Contacts of the helix formed by residues 920 - 929 (chain C) in PDB entry 4AY6
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 HIS 920 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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656C PRO* 3.8 18.6 - - + -
694C PHE* 3.2 23.9 - + + -
917C CYS* 4.7 0.2 - - - -
918C ASN* 3.1 24.2 + - + -
919C GLY* 1.3 75.1 - - - -
921C THR* 1.3 67.8 + - - +
922C THR 3.1 0.4 - - - +
923C GLY 3.3 3.8 + - - -
924C MET* 3.5 1.0 - - - +
942C ALA* 2.9 38.0 + - + -
945C VAL* 3.7 28.0 - - + +
949C GLN* 3.0 22.7 + - - -
1200C 12V 2.8 60.2 + - + +
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Residues in contact with THR 921 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559C PRO* 3.8 12.3 - - + +
562C HIS* 5.4 0.2 - - + -
563C LEU* 3.8 21.0 - - + +
694C PHE* 3.9 7.1 - - - -
698C HIS* 5.4 0.4 - - + +
898C LYS* 3.4 29.6 - - - +
920C HIS* 1.3 77.1 - - - +
922C THR* 1.3 59.1 + - - +
924C MET* 2.9 25.2 + - - +
925C ASP* 3.0 13.3 + - - +
1200C 12V 2.9 50.4 + - - +
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Residues in contact with THR 922 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837C PHE* 4.2 32.6 + - + +
838C ASN* 4.0 30.1 + - - +
901C HIS* 4.7 8.9 + - + +
919C GLY* 4.3 2.0 - - - -
920C HIS 3.1 0.2 - - - -
921C THR* 1.3 75.3 - - - +
923C GLY* 1.3 65.8 + - - +
925C ASP* 2.9 20.8 + - + +
926C VAL* 3.0 19.8 + - + +
1200C 12V 3.3 26.7 + - - -
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Residues in contact with GLY 923 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919C GLY* 3.6 13.9 - - - -
920C HIS 3.3 5.6 + - - -
921C THR 3.2 1.2 - - - -
922C THR* 1.3 79.2 - - - +
924C MET* 1.3 61.3 + - - +
926C VAL* 3.4 3.2 - - - +
927C LEU* 3.1 27.6 + - - +
933C MET* 4.2 16.2 - - - -
949C GLN* 3.5 22.0 - - - -
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Residues in contact with MET 924 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563C LEU* 4.4 4.5 - - + -
694C PHE* 3.7 16.2 - - + -
695C ILE* 3.9 5.4 - - - -
696C GLY 3.7 21.8 - - - +
698C HIS* 3.2 25.8 - - + -
920C HIS 3.5 13.7 - - - +
921C THR* 2.9 8.7 + - - +
923C GLY* 1.3 75.8 - - - +
925C ASP* 1.3 63.8 + - - +
927C LEU* 4.7 1.3 - - - -
928C TRP* 2.9 20.8 + - - +
949C GLN* 3.2 29.8 - - - +
996C LEU* 3.9 26.5 - - + +
997C PHE* 3.2 35.9 - - + -
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Residues in contact with ASP 925 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698C HIS* 2.6 35.8 + - - -
898C LYS* 3.7 14.8 + - - -
901C HIS* 3.3 18.9 + - + +
902C VAL* 3.7 24.4 - - + +
921C THR* 3.0 10.7 + - - +
922C THR* 2.9 16.6 + - + +
924C MET* 1.3 80.8 - - - +
926C VAL* 1.3 61.0 + - - +
928C TRP* 3.4 12.0 + - - +
929C ALA* 3.5 10.4 + - - +
1200C 12V 2.6 31.1 + - - -
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Residues in contact with VAL 926 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835C CYS* 4.3 9.0 - - - -
837C PHE* 5.0 12.1 - - + -
905C GLY* 5.0 5.8 - - - +
911C CYS* 3.8 29.6 - - + -
922C THR* 3.0 17.9 + - + +
923C GLY* 3.4 14.6 - - - +
925C ASP* 1.3 74.4 - - - +
927C LEU* 1.3 72.3 + - + +
929C ALA* 3.4 7.8 + - - +
931C THR* 3.2 54.7 + - + +
933C MET* 4.3 9.6 - - + -
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Residues in contact with LEU 927 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923C GLY 3.1 19.0 + - - +
924C MET* 3.7 4.0 - - - +
926C VAL* 1.3 78.1 - - + +
928C TRP* 1.3 59.9 + - - +
930C GLY* 2.9 19.4 + - - -
931C THR 3.4 20.6 - - - +
932C PRO* 4.6 0.7 - - + -
933C MET* 3.9 35.2 - - + +
949C GLN* 4.4 13.9 - - + +
950C LEU* 4.5 8.1 - - + -
953C LEU* 4.2 23.1 - - + -
987C VAL* 3.9 9.6 - - + +
991C ARG* 3.8 10.1 - - + +
996C LEU* 4.1 22.0 - - + -
997C PHE* 4.2 11.9 - - + -
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Residues in contact with TRP 928 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698C HIS* 3.7 23.8 + - + -
699C ALA* 3.6 29.4 - - + -
702C PHE* 3.3 32.7 + - + +
705C LEU* 3.6 26.4 - - + +
706C LYS* 3.9 17.5 - - + -
902C VAL* 4.2 6.7 - - + -
924C MET 2.9 16.5 + - - +
925C ASP 3.6 6.7 - - - +
926C VAL 3.3 0.4 - - - -
927C LEU* 1.3 77.3 - - - +
929C ALA* 1.3 57.9 + - - +
930C GLY 3.1 0.7 + - - -
991C ARG* 2.8 48.7 + - + +
992C ILE* 3.9 31.2 - - + -
997C PHE* 3.6 47.0 - + + -
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Residues in contact with ALA 929 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705C LEU* 5.7 4.7 - - + -
708C LYS* 4.7 2.4 + - - -
902C VAL* 3.7 20.0 - - + +
905C GLY* 3.7 8.3 - - - +
906C GLN* 3.7 46.6 - - + +
925C ASP 3.5 4.9 + - - +
926C VAL 3.4 9.5 + - - +
927C LEU 3.1 1.2 - - - -
928C TRP* 1.3 79.5 - - - +
930C GLY* 1.3 60.3 + - - +
931C THR* 3.3 4.0 + - - -
984C ARG* 4.7 1.4 + - - -
988C TRP* 3.9 12.6 - - - -
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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