Contacts of the strand formed by residues 234 - 243 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B GLY 3.0 7.1 + - - -
165B PHE* 3.2 9.5 - - - +
166B HIS* 3.1 26.8 + - - -
232B PRO 5.7 0.4 - - - +
233B THR* 1.3 78.8 - - - +
235B TYR* 1.3 67.3 + - - +
236B LEU 3.4 0.3 + - - -
287B SER* 3.2 32.3 + - - +
288B ILE* 3.7 16.6 + - - +
289B ASP* 3.1 46.1 + - - +
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Residues in contact with TYR 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B HIS* 3.4 17.7 - - - +
167B ALA* 3.6 25.8 - - + -
169B ASP* 2.7 43.8 + - + +
195B TYR* 3.8 2.4 - - - -
209B ASP 4.6 0.6 + - - -
212B GLN* 3.2 20.7 - - + +
213B TRP* 3.3 53.1 - + + +
216B ASN* 4.0 16.8 - - + -
234B ARG* 1.3 72.4 - - - +
236B LEU* 1.3 66.0 + - - +
237B LYS 4.5 0.2 - - - -
274B PHE* 4.2 24.9 - + - -
287B SER 4.7 1.6 + - - -
288B ILE* 3.3 11.1 - - + +
289B ASP 2.9 23.0 + - - -
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Residues in contact with LEU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B PHE* 3.8 31.2 - - + -
167B ALA 3.0 17.5 + - - +
168B VAL* 3.7 5.7 - - + -
169B ASP* 2.8 31.2 + - - +
234B ARG 3.4 1.0 + - - -
235B TYR* 1.3 76.1 - - - +
237B LYS* 1.3 68.6 + - - +
238B ILE* 3.8 17.5 - - + -
289B ASP* 3.4 31.6 - - + +
290B ILE 3.8 9.6 - - - +
291B LEU* 4.1 4.9 - - + +
364B MET* 4.0 9.6 - - + -
367B PHE* 3.7 33.0 - - + -
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Residues in contact with LYS 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ASP* 3.0 36.0 + - - +
171B SER* 2.6 32.0 + - - +
197B LYS* 4.4 0.8 - - - +
204B PHE* 3.8 15.0 - - + -
209B ASP* 2.7 30.5 + - - +
235B TYR* 4.1 1.2 + - + -
236B LEU* 1.3 73.6 - - - +
238B ILE* 1.3 68.2 + - - +
271B LEU* 3.5 20.9 - - + +
274B PHE* 3.7 35.4 - - + -
288B ILE* 4.4 2.2 - - + -
289B ASP 2.9 12.0 + - - +
290B ILE* 3.3 5.2 - - + -
291B LEU 3.0 22.2 + - - -
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Residues in contact with ILE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B VAL* 3.8 25.4 - - + -
169B ASP 2.7 14.3 + - - +
170B ILE* 3.3 18.7 - - + -
171B SER 2.8 30.8 + - - -
186B LEU* 5.4 1.8 - - + -
188B LEU* 5.2 2.2 - - + -
236B LEU* 3.8 23.1 - - + -
237B LYS* 1.3 81.3 - - - +
239B ALA* 1.3 60.7 + - - +
240B VAL* 4.3 9.0 - - + -
271B LEU* 4.1 1.8 - - - -
291B LEU* 3.3 20.6 - - + +
293B ILE* 3.9 27.8 - - + -
367B PHE* 4.1 15.0 - - + -
371B LEU* 5.2 1.1 - - + -
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Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B SER 3.4 8.5 - - - +
202B SER* 5.0 2.2 - - - -
204B PHE* 4.3 13.0 - - + -
238B ILE* 1.3 72.0 - - - +
240B VAL* 1.3 64.6 + - - +
267B ALA* 3.9 22.2 - - + +
271B LEU* 3.7 27.6 - - + +
291B LEU 3.1 6.9 + - - +
292B LEU* 3.5 7.1 - - - +
293B ILE 3.1 23.6 + - - -
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Residues in contact with VAL 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ILE* 4.0 14.4 - - + -
171B SER 3.0 7.0 + - - +
172B PRO* 3.9 11.0 - - + -
173B CYS 3.6 11.1 + - - -
178B LEU* 4.3 12.2 - - + +
181B LEU* 4.0 31.0 - - + -
186B LEU* 5.5 0.7 - - + -
202B SER* 2.6 26.5 + - - -
238B ILE* 4.3 4.5 - - + -
239B ALA* 1.3 80.0 - - - +
241B TYR* 1.3 60.1 + - - +
267B ALA* 5.0 0.4 - - - -
293B ILE* 3.2 23.6 - - + +
295B VAL* 3.6 28.7 - - + -
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Residues in contact with TYR 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 5.0 0.2 - - - -
202B SER* 4.1 4.7 - - - +
240B VAL* 1.3 78.9 - - - +
242B HIS* 1.3 70.1 + - - +
243B PHE* 4.0 19.1 - + - -
260B ASP* 4.6 6.3 - - + -
263B ALA* 4.0 23.6 - - + +
264B LEU* 3.6 36.3 - - + +
267B ALA* 4.2 5.8 - - + -
292B LEU* 3.7 23.8 - - + -
293B ILE 2.9 22.2 + - - +
294B GLY* 3.4 25.4 - - - -
295B VAL 2.9 21.1 + - - -
303B ARG* 3.5 18.7 + - - -
305B HIS* 2.7 33.6 + - - -
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Residues in contact with HIS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B CYS* 3.6 18.7 - - + -
175B ASP* 3.4 23.7 + - + +
177B ARG* 4.0 3.5 + - - -
178B LEU* 3.7 17.5 - - + -
241B TYR* 1.3 80.7 - - - +
243B PHE* 1.3 66.8 + - - +
251B SER 5.0 0.2 + - - -
252B GLY* 3.5 8.3 - - - -
253B CYS* 3.5 35.5 + - + +
260B ASP* 4.6 2.3 - - - +
263B ALA* 4.6 7.9 - - - +
295B VAL* 3.1 16.2 - - + +
297B THR* 3.8 22.8 + - + +
720B ZN 2.1 36.1 - - - -
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Residues in contact with PHE 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B TYR* 4.0 22.0 - + - -
242B HIS* 1.3 78.4 + - - +
244B SER* 1.3 59.1 + - - +
245B THR* 4.0 20.2 - - + -
251B SER 4.8 0.2 - - - -
252B GLY* 4.4 8.1 - - - -
260B ASP* 3.4 36.8 - - + +
294B GLY* 4.0 6.3 - - - -
295B VAL* 2.9 24.7 + - - -
296B ASP* 3.1 35.3 - - + -
297B THR* 2.8 32.8 + - - -
301B ALA 5.3 0.9 - - - -
303B ARG* 3.8 37.5 - - + -
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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
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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