Contacts of the helix formed by residues 905 - 910 (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 ILE 905 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809G PHE* 3.5 35.2 - - + -
810G VAL* 4.4 11.7 - - + -
813G ALA* 5.0 1.6 - - + -
814G LEU* 3.8 23.6 - - + +
859G ILE* 4.1 23.3 - - + -
900G VAL* 2.9 31.6 + - + +
901G PHE* 3.1 22.6 + - + -
904G LEU* 1.3 74.2 - - + +
906G CYS* 1.3 68.6 + - - +
908G ALA* 3.1 6.5 + - - +
909G ILE* 3.0 40.9 + - + +
937G VAL* 4.6 1.3 - - + -
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Residues in contact with CYS 906 (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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901G PHE* 3.1 12.4 + - - +
905G ILE* 1.3 75.8 - - - +
907G PRO* 1.3 71.1 - - + +
909G ILE* 2.9 20.5 + - - +
910G LEU* 3.0 19.5 + - - +
934G ALA* 3.6 28.4 - - + +
937G VAL* 4.2 23.1 - - - -
938G GLN* 3.3 25.1 - - - +
36R ILE* 4.3 3.6 - - + -
64R TYR* 3.4 13.9 - - - +
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Residues in contact with PRO 907 (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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803G LYS* 5.2 5.4 - - - +
901G PHE 3.4 4.0 - - - +
902G LEU 3.1 28.5 - - - +
903G ARG* 4.0 12.3 - - - +
904G LEU* 3.7 8.1 - - - +
905G ILE 3.7 2.5 - - - -
906G CYS* 1.3 88.3 - - - +
908G ALA* 1.3 56.4 + - - +
909G ILE 3.2 0.3 + - - -
910G LEU* 3.2 3.6 + - + +
911G ASN* 2.8 33.2 + - - +
914G MET* 5.0 8.7 - - + -
63R GLU* 4.2 22.2 - - + +
64R TYR* 3.3 24.0 - - + +
67R MET* 5.8 0.2 - - - +
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Residues in contact with ALA 908 (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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810G VAL* 3.8 4.5 - - + -
814G LEU* 3.7 16.4 - - + -
818G ILE* 3.8 8.8 - - - +
904G LEU 3.3 11.2 + - - +
905G ILE 3.1 6.8 + - - +
907G PRO* 1.3 78.4 - - - +
909G ILE* 1.3 60.9 + - - +
911G ASN 3.9 7.9 - - - -
912G PRO* 3.4 22.6 - - - +
914G MET* 4.9 0.4 - - - -
915G PHE* 3.3 37.6 - - + -
917G ILE* 4.3 1.6 - - + +
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Residues in contact with ILE 909 (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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814G LEU* 4.0 15.7 - - + -
818G ILE* 4.4 10.7 - - + +
821G ILE* 6.1 0.7 - - + -
855G LEU* 4.8 8.1 - - + -
905G ILE* 3.1 27.8 - - + +
906G CYS* 2.9 18.3 + - - +
908G ALA* 1.3 76.5 - - - +
910G LEU* 1.3 62.2 + - - +
911G ASN 3.5 0.2 + - - -
912G PRO* 4.0 4.9 - - - +
930G LEU* 3.3 53.7 - - + +
933G VAL* 4.4 11.4 - - + -
934G ALA* 3.7 18.6 - - + +
937G VAL* 4.2 16.2 - - + -
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Residues in contact with LEU 910 (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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906G CYS 3.0 13.6 + - - +
907G PRO* 3.9 4.3 - - + +
909G ILE* 1.3 75.6 - - - +
911G ASN* 1.3 59.2 + - - +
912G PRO* 3.7 5.2 - - - +
922G PRO* 5.4 2.1 - - - +
930G LEU* 3.3 37.7 - - + +
931G ILE* 3.5 31.0 - - + -
934G ALA* 3.8 7.6 - - + -
36R ILE* 3.6 24.7 - - + +
37R GLU* 6.4 0.2 - - + -
64R TYR* 3.6 29.4 - - + -
67R MET* 3.9 32.4 - - + +
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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