Contacts of the helix formed by residues 794 - 805 (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 ALA 794 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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770G LEU* 5.5 0.2 - - - +
773G LEU* 3.9 24.7 - - + +
774G ASN* 3.5 22.4 - - - +
777G GLU* 3.6 32.8 + - + +
788G PHE* 4.0 5.2 - - + -
792G THR* 3.4 2.6 + - - +
793G LEU* 1.3 77.7 - - - +
795G SER* 1.3 57.2 + - - +
797G LEU* 3.1 3.9 + - - +
798G MET* 2.9 31.9 + - - +
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Residues in contact with SER 795 (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* 4.7 12.0 - - - -
790G ALA 3.4 14.9 + - - -
791G THR* 3.6 6.2 - - - +
792G THR* 3.2 30.4 + - - -
794G ALA* 1.3 77.6 - - - +
796G THR* 1.3 58.4 + - - +
798G MET* 4.0 9.8 - - - +
799G GLU* 3.3 22.9 + - - +
899G PHE* 4.6 3.6 - - - -
903G ARG* 3.9 23.3 + - - -
63R GLU* 3.9 7.6 - - - +
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Residues in contact with THR 796 (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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749G ARG* 3.3 17.7 - - + -
750G THR* 4.4 12.1 - - + +
753G ALA* 4.1 17.0 - - + +
791G THR* 4.3 6.1 - - - +
792G THR 2.6 22.2 + - - -
793G LEU* 2.9 11.5 + - - -
795G SER* 1.3 78.8 + - - +
797G LEU* 1.3 62.0 + - - +
798G MET 3.3 0.2 - - - -
799G GLU* 3.3 11.5 + - - +
800G GLN* 3.0 41.8 + - + +
62R GLU* 4.5 13.7 + - - +
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Residues in contact with LEU 797 (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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753G ALA* 3.5 40.2 - - + +
756G LEU* 5.0 5.6 - - + -
757G LEU* 4.4 13.1 - - + +
769G LEU* 4.2 19.7 - - + -
770G LEU* 3.8 23.6 - - + +
773G LEU* 3.3 31.0 - - + -
793G LEU* 2.7 26.7 + - + +
794G ALA* 3.4 7.0 - - - +
796G THR* 1.3 75.7 - - - +
798G MET* 1.3 67.7 + - - +
800G GLN* 3.6 1.4 + - + +
801G TYR* 3.1 22.9 + - - +
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Residues in contact with MET 798 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770G LEU* 4.6 15.7 - - - -
774G ASN* 3.4 27.6 - - - +
794G ALA 2.9 19.1 + - - +
795G SER 4.0 3.4 - - - +
797G LEU* 1.3 74.3 - - - +
799G GLU* 1.3 66.5 + - - +
801G TYR* 2.8 18.5 + - + +
802G MET* 2.9 29.9 + - + +
870G LEU* 4.8 3.8 - - + -
873G ILE* 4.4 15.9 - - + -
874G TYR* 4.1 24.7 - - + -
877G LEU* 4.8 0.9 - - + -
899G PHE* 3.3 48.5 - - + -
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Residues in contact with GLU 799 (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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791G THR* 5.9 0.3 - - - +
795G SER 3.3 15.7 + - - +
796G THR* 3.3 15.4 + - - +
798G MET* 1.3 79.0 - - - +
800G GLN* 1.3 68.5 + - + +
802G MET* 3.7 9.4 + - - +
803G LYS* 3.0 39.9 + - + +
903G ARG* 6.3 0.4 - - - +
62R GLU* 3.7 30.8 - - - +
63R GLU* 3.3 40.3 + - - +
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Residues in contact with GLN 800 (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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750G THR* 3.3 41.8 + - - +
753G ALA* 4.3 8.7 - - + -
754G SER* 3.1 27.8 + - - -
757G LEU* 4.0 12.3 - - + +
796G THR* 3.0 25.9 + - + +
797G LEU* 4.4 2.2 - - - +
799G GLU* 1.3 85.5 + - + +
801G TYR* 1.3 64.8 + - - +
803G LYS* 3.8 7.2 + - - +
804G ALA* 3.5 18.0 + - - +
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Residues in contact with TYR 801 (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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757G LEU* 3.7 22.6 - - + +
761G LEU* 4.1 22.4 - - + -
766G GLU* 3.3 19.7 + - + -
770G LEU* 3.6 24.5 - - + -
797G LEU 3.1 19.7 + - - +
798G MET* 2.8 8.1 + - - +
800G GLN* 1.3 75.5 - - - +
802G MET* 1.3 61.7 + - + +
804G ALA* 2.8 23.7 + - + +
805G THR* 3.0 45.7 + - + +
869G THR* 3.9 17.7 - - - +
870G LEU* 4.2 22.4 + - + -
873G ILE* 3.8 20.4 - - + -
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Residues in contact with MET 802 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798G MET* 2.9 30.3 + - + +
799G GLU* 4.1 6.7 - - - +
801G TYR* 1.3 77.0 - - + +
803G LYS* 1.3 63.6 + - + +
804G ALA 3.0 0.2 - - - -
805G THR* 3.9 6.7 - - - -
806G ALA* 2.9 36.0 + - + +
870G LEU* 4.3 16.6 - - + -
874G TYR* 3.3 28.9 - - - -
899G PHE* 3.9 41.7 - - + +
903G ARG* 4.1 18.2 - - + +
904G LEU* 4.1 21.8 - - + -
915G PHE* 4.7 1.2 - - - -
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Residues in contact with LYS 803 (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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799G GLU* 3.0 31.6 + - + +
800G GLN* 4.0 8.5 - - - +
801G TYR 3.2 1.0 - - - -
802G MET* 1.3 81.2 - - + +
804G ALA* 1.3 56.1 + - - +
807G THR* 3.0 21.8 + - - -
903G ARG 3.6 18.3 + - - -
904G LEU* 3.3 14.1 + - - +
907G PRO* 5.2 5.1 - - - +
914G MET* 4.3 27.9 - - + +
915G PHE* 2.8 45.2 - - + -
63R GLU* 4.3 10.5 - - - -
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Residues in contact with ALA 804 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757G LEU* 5.6 2.9 - - + -
761G LEU* 6.1 4.5 - - + -
800G GLN 3.5 10.7 + - - +
801G TYR* 2.8 16.0 + - + +
803G LYS* 1.3 81.2 - - - +
805G THR* 1.3 64.6 + - + +
806G ALA 3.8 0.2 - - - -
807G THR* 4.6 5.4 + - - -
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Residues in contact with THR 805 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761G LEU* 5.8 2.5 - - + -
801G TYR* 3.0 53.5 + - + +
802G MET* 3.9 3.8 - - - -
804G ALA* 1.3 85.7 - - + +
806G ALA* 1.3 60.3 + - - +
807G THR 3.5 2.7 + - - -
808G GLN* 5.1 4.7 + - - +
809G PHE 5.6 0.3 + - - -
867G PRO* 3.3 30.1 - - - +
870G LEU* 4.5 8.8 - - - +
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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