Contacts of the helix formed by residues 855 - 857 (chain A) in PDB entry 4FYT
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 ARG 855 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A GLU* 3.0 25.3 + - - +
305A ARG* 3.9 8.7 - - - +
347A PRO* 3.5 21.6 + - - +
348A ASP* 2.8 39.2 + - - +
364A GLU* 6.0 0.2 - - - -
816A PHE* 5.7 1.4 - - - -
851A PRO 4.4 8.5 + - - +
853A LEU 4.2 0.6 + - - -
854A ILE* 1.3 75.7 - - - +
856A LYS* 1.3 59.6 + - - +
857A GLN* 3.8 22.9 - - + +
858A ASP* 2.8 28.7 + - - +
859A ALA* 3.4 6.9 + - - -
1024A SO4 2.7 43.6 + - - -
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Residues in contact with LYS 856 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ASP* 3.1 52.1 + - + +
189A ASP* 4.1 10.5 - - - +
190A LEU* 4.7 11.9 - - + -
348A ASP* 5.4 1.2 + - - -
851A PRO* 4.0 25.0 - - + +
854A ILE 3.4 2.3 + - - -
855A ARG* 1.3 72.1 - - - +
857A GLN* 1.3 63.3 + - - +
858A ASP 3.0 1.4 + - - -
859A ALA* 3.2 22.4 + - - +
860A THR 4.8 0.7 + - - -
890A ASP 4.9 13.1 + - - -
891A TYR* 5.3 10.6 - - + -
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Residues in contact with GLN 857 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A LEU* 4.1 16.0 - - + +
346A LEU 4.8 0.7 - - - +
347A PRO 3.3 21.5 + - - +
348A ASP* 3.4 4.6 + - + +
349A PHE* 3.0 47.3 + - - +
350A ASN* 4.8 1.3 - - - +
363A ARG* 2.9 37.8 + - - +
822A VAL* 5.4 12.3 - - - +
855A ARG* 3.8 16.7 - - + +
856A LYS* 1.3 76.6 - - - +
858A ASP* 1.3 83.3 + - - +
860A THR* 5.4 1.6 + - - -
861A SER* 5.2 4.2 + - - -
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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
------------------------------------------------------------
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