Contacts of the helix formed by residues 583 - 592 (chain G) in PDB entry 5ZRV
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 GLY 583 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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571G LEU 5.6 0.2 - - - -
572G ASP* 4.6 22.9 - - - -
575G THR* 5.9 2.2 - - - -
576G THR* 5.5 3.6 - - - +
582G VAL* 1.3 76.2 - - - +
584G ALA* 1.3 54.9 + - - -
585G ALA 3.2 3.1 - - - -
586G THR* 2.8 9.9 + - - +
587G LEU* 2.6 31.7 + - - -
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Residues in contact with ALA 584 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558G VAL* 6.5 1.8 - - - +
571G LEU 5.4 3.0 + - - -
572G ASP* 5.3 2.8 - - - +
575G THR* 6.3 0.6 - - - +
582G VAL 3.9 0.4 + - - -
583G GLY* 1.3 68.9 - - - -
585G ALA* 1.3 61.1 + - - +
587G LEU* 3.5 4.7 - - - +
588G VAL* 2.9 23.2 + - - -
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Residues in contact with ALA 585 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568G PRO 6.1 0.9 - - - -
572G ASP* 6.0 1.6 - - - +
583G GLY* 3.2 0.8 - - - -
584G ALA* 1.3 77.1 - - - +
586G THR* 1.3 55.3 + - - +
588G VAL* 3.2 2.8 + - - +
589G ASP* 2.9 23.9 + - - -
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Residues in contact with THR 586 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582G VAL* 5.6 1.3 - - - +
583G GLY* 2.8 15.7 + - - +
585G ALA* 1.3 74.2 - - - +
587G LEU* 1.3 58.0 + - - +
589G ASP* 3.5 4.9 - - - +
590G GLU* 2.8 23.4 + - - -
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Residues in contact with LEU 587 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583G GLY 2.6 16.1 + - - -
584G ALA* 3.2 7.3 + - - +
585G ALA 3.1 0.6 - - - -
586G THR* 1.3 74.5 - - - +
588G VAL* 1.3 57.9 + - - +
590G GLU* 3.2 1.8 + - - +
591G VAL* 3.1 22.7 + - - -
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Residues in contact with VAL 588 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584G ALA 2.9 14.1 + - - -
585G ALA 3.2 3.5 + - - -
587G LEU* 1.3 75.4 - - - +
589G ASP* 1.3 58.9 + - - +
590G GLU 3.2 1.5 + - - -
591G VAL* 4.1 5.5 + - - +
592G GLY* 4.1 12.8 + - - -
593G VAL* 4.8 3.8 + - - -
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Residues in contact with ASP 589 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585G ALA 2.9 15.9 + - - -
586G THR* 3.5 7.1 + - - +
587G LEU 3.2 0.2 - - - -
588G VAL* 1.3 75.8 - - - +
590G GLU* 1.3 58.2 + - - +
591G VAL 3.7 0.2 - - - -
592G GLY* 4.6 4.1 + - - -
629G GLY* 5.8 4.5 - - - -
630G ARG* 4.7 19.4 + - - +
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Residues in contact with GLU 590 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586G THR 2.8 16.2 + - - -
587G LEU* 3.2 4.6 + - - +
589G ASP* 1.3 78.7 - - - +
591G VAL* 1.3 62.8 + - - +
592G GLY 3.4 0.8 + - - -
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Residues in contact with VAL 591 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587G LEU 3.1 12.0 + - - -
588G VAL* 4.1 2.8 + - - +
590G GLU* 1.3 76.5 - - - +
592G GLY* 1.3 65.6 + - - +
595G VAL* 5.4 2.8 + - - -
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Residues in contact with GLY 592 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588G VAL 4.1 9.6 + - - -
589G ASP 4.6 2.5 - - - -
590G GLU 3.4 4.4 + - - +
591G VAL* 1.3 82.3 - - - +
593G VAL* 1.3 64.3 + - - -
594G ASP 3.2 4.3 + - - -
595G VAL 3.6 2.6 + - - -
596G ALA* 3.6 14.9 + - - -
628G LEU 6.1 0.2 - - - -
629G GLY* 6.0 0.2 - - - -
630G ARG 5.9 5.2 - - - -
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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