Contacts of the helix formed by residues 833 - 844 (chain A) in PDB entry 2G30
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 GLU 833 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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831A LYS 3.6 3.0 + - - +
832A MET* 1.3 77.7 - - - +
834A ARG* 1.3 61.4 + - - +
835A GLN* 3.3 24.8 + - - +
836A VAL* 3.2 24.6 + - + +
837A PHE* 2.9 24.9 + - - +
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Residues in contact with ARG 834 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832A MET 5.0 0.7 - - - +
833A GLU* 1.3 74.4 - - - +
835A GLN* 1.3 68.4 + - - +
837A PHE* 3.2 4.2 + - - +
838A LEU* 3.1 26.0 + - - +
876A ILE* 3.0 46.2 + - + -
877A ALA* 3.5 19.0 - - - +
2P ASP* 2.8 42.3 + - - +
4P LEU* 3.7 13.8 - - + +
5P ASP* 3.1 39.6 + - - +
8P PHE* 3.9 14.6 - - + -
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Residues in contact with GLN 835 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833A GLU* 3.3 27.8 + - - +
834A ARG* 1.3 90.0 + - - +
836A VAL* 1.3 63.9 + - + +
838A LEU* 3.3 9.0 + - - +
839A ALA* 3.1 23.3 + - - +
2P ASP* 4.6 6.7 - - + +
4P LEU* 3.7 23.8 - - + +
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Residues in contact with VAL 836 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832A MET* 4.0 19.1 - - + -
833A GLU* 3.2 37.4 + - + +
834A ARG 3.2 0.4 - - - -
835A GLN* 1.3 77.6 - - + +
837A PHE* 1.3 57.2 + - - +
839A ALA* 3.3 5.8 + - + +
840A THR* 2.7 47.7 + - - +
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Residues in contact with PHE 837 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832A MET* 3.6 13.8 - - + -
833A GLU 2.9 14.1 + - - +
834A ARG* 3.2 12.8 + - - +
836A VAL* 1.3 75.7 - - - +
838A LEU* 1.3 60.0 + - + +
840A THR* 3.9 0.6 - - - -
841A TRP* 2.8 59.8 + + + +
876A ILE* 4.1 22.4 - - + -
888A TYR* 3.9 33.2 - + + -
889A GLN 3.3 28.5 - - - -
890A SER* 4.6 0.2 - - - -
900A LEU* 3.6 23.6 - - + +
901A ALA 3.9 8.5 - - - -
8P PHE* 3.8 15.3 - + + -
11P LEU* 4.8 2.5 - - + -
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Residues in contact with LEU 838 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834A ARG 3.1 13.5 + - - +
835A GLN* 3.3 7.2 + - - +
837A PHE* 1.3 76.0 - - - +
839A ALA* 1.3 62.7 + - - +
841A TRP* 3.5 3.5 + - - +
842A LYS* 3.2 24.1 + - - +
4P LEU* 4.0 27.4 - - + -
7P ALA* 4.1 22.9 - - + +
8P PHE* 3.6 47.1 - - + -
11P LEU* 4.3 16.4 - - + -
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Residues in contact with ALA 839 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835A GLN 3.1 16.4 + - - +
836A VAL* 3.8 6.7 - - + +
838A LEU* 1.3 78.7 - - - +
840A THR* 1.3 57.5 + - - +
842A LYS* 3.5 6.9 + - - +
843A ASP* 2.9 31.0 + - - +
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Residues in contact with THR 840 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832A MET* 4.1 12.6 - - + +
836A VAL* 2.7 37.5 + - - +
839A ALA* 1.3 75.1 - - - +
841A TRP* 1.3 59.2 + - - +
843A ASP* 4.2 4.5 - - - -
844A ILE* 2.8 47.9 + - + +
898A TRP* 6.0 2.0 - - + -
900A LEU* 3.8 18.4 - - + -
919A ARG* 3.7 22.4 + - - +
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Residues in contact with TRP 841 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837A PHE* 2.8 39.8 + + + +
838A LEU* 3.9 4.5 - - - +
840A THR* 1.3 72.4 - - - +
842A LYS* 1.3 60.9 + - - +
844A ILE* 3.6 1.0 - - - +
849A GLU* 4.2 1.8 - - - -
888A TYR* 5.0 2.2 - + - -
900A LEU* 3.8 45.2 - - + +
901A ALA 3.9 7.2 - - - -
902A GLU* 3.9 23.8 - - + -
915A SER* 4.1 8.3 - - - -
917A LYS* 2.7 66.0 + - + +
11P LEU* 3.8 34.4 - - + +
15P ARG* 3.7 39.1 - - - +
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Residues in contact with LYS 842 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838A LEU 3.2 16.7 + - - +
839A ALA* 3.7 6.7 - - - +
841A TRP* 1.3 80.6 - - - +
843A ASP* 1.3 61.6 + - - +
844A ILE 3.5 7.1 - - - +
845A PRO* 5.4 0.2 - - - +
846A ASN* 4.8 5.4 - - - +
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Residues in contact with ASP 843 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839A ALA 2.9 19.8 + - - +
840A THR* 3.8 2.9 - - - +
842A LYS* 1.3 74.8 - - - +
844A ILE* 1.3 66.6 + - - +
845A PRO* 3.2 8.8 - - - +
919A ARG* 3.0 30.8 + - - +
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Residues in contact with ILE 844 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840A THR* 2.8 38.9 + - + +
842A LYS 3.5 6.2 - - - +
843A ASP* 1.3 72.1 - - - +
845A PRO* 1.3 84.1 - - + +
846A ASN* 3.5 1.0 + - - +
848A ASN* 3.8 19.7 - - + +
898A TRP* 5.7 2.0 - - + +
900A LEU* 4.7 5.4 - - + -
917A LYS* 3.2 58.3 + - + +
918A CYS* 4.3 5.8 - - - +
919A ARG* 3.4 35.9 - - + +
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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