Contacts of the strand formed by residues 288 - 297 (chain A) in PDB entry 2O39
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 TYR 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A PHE* 3.6 2.4 - - - +
199A PHE* 3.1 28.3 + - + +
200A ASP 3.5 22.2 - - - -
201A SER* 4.4 8.2 + - - -
203A GLY 4.9 0.2 - - - -
233A LYS* 3.2 20.0 + - + +
236A MET* 3.4 49.4 - - + -
237A PRO* 3.6 20.0 - - + -
239A THR* 4.0 8.3 - - + -
244A PHE* 4.1 0.2 - - - -
278A ASN* 3.9 11.7 - - - +
286A THR 3.5 0.6 - - - -
287A SER* 1.3 90.5 + - - +
289A CYS* 1.3 71.3 + - - +
323A GLU* 3.0 43.8 + - + +
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Residues in contact with CYS 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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197A LEU 3.4 8.7 - - - +
198A PHE* 3.7 20.6 - - + -
199A PHE* 4.8 0.7 - - - -
237A PRO* 3.8 3.0 - - - +
244A PHE* 3.9 15.9 - - - -
276A MET 4.4 0.2 - - - -
277A LEU* 3.6 1.9 - - - -
278A ASN* 2.6 42.4 + - - +
280A ARG 3.6 20.6 - - - -
281A ALA* 4.4 4.5 - - - -
286A THR* 4.5 4.0 - - - -
288A TYR* 1.3 82.8 - - - +
290A ILE* 1.3 69.2 + - - +
291A ARG* 3.5 16.8 - - + +
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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
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160A LEU* 5.9 2.7 - - + -
162A LEU* 4.9 11.0 - - + -
195A ALA 3.7 1.9 - - - +
197A LEU* 2.8 52.7 + - + +
199A PHE* 4.4 16.8 - - + -
236A MET* 6.1 0.7 - - + -
237A PRO* 4.0 18.6 - - + -
275A VAL* 4.9 0.7 - - + -
276A MET 3.8 3.1 - - - -
277A LEU* 4.3 10.5 - - + -
289A CYS* 1.3 80.9 - - - +
291A ARG* 1.3 62.9 + - - +
292A ILE* 3.5 27.1 - - + -
318A PHE* 4.7 7.9 - - + -
320A TYR* 3.8 32.3 - - + +
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Residues in contact with ARG 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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194A THR* 4.6 6.1 - - + -
195A ALA 3.6 4.5 - - - -
196A GLU* 3.0 39.9 + - + -
197A LEU 4.8 0.7 - - - +
198A PHE* 3.1 26.8 - - + -
274A SER 3.7 1.0 - - - +
275A VAL* 3.5 4.1 - - - +
276A MET* 2.8 80.1 + - + +
278A ASN* 4.7 0.2 - - - +
279A ARG 4.4 0.2 - - - +
280A ARG* 2.9 31.9 + - - +
282A ILE* 4.1 10.5 - - - +
289A CYS* 3.5 16.3 - - + +
290A ILE* 1.3 77.0 - - - +
292A ILE* 1.3 63.9 + - - +
293A THR* 4.0 4.0 + - + +
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Residues in contact with ILE 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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158A LEU* 6.2 0.7 - - + -
160A LEU* 5.9 3.6 - - + -
173A VAL* 4.6 15.9 - - + -
194A THR* 3.3 3.7 - - - +
195A ALA* 2.8 40.2 + - + +
197A LEU* 5.3 7.2 - - + -
273A ILE* 3.9 14.4 - - + -
274A SER 3.7 1.8 - - - -
275A VAL* 3.8 18.2 - - + -
290A ILE* 3.5 27.8 - - + +
291A ARG* 1.3 73.3 - - - +
293A THR* 1.3 63.3 + - - +
294A TRP* 3.8 34.6 - - + -
318A PHE* 3.9 24.5 - - + -
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Residues in contact with THR 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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192A ASN* 4.7 7.4 + - - +
193A PHE 3.4 7.6 + - - -
194A THR* 3.0 26.6 + - + +
272A ASP 3.4 4.7 - - - +
273A ILE* 3.5 2.1 - - - -
274A SER* 3.0 58.9 + - - +
291A ARG* 4.5 5.2 - - + +
292A ILE* 1.3 75.2 - - - +
294A TRP* 1.3 66.1 + - - +
295A SER* 4.5 3.3 + - - -
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Residues in contact with TRP 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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147A ILE* 4.2 4.9 - - + -
158A LEU* 4.4 10.1 - - + -
173A VAL* 4.4 27.8 - - + -
174A TYR* 4.5 13.0 - - - +
175A VAL* 5.0 2.9 - - + -
192A ASN* 3.0 22.9 - - - +
193A PHE* 3.0 62.0 + + + +
195A ALA* 4.0 17.0 - - + -
259A CYS* 3.4 28.0 - - - -
271A ILE* 3.8 8.7 - - + -
272A ASP 3.2 5.2 - - - -
273A ILE* 3.2 24.9 - - + +
292A ILE* 3.8 35.7 - - + -
293A THR* 1.3 75.7 - - - +
295A SER* 1.3 64.5 + - - +
313A THR* 3.8 16.8 + - + +
314A SER 5.6 0.2 + - - -
316A PHE* 5.3 0.8 - - - +
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Residues in contact with SER 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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191A ILE 3.4 6.7 - - - -
192A ASN* 3.3 19.7 - - - +
271A ILE* 3.5 6.1 - - - +
272A ASP* 2.7 55.2 + - - +
274A SER* 5.3 3.5 + - - -
293A THR* 4.5 5.1 + - - -
294A TRP* 1.3 77.9 - - - +
296A TRP* 1.3 67.1 + - - +
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Residues in contact with TRP 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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185A LEU 3.8 15.3 - - - -
186A THR* 4.2 2.7 - - - -
188A HIS 3.1 19.2 + - - -
189A ARG 3.9 10.5 - - - -
190A ASN* 3.3 0.9 - - - +
191A ILE* 2.8 67.5 + - + +
193A PHE* 4.3 14.6 - + - -
261A TYR* 6.3 0.2 - - + -
269A PHE* 3.6 30.5 - + + -
270A PRO 4.3 8.5 - - - +
271A ILE* 3.6 39.7 - - + -
272A ASP* 5.4 4.7 - - - -
295A SER* 1.3 79.3 - - - +
297A ASN* 1.3 64.6 + - - +
298A THR* 4.9 1.8 - - + -
300A ASP 5.8 0.2 - - - -
302A PRO* 3.8 18.4 - - + +
311A LEU* 4.0 29.6 - - + -
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Residues in contact with ASN 297 (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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189A ARG* 3.4 8.0 - - - +
190A ASN* 3.1 37.2 + - - +
296A TRP* 1.3 72.5 - - - +
298A THR* 1.3 71.1 + - - +
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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