Contacts of the helix formed by residues 891 - 900 (chain G) in PDB entry 1WQ1
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 MET 891 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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784G ALA* 4.1 33.2 - - + +
787G LEU* 3.9 28.7 - - + -
881G VAL* 4.4 19.5 - - + +
885G TRP* 4.6 11.4 - - + -
888G ASN* 3.2 38.6 + - + +
889G THR 3.4 1.0 - - - -
890G THR* 1.3 82.9 - - + +
892G ARG* 1.3 62.1 + - - +
893G THR 3.0 0.9 - - - -
894G ARG* 4.3 27.8 - - + -
895G VAL* 3.0 37.9 + - + +
32R TYR* 6.1 3.1 - - + -
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Residues in contact with ARG 892 (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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878G GLN* 3.1 36.5 + - + +
881G VAL* 3.9 19.2 - - + +
882G GLN* 4.4 23.8 - - + +
888G ASN 5.0 1.2 + - - +
889G THR* 2.7 50.8 + - - +
890G THR* 3.3 2.8 + - - +
891G MET* 1.3 76.2 - - - +
893G THR* 1.3 77.2 + - - +
895G VAL* 3.7 1.3 - - - +
896G VAL* 3.6 6.2 - - - +
968G ILE* 3.7 23.0 - - - +
972G ASP* 2.8 32.5 + - - +
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Residues in contact with THR 893 (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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890G THR* 2.8 19.4 + - - -
892G ARG* 1.3 100.0 + - - +
894G ARG* 1.3 64.4 + - - +
895G VAL 3.2 1.3 - - - -
896G VAL* 3.0 7.7 + - - +
897G SER* 3.0 20.3 + - - -
943G LEU* 4.9 12.3 - - - +
968G ILE* 4.0 27.0 - - + +
971G LEU* 3.9 27.3 - - + +
972G ASP* 3.7 19.1 - - - +
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Residues in contact with ARG 894 (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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784G ALA* 6.3 0.2 - - - +
785G THR* 4.1 13.3 - - - +
888G ASN* 5.8 0.8 - - - +
890G THR* 3.9 35.1 + - - +
891G MET* 3.8 29.0 - - + +
893G THR* 1.3 80.6 + - - +
895G VAL* 1.3 57.6 + - - +
897G SER* 2.8 26.0 + - - -
898G GLY* 2.9 14.0 + - - -
941G ALA 5.3 0.4 - - - -
942G ASN* 4.7 20.5 + - - +
943G LEU* 6.0 3.3 - - + +
971G LEU* 5.0 0.4 - - - +
31R GLU* 5.3 4.6 - - - +
32R TYR* 2.9 71.1 + - + +
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Residues in contact with VAL 895 (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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778G ILE* 4.9 0.2 - - + -
787G LEU* 3.9 17.9 - - + -
788G PHE* 4.4 14.1 - - + -
877G LEU* 3.9 25.6 - - + +
878G GLN* 4.6 0.4 - - + -
881G VAL* 3.8 28.9 - - + -
891G MET* 3.0 27.6 + - + +
892G ARG* 3.7 14.6 - - - +
894G ARG* 1.3 76.7 - - - +
896G VAL* 1.3 66.4 + - + +
898G GLY* 4.1 3.4 + - - -
899G PHE* 3.3 23.4 - - - -
32R TYR* 5.6 2.2 - - - -
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Residues in contact with VAL 896 (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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874G TYR* 4.2 36.1 - - + +
877G LEU* 5.2 3.1 - - + -
878G GLN* 3.6 26.0 - - + +
892G ARG 3.6 20.4 - - - +
893G THR 3.0 6.3 + - - +
895G VAL* 1.3 78.7 - - + +
897G SER* 1.3 67.2 + - - +
898G GLY 3.2 1.3 - - - -
899G PHE* 3.0 8.1 + - - +
900G VAL* 3.0 36.7 + - + +
971G LEU* 3.9 20.4 - - + +
974G LEU* 4.5 6.3 - - + -
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Residues in contact with SER 897 (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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893G THR 3.0 11.6 + - - -
894G ARG* 2.8 13.1 + - - -
896G VAL* 1.3 76.4 - - - +
898G GLY* 1.3 57.2 + - - +
899G PHE 3.0 1.4 + - - -
900G VAL* 3.9 2.2 - - - -
901G PHE* 2.9 27.0 + - - +
902G LEU* 3.2 6.6 + - - -
938G GLN* 4.6 0.5 + - - -
941G ALA* 2.7 41.6 + - - +
942G ASN* 3.9 8.8 + - - -
971G LEU* 3.8 20.6 - - - +
32R TYR* 6.0 0.2 - - - -
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Residues in contact with GLY 898 (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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788G PHE* 5.4 2.4 - - - +
894G ARG 2.9 12.8 + - - -
895G VAL 4.1 3.1 - - - -
896G VAL 3.2 0.6 - - - -
897G SER* 1.3 77.3 - - - +
899G PHE* 1.3 59.4 - - - +
902G LEU* 3.2 30.7 - - - +
903G ARG* 3.2 18.8 + - - +
938G GLN* 5.9 0.7 - - - -
942G ASN* 6.0 0.4 - - - -
32R TYR* 4.1 18.6 - - - -
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Residues in contact with PHE 899 (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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774G ASN* 4.9 0.4 - - - -
788G PHE* 3.6 47.6 - + + -
795G SER* 4.6 5.8 - - - -
798G MET* 3.3 45.8 - - + -
802G MET* 3.9 11.8 - - + +
874G TYR* 4.2 14.8 - - + -
877G LEU* 3.5 27.6 - - + -
895G VAL 3.3 20.2 - - - -
896G VAL* 3.0 6.7 + - - +
898G GLY* 1.3 80.1 - - - +
900G VAL* 1.3 64.7 + - - +
901G PHE 3.3 1.6 - - - -
903G ARG* 3.1 29.6 + - - +
904G LEU* 3.0 23.9 + - - +
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Residues in contact with VAL 900 (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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809G PHE* 4.5 14.1 - - + -
866G LEU* 5.2 2.5 - - + -
874G TYR* 3.9 19.7 - - + +
896G VAL* 3.0 30.5 + - + +
899G PHE* 1.3 77.9 - - - +
901G PHE* 1.3 78.4 + - + +
904G LEU* 3.2 9.6 - - + +
905G ILE* 2.9 41.8 + - + +
970G PHE* 4.5 8.7 - - + -
971G LEU* 3.9 8.3 - - + -
974G LEU* 4.0 22.4 - - + -
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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