Contacts of the helix formed by residues 568 - 579 (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 PRO 568 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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562G LEU* 5.9 7.3 - - - +
566G VAL 3.8 1.7 - - - +
567G ASP* 1.3 67.6 - - - +
569G LYS* 1.3 63.6 + - - -
570G LYS 3.2 0.7 - - - -
571G LEU* 3.1 17.2 + - - +
572G ASP 3.6 7.1 + - - -
585G ALA* 6.0 1.2 + - - -
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Residues in contact with LYS 569 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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567G ASP 2.8 2.6 + - - -
568G PRO* 1.3 75.2 - - - +
570G LYS* 1.3 61.3 + - - +
571G LEU 3.4 0.2 + - - -
572G ASP* 3.5 10.8 + - - +
573G SER 4.1 3.3 + - - -
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Residues in contact with LYS 570 (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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566G VAL 5.1 2.2 - - - -
567G ASP 2.7 19.0 + - - -
569G LYS* 1.3 70.6 - - - +
571G LEU* 1.3 55.3 - - - +
573G SER* 3.3 4.5 + - - -
574G LEU* 2.9 24.1 + - - -
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Residues in contact with LEU 571 (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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566G VAL 5.5 0.6 + - - -
567G ASP 4.0 0.2 + - - -
568G PRO* 3.1 17.6 + - - +
570G LYS* 1.3 73.8 - - - +
572G ASP* 1.3 59.8 + - - +
574G LEU* 3.6 3.5 - - - +
575G THR* 2.9 26.7 + - - -
583G GLY* 5.6 0.2 - - - -
584G ALA 5.4 3.4 + - - -
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Residues in contact with ASP 572 (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 3.6 6.0 + - - -
569G LYS* 3.5 8.2 + - - +
570G LYS 3.2 1.2 - - - -
571G LEU* 1.3 75.3 - - - +
573G SER* 1.3 56.8 + - - +
575G THR 3.9 0.2 - - - -
576G THR* 2.9 27.4 + - - -
583G GLY* 4.6 20.6 - - - -
584G ALA 5.3 1.1 - - - +
585G ALA 6.0 1.3 - - - +
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Residues in contact with SER 573 (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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569G LYS 4.1 4.0 + - - -
570G LYS 3.3 7.7 + - - -
572G ASP* 1.3 74.3 - - - +
574G LEU* 1.3 56.6 + - - +
576G THR* 3.8 1.0 - - - +
577G SER* 2.9 27.5 + - - -
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Residues in contact with LEU 574 (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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570G LYS 2.9 14.2 + - - -
571G LEU* 3.2 6.4 + - - +
573G SER* 1.3 78.0 - - - +
575G THR* 1.3 56.9 + - - +
577G SER* 3.8 1.4 + - - -
578G PHE* 3.8 11.3 + - - -
670G ASP 5.7 0.7 - - - +
674G GLN* 6.1 1.0 - - - -
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Residues in contact with THR 575 (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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571G LEU 2.9 15.0 + - - -
572G ASP 4.1 0.2 - - - -
574G LEU* 1.3 73.8 - - - +
576G THR* 1.3 64.8 + - - +
577G SER 3.1 1.6 - - - -
578G PHE* 3.3 11.2 + - - +
579G GLY 3.3 8.0 + - - -
580G PHE* 3.4 9.9 + - - -
582G VAL 6.0 0.4 - - - -
583G GLY* 5.9 3.6 - - - -
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Residues in contact with THR 576 (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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295G LYS* 5.8 3.6 - - - -
572G ASP 2.9 16.7 + - - -
573G SER* 3.8 1.3 - - - +
575G THR* 1.3 73.9 - - - +
577G SER* 1.3 63.9 + - - +
578G PHE 3.3 0.2 - - - -
579G GLY* 3.3 12.4 + - - -
580G PHE 3.3 20.0 + - - +
582G VAL 6.0 0.4 - - - -
583G GLY* 5.5 3.7 - - - -
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Residues in contact with SER 577 (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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297G LEU* 6.0 2.3 - - - -
573G SER 2.9 18.7 + - - -
574G LEU 3.8 2.9 + - - -
575G THR 3.1 0.6 - - - -
576G THR* 1.3 78.2 - - - +
578G PHE* 1.3 62.1 + - - +
579G GLY* 3.5 0.5 + - - -
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Residues in contact with PHE 578 (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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574G LEU 3.8 6.5 + - - -
575G THR 3.3 9.1 + - - -
577G SER* 1.3 77.9 - - - +
579G GLY* 1.3 56.8 + - - +
580G PHE 3.9 0.4 - - - -
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Residues in contact with GLY 579 (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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575G THR 3.3 2.6 + - - -
576G THR 3.3 8.0 + - - -
577G SER 3.2 3.7 - - - -
578G PHE* 1.3 81.0 - - - +
580G PHE* 1.3 67.8 + - - +
581G PRO* 3.3 3.6 - - - +
711G PRO* 4.0 18.9 - - - +
712G PRO 5.3 2.1 - - - +
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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