Contacts of the strand formed by residues 771 - 773 (chain G) in PDB entry 6BAA
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 771 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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770G VAL* 1.3 83.3 - - - +
772G TYR* 1.3 62.8 + - - +
843G ALA* 4.5 22.9 - - + +
846G GLN* 5.4 3.8 - - + -
848G THR* 3.8 13.0 - - - -
850G VAL 2.8 20.0 + - - +
851G VAL* 4.0 13.0 - - + -
852G PHE* 3.3 23.3 + - - +
1217G PHE* 3.9 7.2 - - + -
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Residues in contact with TYR 772 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723G LEU* 4.9 23.6 - - + +
724G LEU* 5.8 1.6 + - - -
727G LEU* 5.6 6.3 - - + -
770G VAL* 5.8 0.2 - - + -
771G ALA* 1.3 77.7 - - - +
773G ALA* 1.3 71.2 + - - +
774G SER* 3.5 34.6 + - - -
775G GLN 4.6 2.3 + - - -
839G SER* 5.2 2.4 - - - +
843G ALA* 4.5 9.3 - - - +
852G PHE* 3.6 14.6 - - + -
854G ASP* 5.9 1.1 - - + -
1212G THR* 4.8 14.1 - - + +
1213G THR* 3.8 37.7 - - + +
1216G ALA* 4.6 18.2 - - + -
1217G PHE* 3.3 31.7 - - + -
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Residues in contact with ALA 773 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772G TYR* 1.3 79.8 - - - +
774G SER* 1.3 66.3 + - - +
839G SER* 5.4 14.8 - - - +
840G VAL* 5.6 3.6 - - - +
843G ALA* 5.3 9.2 - - + -
852G PHE 2.7 19.6 + - - +
853G LEU* 3.8 15.7 - - + -
854G ASP* 3.3 22.5 + - - +
856G PRO* 6.1 2.5 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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