Contacts of the strand formed by residues 255 - 257 (chain A) in PDB entry 1FR8
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 LEU 255 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GDU 5.2 0.9 - - - +
198A TRP* 3.4 16.5 + - - -
251A SER* 4.4 1.6 + - - -
252A ASP* 3.6 8.8 + - + +
253A VAL 3.2 4.4 + - - -
254A ASP* 1.3 100.5 - - - +
256A ILE* 1.3 73.5 + - - +
257A PRO* 4.4 2.6 - - - +
264A TYR* 4.6 3.7 + - - -
274A SER* 3.6 15.9 - - - -
277A MET* 3.6 20.2 - - + -
279A LYS* 4.9 5.2 - - - +
292A GLY* 3.5 31.6 - - - -
293A VAL* 3.6 23.3 - - + -
342A CYS* 5.3 3.4 - - + -
343A ARG 3.4 7.4 - - - +
344A MET* 3.8 18.4 - - + -
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Residues in contact with ILE 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ILE* 4.1 15.9 - - + -
149A PHE* 4.0 27.1 - - + -
197A TYR 4.4 3.8 - - - +
198A TRP* 3.7 26.5 - - + +
201A TYR* 3.6 28.0 - - + -
202A LEU* 3.7 15.0 - - + -
205A ILE* 5.0 1.1 - - + -
255A LEU* 1.3 86.1 - - - +
257A PRO* 1.3 79.8 - - + +
264A TYR* 4.9 0.2 - - - -
342A CYS* 3.2 6.3 - - - -
343A ARG* 2.8 37.5 + - - +
345A ILE* 4.1 11.7 - - + -
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Residues in contact with PRO 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A MET* 3.3 13.5 - - + +
147A ILE* 3.9 3.3 - - - +
202A LEU* 3.7 14.6 - - + -
205A ILE* 3.8 21.4 - - + +
209A GLN* 6.1 0.2 - - - +
255A LEU 4.4 0.2 - - - +
256A ILE* 1.3 99.2 - - + +
258A MET* 1.3 60.9 + - - +
259A ASN 3.3 8.7 - - - +
260A ASP* 6.1 0.2 - - - -
262A ASN* 4.3 16.2 - - + +
264A TYR* 3.5 39.7 - - + +
341A LYS 3.8 5.4 - - - +
342A CYS* 3.8 6.5 - - - -
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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
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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