Contacts of the helix formed by residues 787 - 800 (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 GLU 787 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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779E ILE* 3.3 25.8 - - + +
783E ILE* 4.7 9.2 - - + -
785E GLU 3.0 7.6 + - - +
786E GLU* 1.3 68.3 - - - +
788E ALA* 1.3 61.4 + - - +
789E THR* 3.3 3.8 + - - +
790E LEU* 3.6 11.2 + - + +
791E VAL* 3.0 29.2 + - - +
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Residues in contact with ALA 788 (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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776E ASN* 5.4 1.8 - - - -
786E GLU* 3.3 9.9 + - + +
787E GLU* 1.3 71.1 - - - +
789E THR* 1.3 64.2 + - - +
791E VAL* 3.5 11.3 + - - +
792E ASP* 2.9 28.5 + - - +
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Residues in contact with THR 789 (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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787E GLU* 3.3 2.6 - - - -
788E ALA* 1.3 80.8 - - - +
790E LEU* 1.3 61.4 + - - +
792E ASP* 3.8 10.8 + - - +
793E PHE* 4.0 8.7 + - - +
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Residues in contact with LEU 790 (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* 4.9 13.0 - - + -
787E GLU* 3.6 18.3 + - + +
788E ALA 3.4 0.2 - - - -
789E THR* 1.3 77.2 - - - +
791E VAL* 1.3 65.8 + - - +
793E PHE* 3.1 22.9 + - - +
794E VAL* 3.4 12.6 + - + +
814E VAL* 5.8 13.2 - - + -
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Residues in contact with VAL 791 (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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772E ARG* 4.8 4.9 - - + +
775E ILE* 4.0 15.9 - - + -
776E ASN* 3.7 32.1 - - + +
779E ILE* 3.7 23.1 - - + +
787E GLU 3.0 19.5 - - - +
788E ALA* 3.7 9.2 - - - +
789E THR 3.4 0.6 - - - -
790E LEU* 1.3 75.8 - - - +
792E ASP* 1.3 67.8 + - - +
794E VAL* 3.2 14.9 + - - +
795E CYS* 3.2 31.0 + - - -
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Residues in contact with ASP 792 (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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788E ALA* 2.9 18.3 + - - +
789E THR* 4.0 8.1 - - - +
790E LEU 3.3 0.6 - - - -
791E VAL* 1.3 79.1 - - - +
793E PHE* 1.3 63.8 + - - +
795E CYS* 3.4 8.5 + - - +
796E SER* 3.0 26.3 + - - -
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Residues in contact with PHE 793 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789E THR 4.0 5.3 + - - +
790E LEU* 3.1 14.3 + - - +
792E ASP* 1.3 78.9 - - - +
794E VAL* 1.3 70.5 + - + +
796E SER* 2.6 24.1 + - - -
797E LYS* 3.2 31.2 + - + +
807E ILE* 5.6 1.3 - - + -
810E ASP* 3.6 44.2 - - + -
811E VAL* 4.5 13.9 - - + -
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Residues in contact with VAL 794 (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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775E ILE* 3.9 13.5 - - + -
779E ILE* 5.5 4.0 - - + -
790E LEU* 3.7 15.3 - - + +
791E VAL* 3.2 6.1 + - - +
793E PHE* 1.3 79.6 - - + +
795E CYS* 1.3 67.2 + - - +
797E LYS* 3.0 5.8 + - - +
798E VAL* 2.9 32.3 + - + +
807E ILE* 4.5 11.0 - - + -
811E VAL* 4.0 23.6 - - + -
822E PHE* 4.3 13.9 - - + -
826E MET* 3.3 32.8 - - + -
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Residues in contact with CYS 795 (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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767E MET* 3.5 32.3 - - - +
772E ARG* 4.7 12.1 - - - -
775E ILE* 4.1 19.5 - - - -
791E VAL* 3.2 32.1 + - - -
792E ASP* 3.7 8.3 - - - +
794E VAL* 1.3 78.0 - - - +
796E SER* 1.3 57.4 + - - +
798E VAL* 3.4 1.2 + - - -
799E MET* 3.0 29.5 + - - +
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Residues in contact with SER 796 (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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792E ASP 3.0 13.6 + - - -
793E PHE* 2.6 29.3 + - - -
795E CYS* 1.3 77.8 - - - +
797E LYS* 1.3 60.4 + - - +
799E MET* 3.2 8.6 + - - +
800E ALA* 3.1 26.9 + - - +
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Residues in contact with LYS 797 (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* 3.4 38.6 - - + +
794E VAL* 3.0 7.2 + - - +
796E SER* 1.3 84.0 + - - +
798E VAL* 1.3 60.8 + - - +
800E ALA* 3.5 8.8 + - + +
802E SER* 3.3 54.9 + - - +
806E SER* 4.5 10.5 + - - -
807E ILE* 4.2 20.7 - - + +
810E ASP* 3.4 25.1 + - - +
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Residues in contact with VAL 798 (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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767E MET* 4.7 10.5 - - + -
771E ILE* 5.4 4.0 - - + -
775E ILE* 5.1 2.0 - - + -
794E VAL* 2.9 25.1 + - + +
795E CYS* 4.0 4.7 - - - +
797E LYS* 1.3 73.9 - - - +
799E MET* 1.3 60.9 + - - +
800E ALA 3.2 0.7 - - - -
801E HIS* 3.1 28.0 + - + +
802E SER 5.9 0.2 - - - -
807E ILE* 3.9 19.7 - - + -
826E MET* 3.9 25.1 - - - -
827E TRP* 5.0 6.3 - - + -
830E LEU* 4.2 32.5 - - + -
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Residues in contact with MET 799 (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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767E MET* 4.7 9.8 - - + +
795E CYS 3.0 18.4 + - - +
796E SER* 3.2 9.8 + - - +
798E VAL* 1.3 77.2 - - - +
800E ALA* 1.3 55.4 + - - +
801E HIS* 3.2 17.7 + - - -
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Residues in contact with ALA 800 (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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796E SER 3.1 13.9 + - - +
797E LYS* 3.5 10.3 + - + +
798E VAL 3.2 0.6 - - - -
799E MET* 1.3 75.0 - - - +
801E HIS* 1.3 69.5 + - - +
802E SER* 3.1 13.2 + - - +
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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