.0 13.6 - - - +
820E GLU* 3.9 40.2 - - + +
823E ILE* 3.9 16.3 - - + +
824E VAL* 5.6 0.2 - - + -
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Residues in contact with ASP 809 (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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805E GLN* 2.9 46.7 + - - +
806E SER* 3.9 7.6 - - - +
808E LEU* 1.3 80.5 - - - +
810E ASP* 1.3 65.1 + - - +
812E ALA* 4.0 7.5 - - - +
813E MET* 3.5 20.4 - - - +
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Residues in contact with ASP 810 (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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793E PHE* 3.6 28.2 - - + -
797E LYS* 3.4 29.5 + - - -
806E SER* 3.1 13.8 + - - +
807E ILE* 2.9 9.5 + - - +
809E ASP* 1.3 77.9 - - - +
811E VAL* 1.3 66.5 + - - +
812E ALA 3.1 2.0 - - - -
813E MET* 3.0 27.2 + - - +
814E VAL* 5.3 1.2 - - - +
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Residues in contact with VAL 811 (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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779E ILE* 6.1 1.1 - - + -
793E PHE* 4.5 10.3 - - + -
794E VAL* 4.0 21.8 - - + -
807E ILE* 2.8 39.7 + - + +
808E LEU* 4.3 1.8 - - - +
810E ASP* 1.3 72.0 - - - +
812E ALA* 1.3 59.8 + - - +
813E MET 2.9 6.3 + - - -
814E VAL* 3.0 18.0 + - + +
815E LEU* 3.2 33.4 + - + -
819E ALA* 4.0 8.1 - - + -
822E PHE* 4.0 23.6 - - + -
823E ILE* 4.5 2.0 - - + -
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Residues in contact with ALA 812 (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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808E LEU* 3.1 25.0 + - + +
809E ASP* 4.0 9.6 - - - +
810E ASP 3.1 0.2 - - - -
811E VAL* 1.3 76.3 - - - +
813E MET* 1.3 63.3 + - - +
814E VAL 3.2 0.4 - - - -
815E LEU 3.2 27.0 - - - +
816E ASP* 3.4 15.4 - - - +
819E ALA* 3.5 10.0 - - + +
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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