Contacts of the helix formed by residues 803 - 812 (chain C) in PDB entry 3V53
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 SER 803 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801C HIS 3.8 0.8 + - - -
802C SER* 1.3 75.2 - - - +
804C PRO* 1.3 73.3 - - - +
805C GLN* 4.3 5.5 - - - +
806C SER* 2.6 51.9 + - - -
807C ILE* 3.2 8.1 + - - +
827C TRP* 4.4 0.2 - - - -
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Residues in contact with PRO 804 (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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753C PHE* 3.6 50.7 - - + +
802C SER 3.6 0.2 - - - -
803C SER* 1.3 87.4 - - - +
805C GLN* 1.3 56.7 + - + +
807C ILE* 3.4 2.8 + - + +
808C LEU* 2.9 28.9 + - - +
823C ILE* 3.6 8.4 - - + +
827C TRP* 3.4 58.1 - - + +
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Residues in contact with GLN 805 (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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749C LYS* 3.2 34.7 + - - +
753C PHE* 3.4 15.8 - - + -
803C SER* 3.2 6.0 - - - +
804C PRO* 1.3 82.0 - - + +
806C SER* 1.3 57.4 + - - +
808C LEU* 3.2 12.7 - - - +
809C ASP* 2.8 63.0 + - - +
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Residues in contact with SER 806 (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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797C LYS* 6.4 0.9 - - - -
802C SER* 3.9 8.3 - - - -
803C SER* 2.6 42.9 + - - -
805C GLN* 1.3 79.6 - - - +
807C ILE* 1.3 61.4 + - - +
809C ASP* 3.2 11.9 + - - +
810C ASP* 3.0 33.2 + - - +
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Residues in contact with ILE 807 (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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793C PHE* 5.4 0.7 - - + -
794C VAL* 4.5 8.3 - - + +
797C LYS* 3.7 47.1 - - + +
798C VAL* 4.2 15.7 - - + +
802C SER* 3.9 8.3 - - - +
803C SER 3.2 14.9 + - - +
804C PRO* 3.7 6.3 - - + +
805C GLN 3.3 0.2 - - - -
806C SER* 1.3 75.3 + - - +
808C LEU* 1.3 64.2 + - - +
810C ASP* 3.1 9.3 + - - +
811C VAL* 2.9 34.3 + - + +
823C ILE* 3.8 21.3 - - + -
826C MET* 4.3 6.3 - - + -
827C TRP* 4.2 17.7 - - + -
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Residues in contact with LEU 808 (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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749C LYS* 4.3 3.8 - - - -
753C PHE* 3.7 30.7 - - + -
804C PRO 2.9 12.0 + - - +
805C GLN* 3.2 18.8 - - - +
807C ILE* 1.3 77.0 - - - +
809C ASP* 1.3 67.0 + - - +
811C VAL* 3.7 1.4 - - - +
812C ALA* 2.8 36.5 + - + +
819C ALA* 4.3 5.8 - - + +
820C GLU* 4.1 47.8 - - + +
823C ILE* 3.7 22.1 - - + +
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Residues in contact with ASP 809 (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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805C GLN* 2.8 51.5 + - - +
806C SER* 3.2 10.2 + - - +
808C LEU* 1.3 77.5 - - - +
810C ASP* 1.3 66.6 + - - +
812C ALA* 3.7 14.8 - - - +
813C MET* 3.8 15.2 - - - +
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Residues in contact with ASP 810 (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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793C PHE* 3.8 30.1 - - + -
797C LYS* 4.4 12.0 + - - -
806C SER* 3.0 22.1 + - - +
807C ILE* 3.6 8.1 - - - +
809C ASP* 1.3 76.4 - - - +
811C VAL* 1.3 65.9 + - - +
812C ALA 3.0 1.6 - - - -
813C MET* 3.0 28.2 + - - +
814C VAL* 4.3 2.6 + - - +
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Residues in contact with VAL 811 (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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779C ILE* 5.8 0.7 - - + -
793C PHE* 4.4 11.0 - - + -
794C VAL* 3.8 27.4 - - + -
807C ILE* 2.9 33.6 + - + +
808C LEU* 4.0 2.2 - - - +
810C ASP* 1.3 71.4 - - - +
812C ALA* 1.3 55.4 + - - +
814C VAL* 3.0 14.5 + - + +
815C LEU* 2.9 50.3 + - + -
819C ALA* 4.4 5.8 - - + -
822C PHE* 4.0 16.4 - - + -
823C ILE* 4.5 7.4 - - + -
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Residues in contact with ALA 812 (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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808C LEU* 2.8 22.7 + - + +
809C ASP* 3.7 13.0 - - - +
810C ASP 3.0 0.6 - - - -
811C VAL* 1.3 77.7 - - - +
813C MET* 1.3 63.9 + - - +
814C VAL 3.2 0.4 + - - -
815C LEU 3.8 3.8 - - - +
816C ASP* 3.7 27.1 + - - +
819C ALA* 3.7 20.4 - - + +
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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