Contacts of the helix formed by residues 640 - 648 (chain V) in PDB entry 5Z58
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 THR 640 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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628V ILE* 4.4 28.2 - - - +
631V PHE* 4.7 7.2 - - - +
637V GLY* 3.9 21.9 + - - -
638V GLY 3.4 1.6 - - - -
639V LEU* 1.3 78.4 - - - +
641V ASP* 1.3 67.3 + - - +
642V GLU 3.6 1.1 - - - -
643V LEU* 3.4 13.0 + - - +
644V ARG* 3.1 14.8 + - - +
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Residues in contact with ASP 641 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637V GLY 4.7 2.5 + - - +
638V GLY* 4.5 11.1 + - - +
639V LEU* 3.3 3.2 - - - +
640V THR* 1.3 76.2 - - - +
642V GLU* 1.3 56.4 + - - +
644V ARG* 2.4 39.9 + - - +
645V GLU* 3.0 5.7 + - - +
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Residues in contact with GLU 642 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639V LEU 5.2 2.4 + - - +
640V THR 3.6 0.2 - - - -
641V ASP* 1.3 76.3 - - - +
643V LEU* 1.3 57.9 + - - +
645V GLU* 3.2 11.8 + - - +
646V HIS* 2.9 26.0 + - - +
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Residues in contact with LEU 643 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612V PHE* 6.5 1.1 - - + -
613V GLU 5.0 11.4 - - - +
624V THR* 5.2 13.3 - - - +
627V ALA* 6.2 4.0 - - + -
628V ILE* 5.4 9.4 - - + +
639V LEU 5.7 0.2 + - - -
640V THR* 3.4 16.0 + - - +
641V ASP 3.0 0.6 - - - -
642V GLU* 1.3 79.6 - - - +
644V ARG* 1.3 56.4 + - - +
646V HIS* 3.1 10.4 + - - +
647V LEU* 2.9 26.5 + - - +
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Residues in contact with ARG 644 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628V ILE* 5.5 7.8 - - + +
640V THR 3.1 10.8 + - - +
641V ASP* 2.4 30.8 + - - +
643V LEU* 1.3 64.2 - - - +
645V GLU* 1.3 64.9 + - - +
647V LEU* 2.9 20.1 + - - +
648V LYS* 3.1 11.8 + - - +
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Residues in contact with GLU 645 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641V ASP 3.0 7.1 + - - +
642V GLU* 3.3 14.8 - - - +
644V ARG* 1.3 75.9 - - - +
646V HIS* 1.3 58.4 + - - +
648V LYS* 2.8 32.9 + - - +
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Residues in contact with HIS 646 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613V GLU 5.8 4.0 - - - +
642V GLU 2.9 13.8 + - - +
643V LEU* 3.1 13.4 + - + +
645V GLU* 1.3 74.4 - - - +
647V LEU* 1.3 67.6 + - - +
648V LYS 3.2 5.5 + - - -
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Residues in contact with LEU 647 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621V PRO* 6.1 5.4 - - - +
624V THR* 5.4 12.5 - - - -
643V LEU 2.9 11.9 + - - +
644V ARG* 3.1 13.9 - - - +
646V HIS* 1.3 76.5 - - - +
648V LYS* 1.3 63.7 + - - +
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Residues in contact with LYS 648 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644V ARG 3.1 5.5 + - - +
645V GLU* 2.8 21.9 + - - +
646V HIS 3.6 5.4 - - - -
647V LEU* 1.3 86.4 - - - +
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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