Contacts of the strand formed by residues 234 - 243 (chain A) in PDB entry 2FGY
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 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A GLY 2.9 7.4 + - - +
165A PHE* 3.1 10.7 - - - +
166A HIS* 3.0 26.6 + - - -
232A PRO 5.6 1.1 - - - +
233A THR* 1.3 79.7 - - - +
235A TYR* 1.3 69.4 + - - +
236A LEU 3.5 0.5 + - - -
287A SER* 3.3 29.6 + - - +
288A ILE* 3.7 19.0 + - - +
289A ASP* 3.1 42.3 + - - +
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Residues in contact with TYR 235 (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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166A HIS* 3.4 18.2 - - - +
167A ALA* 3.4 28.5 - - + -
169A ASP* 2.6 45.2 + - + +
195A TYR* 3.8 2.9 - + - -
209A ASP 4.5 1.0 + - - -
212A GLN* 3.2 20.8 - - + +
213A TRP* 3.4 52.0 - + + +
216A ASN* 4.0 17.5 - - + -
234A ARG* 1.3 73.0 - - - +
236A LEU* 1.3 66.2 + - - +
274A PHE* 4.3 24.7 - + - -
287A SER 4.8 1.4 + - - -
288A ILE* 3.3 10.7 - - + +
289A ASP 2.9 23.4 + - - -
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Residues in contact with LEU 236 (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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165A PHE* 3.8 31.4 - - + -
167A ALA 3.0 16.7 + - - +
168A VAL* 3.6 6.6 - - + -
169A ASP* 2.8 35.0 + - - +
234A ARG 3.5 0.8 + - - -
235A TYR* 1.3 76.1 - - - +
237A LYS* 1.3 63.5 + - - +
238A ILE* 3.9 17.3 - - + -
289A ASP* 3.5 32.5 - - + +
290A ILE 3.9 9.4 - - - +
291A LEU* 4.2 4.7 - - + -
364A MET* 4.0 9.2 - - + -
367A PHE* 3.7 32.8 - - + -
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Residues in contact with LYS 237 (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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169A ASP* 2.9 38.1 + - - +
171A SER* 2.6 33.2 + - - -
197A LYS* 4.4 1.0 - - - +
204A PHE* 3.9 13.4 - - + -
209A ASP* 2.6 30.7 + - - +
235A TYR* 4.1 1.2 + - + -
236A LEU* 1.3 71.9 - - - +
238A ILE* 1.3 69.4 + - - +
271A LEU* 3.5 21.1 - - + +
274A PHE* 3.8 34.8 - - + -
288A ILE* 4.5 2.9 - - + -
289A ASP 3.0 12.0 + - - +
290A ILE* 3.3 5.8 - - + -
291A LEU 3.1 22.0 + - - -
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Residues in contact with ILE 238 (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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168A VAL* 3.8 26.0 - - + -
169A ASP 2.7 15.1 + - - +
170A ILE* 3.4 17.3 - - + -
171A SER 2.8 25.9 + - - -
186A LEU* 5.6 1.3 - - + -
188A LEU* 5.3 1.8 - - + -
236A LEU* 3.9 22.9 - - + -
237A LYS* 1.3 81.5 - - - +
239A ALA* 1.3 68.5 + - - +
240A VAL* 4.2 9.6 - - + -
271A LEU* 4.0 2.0 - - - -
291A LEU* 3.3 20.9 - - + +
293A ILE* 3.7 28.5 - - + -
367A PHE* 4.1 13.9 - - + -
371A LEU* 5.2 1.3 - - + -
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Residues in contact with ALA 239 (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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171A SER* 3.4 8.5 - - - +
202A SER* 5.1 2.2 - - - -
204A PHE* 4.3 11.9 - - + -
238A ILE* 1.3 72.6 - - - +
240A VAL* 1.3 65.1 + - - +
241A TYR 4.2 0.2 - - - -
267A ALA* 3.8 23.6 - - + +
271A LEU* 3.7 28.4 - - + +
291A LEU 3.1 7.1 + - - +
292A LEU* 3.6 6.1 - - + +
293A ILE 3.0 23.9 + - - +
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Residues in contact with VAL 240 (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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170A ILE* 4.0 14.4 - - + -
171A SER 3.0 7.5 + - - -
172A PRO* 3.9 10.8 - - + -
173A CYS 3.5 11.1 + - - -
178A LEU* 4.4 10.6 - - + +
181A LEU* 3.9 30.1 - - + -
186A LEU* 5.6 0.4 - - + -
202A SER* 2.7 25.6 + - - -
238A ILE* 4.2 4.5 - - + -
239A ALA* 1.3 80.3 - - - +
241A TYR* 1.3 58.1 + - - +
267A ALA* 5.1 0.9 - - - -
293A ILE* 3.2 24.9 - - + +
295A VAL* 3.6 28.7 - - + -
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Residues in contact with TYR 241 (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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202A SER* 4.2 4.7 - - - +
240A VAL* 1.3 79.5 - - - +
242A HIS* 1.3 68.8 + - - +
243A PHE* 4.0 20.6 - + + -
253A CYS* 6.6 0.2 - - - -
260A ASP* 4.6 6.3 - - + -
263A ALA* 3.9 23.8 - - + +
264A LEU* 3.6 34.5 - - + +
267A ALA* 4.3 5.6 - - + -
292A LEU* 3.7 23.8 - - + -
293A ILE 3.0 22.7 + - - -
294A GLY* 3.4 25.5 - - - -
295A VAL 2.9 21.5 + - - -
303A ARG* 3.4 19.2 + - - -
305A HIS* 2.7 32.6 + - - -
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Residues in contact with HIS 242 (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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173A CYS* 3.6 16.8 - - + -
175A ASP* 3.2 24.1 + - - +
177A ARG* 4.0 3.5 + - - -
178A LEU* 3.8 19.7 - - + -
241A TYR* 1.3 79.7 - - - +
243A PHE* 1.3 67.5 + - - +
252A GLY* 3.5 22.1 - - - -
253A CYS* 3.6 23.0 + - + +
260A ASP* 4.5 2.9 - - - +
263A ALA* 4.6 7.3 - - - +
295A VAL 3.1 15.0 - - - +
297A THR* 3.7 23.1 + - + +
620A ZN 2.1 36.0 - - - -
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Residues in contact with PHE 243 (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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241A TYR* 4.0 24.5 - + - -
242A HIS* 1.3 81.2 + - - +
244A SER* 1.3 57.8 + - - +
245A THR* 4.0 21.3 - - + -
251A SER 4.8 0.2 - - - -
252A GLY* 4.4 7.9 - - - -
260A ASP* 3.3 36.6 - - + +
294A GLY* 4.1 4.0 - - - -
295A VAL 2.9 23.0 + - - -
296A ASP* 3.2 33.7 - - + -
297A THR* 2.8 33.8 + - - -
301A ALA 5.4 0.7 - - - -
303A ARG* 3.9 37.7 - - + -
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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