Contacts of the helix formed by residues 268 - 271 (chain A) in PDB entry 1F9O
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 268 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ILE* 3.8 24.4 - - + +
139A GLN* 2.9 31.5 + - - -
140A LEU* 4.2 9.3 - - - +
264A GLY 4.7 0.2 - - - -
265A ASP* 3.1 29.6 + - - +
266A TYR 3.0 0.6 - - - -
267A LEU* 1.3 73.0 - - - +
269A TYR* 1.3 63.1 + - - +
270A SER 3.0 2.7 - - - -
271A PHE* 3.0 40.1 + - + +
272A PHE* 3.5 8.5 - - + -
289A TYR* 3.5 3.6 + - - -
342A SER* 3.0 20.8 + - - -
344A ASN 3.7 5.5 - - - -
345A GLY* 3.9 11.2 - - - -
348A ASP* 2.6 51.7 + - - +
349A TRP* 3.6 20.4 - - - +
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Residues in contact with TYR 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ASP* 2.7 38.2 + - - -
136A ILE* 3.7 18.1 - - + +
137A ASN* 3.0 26.6 + - - +
140A LEU* 3.8 18.2 - - + -
149A LEU* 4.3 30.1 - - + -
266A TYR* 3.2 18.5 + + - +
267A LEU 3.1 1.6 + - - -
268A ARG* 1.3 77.2 - - - +
270A SER* 1.3 60.3 + - - +
271A PHE 3.1 1.4 + - - -
272A PHE* 3.3 15.7 + + - +
276A PHE* 4.3 13.2 - + - -
300A TYR* 3.6 24.7 - + + -
313A ILE* 3.7 25.2 - - + +
314A ILE 5.5 1.1 - - - -
315A GLY* 3.7 16.3 - - - -
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Residues in contact with SER 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PRO* 3.8 25.4 - - - -
267A LEU* 2.8 21.9 + - - +
269A TYR* 1.3 78.3 - - - +
271A PHE* 1.3 61.8 + - - +
272A PHE 3.2 1.9 + - - +
293A HIS* 3.0 14.7 + - - -
295A LEU 3.1 2.7 - - - +
296A LEU* 3.5 21.8 - - - +
297A SER* 2.7 35.9 + - - -
299A TYR 4.4 0.9 - - - -
300A TYR* 3.9 11.6 - - - -
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Residues in contact with PHE 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ARG* 3.0 37.2 + - + +
270A SER* 1.3 82.5 - - - +
272A PHE* 1.3 65.0 + + + +
289A TYR* 6.4 0.4 - + - -
292A ALA* 3.3 5.5 - - + -
293A HIS* 2.8 35.9 + - - -
294A TYR* 3.9 28.0 - + - +
295A LEU 3.3 20.0 - - - -
296A LEU* 4.0 10.8 - - + -
348A ASP* 3.9 18.8 - - + -
349A TRP* 3.6 35.4 - + - -
352A SER* 3.6 35.0 - - - -
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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