Contacts of the strand formed by residues 288 - 296 (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 ILE 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A TRP* 3.7 27.6 - - + +
234A ARG* 3.7 13.7 - - - +
235A TYR* 3.3 19.7 - - + +
237A LYS* 4.5 1.1 - - + -
274A PHE* 3.4 36.8 - - + +
275A ARG* 3.0 53.8 + - + +
278A VAL* 4.0 12.8 - - + -
279A GLU* 5.3 0.2 + - - -
287A SER* 1.3 83.3 - - - +
289A ASP* 1.3 64.3 + - - +
290A ILE* 3.8 17.0 - - + -
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Residues in contact with ASP 289 (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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164A GLY 4.3 1.9 - - - +
165A PHE* 3.2 25.8 - - + -
234A ARG* 3.1 45.9 + - - +
235A TYR 2.9 9.9 + - - +
236A LEU* 3.5 17.3 - - + -
237A LYS 3.0 24.1 + - - -
275A ARG* 3.9 4.6 + - - +
288A ILE* 1.3 78.3 - - - +
290A ILE* 1.3 65.5 + - - +
311A GLY* 5.4 5.2 - - - -
364A MET* 4.1 9.0 - - + +
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LEU* 4.0 1.8 - - - -
237A LYS* 3.3 10.1 - - + +
268A LEU* 4.9 0.4 - - + -
271A LEU* 3.9 40.8 - - + +
272A MET* 4.6 14.1 - - + +
275A ARG* 3.5 33.0 - - + +
288A ILE* 3.8 22.7 - - + -
289A ASP* 1.3 80.5 - - - +
291A LEU* 1.3 64.4 + - - +
307A PRO* 4.1 10.4 - - - +
311A GLY 3.7 8.4 + - - +
312A PHE* 5.4 0.2 - - - -
313A LEU* 3.7 26.9 - - + +
364A MET* 4.0 12.3 - - - +
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Residues in contact with LEU 291 (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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236A LEU* 4.2 7.2 - - + -
237A LYS 3.1 5.3 + - - -
238A ILE* 3.3 19.4 - - + +
239A ALA 3.1 25.1 + - - -
271A LEU* 3.4 6.4 - - - +
290A ILE* 1.3 75.9 - - - +
292A LEU* 1.3 60.7 + - - +
293A ILE* 4.1 13.7 - - + -
304A VAL* 3.8 8.3 - - + -
305A HIS 3.3 25.8 - - - +
307A PRO* 4.2 7.9 - - + -
313A LEU* 4.0 2.5 - - - -
364A MET* 4.3 7.2 - - + -
367A PHE* 4.0 27.8 - - + -
368A ILE* 3.8 26.9 - - + -
371A LEU* 4.1 15.3 - - + -
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Residues in contact with LEU 292 (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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239A ALA 3.6 14.1 - - - +
241A TYR* 3.7 17.0 - - + -
264A LEU* 3.7 29.4 - - + -
267A ALA* 3.7 29.2 - - + -
268A LEU* 4.0 22.0 - - + +
271A LEU* 4.0 7.9 - - + -
291A LEU* 1.3 75.9 - - - +
293A ILE* 1.3 65.9 + - - +
304A VAL* 4.2 0.7 - - - +
305A HIS* 2.9 54.6 + - + +
313A LEU* 3.7 19.5 - - + +
314A ASN 5.8 0.2 - - - +
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Residues in contact with ILE 293 (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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181A LEU* 5.8 0.4 - - + -
186A LEU* 4.4 19.1 - - + -
238A ILE* 3.7 24.2 - - + -
239A ALA 3.0 6.5 + - - -
240A VAL* 3.2 17.6 - - + +
241A TYR* 3.0 29.4 + - - -
291A LEU* 4.1 8.5 - - + -
292A LEU* 1.3 79.7 - - - +
294A GLY* 1.3 73.2 + - - +
295A VAL* 4.3 6.5 - - + -
302A ILE* 3.9 22.9 - - + -
303A ARG 3.4 7.2 - - - +
304A VAL* 4.2 12.1 - - + -
371A LEU* 3.9 27.6 - - + -
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Residues in contact with GLY 294 (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* 3.4 34.3 - - - -
243A PHE* 4.1 7.4 - - - -
293A ILE* 1.3 74.6 - - - +
295A VAL* 1.3 62.2 + - - +
296A ASP 4.4 0.2 + - - -
301A ALA 4.0 0.2 - - - +
302A ILE* 3.3 6.9 - - - +
303A ARG* 2.8 35.2 + - - +
305A HIS* 4.6 0.2 - - - -
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Residues in contact with VAL 295 (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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178A LEU* 4.0 18.6 - - + -
181A LEU* 4.5 1.8 - - + -
185A ILE* 3.9 28.7 - - + -
240A VAL* 3.6 23.3 - - + -
241A TYR 2.9 11.3 + - - +
242A HIS* 3.1 5.5 - - - +
243A PHE* 2.9 32.2 + - - +
293A ILE* 4.3 2.0 - - + -
294A GLY* 1.3 78.0 - - - +
296A ASP* 1.3 73.8 + - - +
297A THR* 4.3 4.3 - - + +
300A ASP* 4.3 8.7 - - - +
301A ALA 3.7 7.2 - - - +
302A ILE* 3.9 17.5 - - + -
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Residues in contact with ASP 296 (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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39A PRO* 4.9 4.0 - - - +
243A PHE* 3.2 23.8 - - + +
245A THR* 2.7 50.8 + - + +
295A VAL* 1.3 71.3 - - - +
297A THR* 1.3 59.4 + - - +
298A ASP* 3.1 15.9 + - - +
299A THR* 3.4 25.3 + - - +
300A ASP* 2.8 30.0 + - - -
301A ALA* 3.1 14.8 + - + +
322A THR* 5.8 0.3 + - - -
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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