Contacts of the helix formed by residues 757 - 765 (chain A) in PDB entry 3ZHT
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 GLN 757 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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680A ILE* 3.7 23.6 - - + -
683A THR 3.0 24.4 + - - +
685A ALA* 3.9 28.6 - - - +
753A PRO 3.0 14.2 + - - +
756A THR* 1.4 93.7 + - - +
758A PRO* 1.4 64.6 - - - +
759A TYR 3.4 3.1 + - - -
760A MET* 3.6 15.4 + - + +
761A TYR* 3.1 34.1 + - + +
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Residues in contact with PRO 758 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754A SER* 3.3 28.2 - - - +
755A MET 4.5 2.7 - - - +
756A THR* 3.5 8.5 - - - +
757A GLN* 1.4 86.2 - - - +
759A TYR* 1.3 58.0 + - + +
761A TYR* 3.7 1.0 - - - +
762A ASP* 2.9 41.4 + - - +
857B HIS* 5.7 1.8 - - + -
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Residues in contact with TYR 759 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A ARG 4.4 1.9 + - - -
392A LEU* 3.2 44.2 + - + +
394A ASN* 3.0 28.5 + - - -
757A GLN 3.4 0.6 - - - -
758A PRO* 1.3 77.3 - - + +
760A MET* 1.4 67.6 + - + +
762A ASP* 3.2 16.7 + - + +
763A VAL* 3.2 30.6 + - + +
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Residues in contact with MET 760 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A LEU* 4.2 10.5 - - + +
392A LEU* 3.7 35.0 - - + -
678A ASN 4.2 4.3 - - - +
679A GLN* 3.2 37.0 - - + +
680A ILE* 3.9 19.3 - - - -
686A PRO* 5.7 1.1 - - + -
743A ARG 6.3 0.2 - - - -
757A GLN* 3.6 19.1 + - + +
758A PRO 3.5 0.2 - - - -
759A TYR* 1.4 79.0 - - + +
761A TYR* 1.3 79.1 + - + +
763A VAL* 3.3 4.9 + - - +
764A ILE* 2.9 44.0 + - + +
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Residues in contact with TYR 761 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680A ILE* 4.1 11.2 - - + +
743A ARG* 2.8 63.0 + - - +
744A ARG 3.6 11.7 - - - -
745A ARG 3.8 1.6 - - - -
753A PRO* 3.5 37.7 - - + -
754A SER* 4.3 19.1 - - - +
757A GLN* 3.1 22.0 + - + +
758A PRO 3.7 0.4 - - - -
760A MET* 1.3 95.6 - - + +
762A ASP* 1.3 63.7 + - - +
764A ILE* 3.6 20.0 - - + +
765A ASP* 3.0 38.9 + - - +
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Residues in contact with ASP 762 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754A SER* 5.4 4.9 - - - -
758A PRO* 2.9 30.2 + - - +
759A TYR* 3.2 8.6 + - + +
761A TYR* 1.3 79.8 - - - +
763A VAL* 1.3 62.9 + - + +
765A ASP* 3.6 14.8 + - - +
766A THR* 3.5 20.1 + - - +
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Residues in contact with VAL 763 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A LEU* 3.3 42.8 - - + +
392A LEU* 4.0 16.2 - - + -
759A TYR* 3.2 31.5 + - + +
760A MET 3.6 6.7 - - - +
762A ASP* 1.3 76.7 - - + +
764A ILE* 1.4 63.6 + - - +
766A THR* 2.6 28.8 + - - +
767A LYS* 3.6 9.5 - - + +
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Residues in contact with ILE 764 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A LEU* 3.7 18.8 - - + -
742A TYR* 3.8 21.5 - - + -
743A ARG 3.5 18.8 - - - +
744A ARG* 2.6 66.1 + - - +
760A MET* 2.9 33.5 + - + +
761A TYR* 3.6 28.3 - - + +
762A ASP 3.5 0.2 - - - -
763A VAL* 1.4 73.7 - - - +
765A ASP* 1.4 53.5 + - - +
767A LYS* 3.0 21.0 + - - +
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Residues in contact with ASP 765 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744A ARG* 3.9 22.7 + - - +
761A TYR* 3.0 27.6 + - - +
762A ASP* 3.8 14.2 - - - +
763A VAL 3.3 0.2 - - - -
764A ILE* 1.4 76.9 - - - +
766A THR* 1.3 59.7 + - + +
767A LYS 3.3 2.3 + - - +
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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