Contacts of the helix formed by residues 747 - 758 (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 HIS 747 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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736G ARG* 4.2 10.4 + - - -
745G ASP* 3.3 10.3 + - - +
746G ALA* 1.3 83.8 + - - +
748G THR* 1.3 60.7 + - - +
749G PRO 3.4 2.0 - - - -
750G MET* 3.3 2.9 + - - +
751G LEU* 2.8 36.5 + - + +
767G PHE* 4.3 4.4 - + - -
780G TYR* 2.7 37.9 + + - -
785G TRP* 3.8 23.9 - + + -
788G LYS* 6.1 2.2 - - - -
789G PHE* 3.8 32.9 - + + -
829G ASP* 4.1 28.7 + - - +
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Residues in contact with THR 748 (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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409G PHE* 3.5 29.9 - - + -
710G ILE* 4.7 4.3 - - + -
744G GLU* 6.1 0.4 - - - +
745G ASP* 3.1 15.9 + - - -
747G HIS* 1.3 75.4 - - - +
749G PRO* 1.3 73.2 - - + +
751G LEU* 3.4 8.9 + - - +
752G GLN* 3.1 44.3 + - - +
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Residues in contact with PRO 749 (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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409G PHE* 5.8 0.2 - - + -
709G SER* 6.4 0.2 - - - -
710G ILE* 3.9 29.6 - - + +
713G ILE* 4.3 4.0 - - + -
732G TRP* 3.3 30.5 - - + -
744G GLU* 4.7 13.5 - - + +
745G ASP* 3.1 27.6 - - + +
747G HIS 3.5 3.6 - - - +
748G THR* 1.3 99.7 - - + +
750G MET* 1.3 57.8 + - - +
752G GLN* 3.3 1.2 + - - +
753G MET* 2.9 35.7 + - - +
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Residues in contact with MET 750 (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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713G ILE* 3.6 14.8 - - + -
730G LEU* 6.0 0.4 - - + -
732G TRP* 2.8 70.4 - - + +
746G ALA 4.4 3.4 - - - +
747G HIS 3.3 6.8 + - - +
749G PRO* 1.3 75.6 - - - +
751G LEU* 1.3 58.2 + - - +
752G GLN 2.9 4.5 - - - -
753G MET 4.4 0.2 - - - +
754G TYR* 2.9 38.1 + - + +
757G ILE* 4.0 22.7 - - + -
765G LEU* 4.3 4.9 - - + -
767G PHE* 4.2 2.0 - - + -
785G TRP* 4.4 8.7 - - + -
796G PHE* 3.1 38.1 - - + -
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Residues in contact with LEU 751 (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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747G HIS* 2.8 21.7 + - + +
748G THR* 3.4 8.5 - - - +
750G MET* 1.3 75.7 - - - +
752G GLN* 1.3 58.5 + - + +
754G TYR* 4.5 1.4 + - - +
785G TRP* 3.6 15.1 - - + -
789G PHE* 3.4 43.7 - - + -
791G TYR* 3.1 77.5 - - + +
794G MET* 3.5 25.1 - - + +
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Residues in contact with GLN 752 (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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710G ILE* 3.4 34.5 - - + +
748G THR* 3.1 28.9 + - - +
749G PRO* 3.6 4.5 - - + +
750G MET 2.9 0.8 - - - -
751G LEU* 1.3 80.2 - - - +
753G MET* 1.3 69.5 + - + +
754G TYR 3.5 0.7 - - - -
755G SER* 5.2 2.0 + - - -
756G LYS* 5.3 5.9 + - - +
791G TYR* 5.3 3.8 - - - +
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Residues in contact with MET 753 (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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710G ILE* 4.2 27.1 - - + +
713G ILE* 3.7 35.0 - - + -
714G SER* 4.1 18.2 - - - +
717G ILE* 3.8 21.3 - - + -
749G PRO 2.9 18.9 + - - +
750G MET 4.5 0.2 - - - +
752G GLN* 1.3 84.5 - - - +
754G TYR* 1.3 66.9 + - - +
755G SER 3.0 3.6 + - - -
756G LYS* 3.0 34.2 + - + +
757G ILE* 3.1 27.6 + - + +
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Residues in contact with TYR 754 (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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561G TRP* 3.5 26.9 - + - -
565G TYR* 3.8 5.5 - - - -
750G MET* 2.9 20.4 + - + +
751G LEU 4.6 2.0 + - - +
752G GLN 3.5 1.6 - - - -
753G MET* 1.3 75.9 - - - +
755G SER* 1.3 65.3 + - - +
757G ILE* 3.3 9.1 + - - +
758G ARG* 3.0 53.9 + - + +
765G LEU* 3.5 32.3 - - + -
794G MET* 3.0 48.5 - - + -
795G PRO* 2.7 37.7 + - - +
796G PHE* 4.5 7.4 - + - -
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Residues in contact with SER 755 (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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521G ASP* 2.7 33.4 + - - -
561G TRP* 3.5 26.7 + - - -
751G LEU 5.8 0.2 + - - -
752G GLN 5.2 1.9 + - - -
753G MET 3.0 1.4 + - - -
754G TYR* 1.3 76.5 - - - +
756G LYS* 1.3 64.9 + - - +
758G ARG* 3.3 12.4 + - - +
759G ARG* 3.4 33.1 + - - +
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Residues in contact with LYS 756 (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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714G SER* 6.1 0.4 - - - +
717G ILE* 4.0 16.6 - - + -
752G GLN 5.3 5.8 + - - +
753G MET* 3.0 27.9 + - + +
755G SER* 1.3 76.3 - - - +
757G ILE* 1.3 65.7 + - - +
758G ARG 3.1 1.6 - - - -
759G ARG* 3.1 24.4 + - - +
760G HIS* 3.2 19.2 + - + -
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Residues in contact with ILE 757 (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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713G ILE* 3.8 27.4 - - + -
717G ILE* 3.9 10.5 - - + +
730G LEU* 3.9 7.4 - - + -
750G MET* 4.0 14.4 - - - -
753G MET* 3.1 29.3 + - + +
754G TYR* 3.5 8.7 - - - +
756G LYS* 1.3 75.1 - - - +
758G ARG* 1.3 62.3 + - - +
759G ARG 3.3 0.2 - - - -
760G HIS 3.4 15.1 + - - +
763G ILE* 3.5 36.7 - - + +
765G LEU* 3.5 40.8 - - + -
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Residues in contact with ARG 758 (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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561G TRP* 4.2 13.0 - - + +
565G TYR* 3.2 59.6 + - + +
582G LYS* 4.2 4.2 - - - +
754G TYR* 3.0 52.5 + - + +
755G SER 3.6 6.5 - - - +
756G LYS 3.1 0.6 - - - -
757G ILE* 1.3 78.7 + - + +
759G ARG* 1.3 58.8 + - - +
760G HIS 3.2 10.3 + - - -
761G PRO* 5.1 0.7 - - - +
763G ILE 3.6 16.0 + - - -
765G LEU* 4.0 17.9 - - - +
795G PRO 3.3 17.4 + - - -
797G ASP* 2.3 45.3 + - - -
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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