Contacts of the helix formed by residues 879 - 888 (chain C) in PDB entry 4YZ9
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 THR 879 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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835A LEU* 5.7 1.6 - - - +
927A ASP* 5.6 1.2 - - - +
928A ASP* 3.0 18.4 + - - -
931A CYS* 4.4 17.4 - - - +
878C ILE* 1.3 77.3 - - - +
880C VAL* 1.3 61.6 + - - +
881C PRO* 3.7 5.8 - - + +
882C LEU* 3.8 5.2 - - - +
883C GLN* 2.9 25.3 + - - +
921C THR* 3.4 36.6 - - + +
932C TYR* 3.0 27.4 + - + +
936C ARG* 4.8 11.1 - - - +
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Residues in contact with VAL 880 (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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835A LEU* 5.1 15.7 - - + -
927A ASP* 6.1 0.7 - - - +
878C ILE 5.5 0.4 - - - +
879C THR* 1.3 74.1 + - - +
881C PRO* 1.3 69.8 - - + +
883C GLN* 2.9 20.2 + - + +
884C THR* 2.8 41.3 + - - +
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Residues in contact with PRO 881 (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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924A SER* 5.6 2.5 - - - +
927A ASP* 6.1 6.1 - - + +
928A ASP* 4.6 4.9 - - - +
879C THR* 3.7 13.2 - - + +
880C VAL* 1.3 96.3 - - + +
882C LEU* 1.3 60.5 + - - +
884C THR* 3.4 6.8 + - - +
885C ASP* 3.1 21.7 + - - +
917C GLU* 3.7 40.0 - - + +
918C VAL* 3.8 7.1 - - - +
921C THR* 3.3 24.5 - - + -
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Residues in contact with LEU 882 (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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878C ILE* 3.9 14.8 - - + -
879C THR* 3.4 9.0 + - + +
880C VAL 3.3 0.6 - - - -
881C PRO* 1.3 75.8 - - - +
883C GLN* 1.3 65.1 + - - +
885C ASP* 3.4 2.8 + - + -
886C LEU* 3.2 46.7 + - + +
907C LYS* 4.3 17.3 - - + -
918C VAL* 4.2 22.2 - - + +
921C THR* 4.3 7.9 - - - +
922C LEU* 4.6 9.4 - - + -
932C TYR* 3.3 41.3 - - + +
933C PHE* 4.1 16.4 - - + -
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Residues in contact with GLN 883 (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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875C ARG* 3.4 32.0 + - + +
876C GLU* 4.4 17.3 + - - +
878C ILE* 3.9 20.4 + - + +
879C THR 2.9 11.9 + - - +
880C VAL* 2.9 24.1 + - + +
882C LEU* 1.3 77.5 - - - +
884C THR* 1.3 64.0 + - - +
886C LEU* 3.5 1.9 + - - +
887C ARG* 2.8 50.7 + - - +
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Residues in contact with THR 884 (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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880C VAL* 2.8 29.4 + - - +
881C PRO* 3.7 10.1 - - - +
883C GLN* 1.3 75.0 - - - +
885C ASP* 1.3 63.1 + - - +
886C LEU 3.4 0.3 + - - -
887C ARG* 3.4 28.1 + - - +
888C LYS* 4.0 4.5 + - - +
917C GLU* 4.7 9.0 - - - +
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Residues in contact with ASP 885 (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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881C PRO 3.1 13.7 + - - +
882C LEU* 3.9 6.7 - - + +
883C GLN 3.3 0.2 - - - -
884C THR* 1.3 79.9 - - - +
886C LEU* 1.3 60.4 + - + +
888C LYS* 3.3 38.6 + - - +
889C PHE* 3.4 6.6 - - - -
907C LYS* 3.1 32.4 + - - -
914C LEU* 4.6 3.2 - - - +
915C PRO* 3.9 24.4 - - - +
917C GLU* 5.9 0.2 - - - +
918C VAL* 4.1 18.6 - - + -
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Residues in contact with LEU 886 (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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874C TRP* 3.8 29.6 - - + -
875C ARG* 6.3 4.7 - - + -
878C ILE* 4.2 6.5 - - + -
882C LEU* 3.2 39.0 + - + +
883C GLN* 4.3 2.7 - - - +
885C ASP* 1.3 74.0 - - - +
887C ARG* 1.3 61.9 + - - +
888C LYS 3.0 7.1 + - - -
889C PHE* 3.2 23.4 + - + +
892C TYR* 3.7 30.2 - - + +
903C ALA* 4.3 10.5 - - + -
907C LYS* 3.5 39.3 - - + +
933C PHE* 6.3 1.3 - - + -
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Residues in contact with ARG 887 (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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875C ARG* 6.0 6.3 - - - +
876C GLU* 5.6 0.8 + - - -
883C GLN* 2.8 54.2 + - - +
884C THR* 3.7 22.7 + - - +
885C ASP 3.4 0.4 - - - -
886C LEU* 1.3 76.1 - - - +
888C LYS* 1.3 61.4 + - - +
889C PHE 3.1 7.2 + - - +
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Residues in contact with LYS 888 (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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884C THR 4.0 4.2 + - - +
885C ASP* 3.3 33.8 + - - +
886C LEU 3.0 0.2 - - - -
887C ARG* 1.3 78.8 - - - +
889C PHE* 1.3 88.9 + - + +
890C ARG* 4.1 2.6 + - - +
915C PRO* 6.1 0.4 - - - +
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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