Contacts of the helix formed by residues 581 - 588 (chain G) in PDB entry 2VKZ
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 581 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565G TYR 5.8 1.8 - - - +
566G HIS 5.7 1.1 - - - -
567G PRO* 4.6 5.2 - - + -
579G VAL* 4.2 9.2 - - + +
580G GLU* 1.3 80.0 - - - +
582G LYS* 1.3 65.1 + - - +
583G PHE 3.5 3.5 + - - -
584G SER* 3.0 13.6 + - - -
585G LYS* 2.9 26.1 + - - +
591G PRO* 3.6 7.6 - - + +
781G LEU* 3.9 28.0 - - + -
796G PHE 4.3 4.9 - - - +
797G ASP* 2.7 33.7 + - - +
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Residues in contact with LYS 582 (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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565G TYR* 3.9 29.3 + - + -
581G THR* 1.3 75.1 - - - +
583G PHE* 1.3 63.8 + - - +
585G LYS* 3.9 6.3 - - - +
586G LEU* 3.7 14.6 + - - +
758G ARG* 4.2 5.7 - - - +
760G HIS 4.8 0.8 + - - -
761G PRO* 3.0 43.1 + - - +
763G ILE 3.9 12.4 + - - +
764G MET* 4.1 8.7 - - + +
797G ASP* 3.3 26.5 - - - +
1106G GLU 4.7 1.2 - - - +
1108G PRO* 3.7 31.5 + - + +
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Residues in contact with PHE 583 (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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581G THR* 3.1 0.6 + - - -
582G LYS* 1.3 77.3 - - - +
584G SER* 1.3 55.8 + - - +
586G LEU* 2.8 27.2 + - - +
587G ILE* 2.8 38.5 + - + +
591G PRO* 3.8 27.6 - - + -
592G LEU 4.6 1.6 - - - -
593G LEU* 4.6 13.0 - - + -
616G THR* 4.8 7.9 - - + -
702G TYR* 4.1 24.9 - + - -
764G MET* 3.2 36.3 - - + -
766G ILE* 3.7 30.3 - - + -
797G ASP* 3.0 30.6 - - + +
798G GLY* 4.3 1.1 - - - -
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Residues in contact with SER 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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578G PHE* 5.9 0.2 - - - -
579G VAL 2.9 19.3 + - - -
580G GLU* 3.6 3.8 - - - -
581G THR* 3.0 16.1 + - - -
583G PHE* 1.3 79.3 - - - +
585G LYS* 1.3 56.2 + - - +
587G ILE* 3.6 7.2 - - - -
588G GLY* 2.7 31.2 + - - -
589G ARG 3.0 25.8 - - - -
591G PRO* 3.4 19.9 - - - +
1103G PHE* 3.6 11.8 - - - -
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Residues in contact with LYS 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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570G ILE* 4.6 6.7 - - - +
580G GLU* 3.5 25.2 + - + +
581G THR 2.9 21.1 + - - +
582G LYS* 3.9 8.1 - - - +
583G PHE 3.1 0.2 + - - -
584G SER* 1.3 78.2 + - - +
586G LEU* 1.3 57.2 + - - +
1100G VAL* 5.2 3.0 - - - +
1102G TYR 5.6 0.8 + - - -
1103G PHE* 3.4 34.8 - - + +
1104G GLY* 3.2 13.9 - - - +
1105G GLY 3.1 9.7 + - - -
1106G GLU* 3.0 67.8 + - + +
1147G ILE* 5.0 13.9 - - - +
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Residues in contact with LEU 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 LYS 3.7 6.8 + - - +
583G PHE 2.8 10.2 + - - +
585G LYS* 1.3 79.0 - - - +
587G ILE* 1.3 64.7 + - + +
701G LYS* 4.5 28.5 - - + +
702G TYR* 4.6 14.4 - - + -
727G PRO* 3.9 18.4 - - + -
764G MET* 3.5 31.9 - - + -
1105G GLY* 3.2 22.0 + - - -
1106G GLU 3.2 23.6 + - - +
1107G SER* 4.6 3.4 - - - +
1108G PRO* 4.1 10.8 - - + -
1248G PHE* 3.9 10.4 - - + -
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Residues in contact with ILE 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 PHE* 2.8 50.9 - - + +
584G SER* 3.6 4.7 - - - -
586G LEU* 1.3 80.7 - - + +
588G GLY* 1.3 58.8 + - - +
589G ARG* 3.7 36.8 + - + +
590G PRO 3.9 8.7 - - - +
616G THR* 3.3 35.9 - - + -
702G TYR* 5.8 6.1 - - + +
1248G PHE* 3.8 24.2 - - - +
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Residues in contact with GLY 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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578G PHE* 4.2 11.1 - - - -
584G SER 2.7 20.4 + - - -
586G LEU 3.4 2.0 - - - -
587G ILE* 1.3 74.0 - - - +
589G ARG* 1.3 63.6 + - - +
1103G PHE* 3.3 34.4 - - - +
1104G GLY* 3.8 5.4 - - - -
1247G GLY* 5.0 8.5 + - - -
1248G PHE 5.1 1.1 + - - -
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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