Contacts of the helix formed by residues 734 - 746 (chain C) in PDB entry 2W4V
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 734 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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717C LYS* 5.0 0.9 - - - +
735C GLY* 1.3 58.8 + - - +
736C LYS* 2.7 45.4 + - - +
737C THR* 3.1 30.4 + - + +
738C VAL* 2.7 35.3 + - - +
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Residues in contact with GLY 735 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713C TYR* 3.4 27.0 - - - +
714C SER* 5.2 3.1 - - - -
717C LYS* 4.0 8.5 - - - +
734C ASP* 1.3 74.9 + - - +
736C LYS* 1.3 56.9 + - - +
738C VAL* 2.6 27.8 - - - +
739C SER* 3.5 5.9 + - - -
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Residues in contact with LYS 736 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713C TYR* 3.4 28.3 - - + -
734C ASP* 2.7 22.2 + - - +
735C GLY* 1.3 71.5 - - - +
737C THR* 1.3 52.6 + - + -
739C SER* 3.3 5.6 + - - -
740C GLU* 2.4 35.0 - - - +
757C THR* 2.2 41.6 + - - +
758C THR* 3.7 17.0 - - - +
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Residues in contact with THR 737 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734C ASP* 3.1 32.6 + - + +
736C LYS* 1.3 79.2 - - + +
738C VAL* 1.3 62.6 + - - +
739C SER 3.1 1.8 - - - -
740C GLU* 2.8 12.1 + - + +
741C LYS* 2.8 51.3 + - - +
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Residues in contact with VAL 738 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717C LYS* 2.5 66.6 - - + +
728C ILE* 5.6 2.4 - - + +
729C PRO* 6.6 0.2 - - + -
734C ASP 2.7 26.2 - - - +
735C GLY 2.6 31.2 - - - +
737C THR* 1.3 84.7 + - - +
739C SER* 1.3 56.9 + - - +
741C LYS* 3.0 16.8 - - + +
742C ILE* 2.7 40.1 + - + +
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Residues in contact with SER 739 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713C TYR* 2.8 39.1 - - - -
716C PHE* 3.5 29.2 - - - -
735C GLY 3.5 4.2 + - - -
736C LYS 3.3 3.3 + - - -
738C VAL* 1.3 79.1 - - - +
740C GLU* 1.3 71.1 + - - +
741C LYS 2.9 1.8 - - - -
742C ILE* 3.2 12.1 - - - +
743C LEU* 3.1 29.1 + - - +
760C VAL* 4.3 3.7 - - - +
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Residues in contact with GLU 740 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501C LYS 4.6 3.6 - - - +
502C LYS 4.5 1.5 - - - +
504C GLY* 4.8 2.6 - - - -
713C TYR* 4.4 7.4 - - - -
736C LYS 2.4 30.5 - - - +
737C THR* 2.8 18.6 + - + +
739C SER* 1.3 87.1 + - - +
741C LYS* 1.3 50.0 + - + +
743C LEU* 4.3 1.4 - - - +
744C ALA* 2.8 33.4 + - - +
755C LEU* 3.8 27.2 - - - +
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Residues in contact with LYS 741 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724C ALA* 5.5 0.7 - - - -
727C ALA* 3.3 29.9 + - + +
728C ILE* 4.8 3.4 - - + -
729C PRO* 2.9 36.8 - - + +
737C THR* 2.8 30.9 + - - +
738C VAL* 3.0 14.6 - - + +
739C SER 2.9 0.4 - - - -
740C GLU* 1.3 77.7 - - + +
742C ILE* 1.3 55.3 + - + +
744C ALA* 2.7 9.4 + - - +
745C GLY* 2.5 35.9 + - - -
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Residues in contact with ILE 742 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716C PHE* 3.4 29.8 - - + -
717C LYS* 5.9 2.7 - - + +
720C TYR* 3.9 24.2 - - + +
721C SER* 4.7 11.7 - - - +
723C LEU* 5.5 2.7 - - + -
724C ALA* 4.2 19.1 - - + +
728C ILE* 5.2 10.3 - - + +
738C VAL* 2.7 25.8 + - + +
739C SER* 3.2 12.1 - - - +
741C LYS* 1.3 71.7 - - + +
743C LEU* 1.3 103.6 + - + +
745C GLY* 3.1 1.2 + - - -
746C LEU* 2.9 38.6 + - + +
770C LEU* 5.4 1.8 - - + -
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Residues in contact with LEU 743 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504C GLY* 4.8 5.6 - - - +
505C ILE 3.8 4.0 - - - +
716C PHE* 4.1 2.7 - - + -
739C SER* 3.1 12.9 + - - +
740C GLU* 4.7 1.3 - - - +
742C ILE* 1.3 103.5 - - + +
744C ALA* 1.3 59.8 + - - +
746C LEU* 4.9 0.7 - - + -
748C MET* 2.7 77.0 + - + +
753C TYR* 4.5 21.2 + - + -
760C VAL* 5.5 1.1 - - + -
762C PHE* 2.8 40.6 - - + -
770C LEU* 4.5 4.3 - - + -
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Residues in contact with ALA 744 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740C GLU 2.8 23.7 + - - +
741C LYS* 2.7 12.1 + - - +
743C LEU* 1.3 77.4 - - - +
745C GLY* 1.3 64.7 + - - +
747C GLN* 2.8 24.1 + - - +
748C MET 5.1 0.4 - - - +
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Residues in contact with GLY 745 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724C ALA* 4.7 11.2 - - - -
727C ALA* 5.7 5.6 - - - -
741C LYS 2.5 17.6 + - - -
742C ILE 3.6 1.8 - - - -
744C ALA* 1.3 69.5 - - - +
746C LEU* 1.3 53.3 + - - +
747C GLN* 2.5 33.3 + - - +
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Residues in contact with LEU 746 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723C LEU* 3.9 37.0 - - + +
724C ALA* 4.9 1.8 - - - +
742C ILE* 2.9 17.0 + - + +
743C LEU* 4.9 3.1 - - + -
745C GLY* 1.3 70.3 - - - +
747C GLN* 1.3 69.6 + - - +
748C MET* 3.2 37.9 + - + +
770C LEU* 3.9 22.9 - - + -
773C MET* 4.6 21.1 - - + -
777C ARG* 5.0 6.3 - - - +
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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