Contacts of the helix formed by residues 1047 - 1051 (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 ASP1047 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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860G ARG* 2.7 26.2 + - - -
897G ALA 5.0 0.2 - - - +
1040G LEU* 3.9 1.3 - - - -
1043G VAL* 3.8 8.8 - - - +
1045G ASP* 3.0 20.9 - - - +
1046G GLN* 1.3 74.5 - - - +
1048G VAL* 1.3 67.0 + - - +
1049G GLN* 3.0 21.9 + - - +
1050G ARG* 3.1 39.2 + - + +
1051G THR* 3.9 1.7 + - - -
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Residues in contact with VAL1048 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816G ASP* 3.3 37.7 - - + +
817G ALA* 3.8 16.4 - - + -
820G CYS* 4.4 10.8 - - + -
859G THR* 3.5 7.5 - - - +
1040G LEU* 3.3 22.0 - - + -
1046G GLN 3.3 3.9 + - - +
1047G ASP* 1.3 72.8 + - - +
1049G GLN* 1.3 54.2 + - - +
1050G ARG 3.0 0.4 - - - -
1051G THR* 2.8 33.3 + - - -
1053G ILE* 3.7 28.7 - - + +
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Residues in contact with GLN1049 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820G CYS* 4.8 7.1 - - - -
858G ALA 4.1 3.6 + - - -
859G THR* 3.2 36.7 - - - +
860G ARG* 2.8 66.7 + - + +
861G GLY 2.8 7.6 + - - -
1047G ASP* 3.0 17.3 + - - +
1048G VAL* 1.3 79.1 - - - +
1050G ARG* 1.3 55.7 + - - +
1051G THR 3.3 1.8 - - - -
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Residues in contact with ARG1050 (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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860G ARG* 4.7 0.7 - - - +
861G GLY* 4.1 7.5 - - - -
895G LEU 4.4 0.2 + - - -
896G ASN* 2.6 33.9 + - - +
897G ALA* 3.2 17.9 + - - +
898G ASP* 3.3 18.6 - - - +
899G PHE* 2.8 30.6 + - - +
900G GLN* 3.1 27.7 + - - +
902G PRO* 6.0 0.4 - - - +
1043G VAL* 3.8 11.0 - - + -
1044G VAL* 3.0 36.1 - - - +
1045G ASP* 2.8 29.5 + - - -
1047G ASP* 3.1 28.4 + - + +
1048G VAL 2.9 0.8 + - - -
1049G GLN* 1.3 78.2 - - - +
1051G THR* 1.3 56.9 - - - +
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Residues in contact with THR1051 (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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859G THR* 2.7 27.5 + - - +
862G VAL* 3.6 4.2 - - - +
900G GLN* 3.2 13.8 + - - +
1036G GLN* 3.7 11.1 + - + +
1037G SER* 3.7 28.9 - - - +
1040G LEU* 4.7 1.9 - - + +
1043G VAL* 4.0 10.0 - - - +
1047G ASP 3.9 8.1 + - - -
1048G VAL* 2.8 22.8 + - + +
1049G GLN 3.3 1.6 + - - -
1050G ARG* 1.3 78.1 - - - +
1052G CYS* 1.3 78.4 + - - +
1053G ILE* 3.3 12.1 + - + +
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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
------------------------------------------------------------
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