Contacts of the helix formed by residues 804 - 810 (chain A) in PDB entry 5C51
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 804 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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800A PHE* 3.4 37.4 + - + +
801A TRP* 4.8 1.1 - - - -
802A ARG 3.4 1.4 + - - -
803A ASN* 1.3 80.1 - - - +
805A HIS* 1.3 69.8 + - - +
806A LYS 3.1 2.9 - - - -
807A ARG* 2.9 39.1 + - - +
808A ILE* 2.9 22.8 + - + +
10T G 4.8 1.5 - - - -
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Residues in contact with HIS 805 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A GLN* 4.3 11.9 + - - +
452A TYR* 5.0 11.4 + + - -
801A TRP* 3.1 59.6 + + + +
802A ARG* 3.4 20.2 + - - -
804A ALA* 1.3 77.6 - - - +
806A LYS* 1.3 69.3 + - + +
808A ILE* 4.5 3.1 - - - -
809A SER* 2.7 42.4 + - - -
10T G 5.3 2.7 + - - -
11T C 4.6 10.3 + - - -
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Residues in contact with LYS 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804A ALA* 3.0 1.7 + - - +
805A HIS* 1.3 100.2 - - + +
807A ARG* 1.3 57.6 + - + +
809A SER* 3.3 5.1 + - - -
810A SER* 2.4 46.9 + - - +
10T G 3.4 35.4 - - - +
11T C 6.1 0.9 - - - -
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Residues in contact with ARG 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800A PHE* 5.1 2.2 - - - -
803A ASN 3.0 28.8 + - - -
804A ALA* 2.9 22.1 + - - +
806A LYS* 1.3 81.8 - - + +
808A ILE* 1.3 58.2 + - + +
810A SER* 3.7 5.6 + - - -
811A GLN* 3.2 32.9 + - - +
857A PRO* 2.8 31.5 + - - -
858A THR* 3.2 22.8 + - + +
861A THR* 3.2 26.2 + - - -
8T T 5.0 2.7 + - - -
9T G 3.4 52.2 + - - +
10T G 5.1 2.0 - - - +
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Residues in contact with ILE 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A TRP* 3.5 15.7 - - + -
444A TYR* 3.9 16.4 - - + -
445A LEU* 4.2 5.5 - - + +
800A PHE* 5.1 6.5 - - + -
801A TRP* 4.1 22.2 - - + -
804A ALA* 2.9 34.8 + - + +
805A HIS* 4.0 3.4 - - - +
807A ARG* 1.3 77.0 - - + +
809A SER* 1.3 65.3 + - - +
811A GLN* 3.2 19.3 - - - +
858A THR* 3.6 26.2 - - + +
874A LEU* 3.6 41.1 - - + -
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Residues in contact with SER 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A LEU* 4.1 25.8 - - - +
449A GLN* 5.8 4.0 - - - -
801A TRP* 5.8 3.8 - - - -
805A HIS* 2.7 25.9 + - - -
806A LYS* 3.3 6.4 + - - -
808A ILE* 1.3 77.4 - - - +
810A SER* 1.3 62.1 + - - +
811A GLN 3.2 3.7 + - - +
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Residues in contact with SER 810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A THR* 4.5 10.0 - - - +
806A LYS* 2.4 33.6 + - - +
807A ARG* 3.7 6.2 + - - -
809A SER* 1.3 77.5 + - - +
811A GLN* 1.3 53.8 + - - +
812A MET* 2.8 22.1 + - - +
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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