Contacts of the strand formed by residues 303 - 314 (chain K) in PDB entry 7JOA
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 GLU 303 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210K ASN* 2.7 32.2 + - - -
297K LEU* 3.5 36.4 - - + +
298K ILE 3.3 5.2 - - - +
299K ARG* 2.8 45.0 + - + +
301K PRO 3.9 1.4 + - - -
302K GLU* 1.3 74.3 - - - +
304K ILE* 1.3 55.1 + - - +
305K SER* 5.1 1.2 + - - +
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Residues in contact with ILE 304 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167K ALA* 4.0 32.1 - - + +
170K THR* 4.3 19.7 - - + -
171K VAL* 3.8 24.2 - - + -
210K ASN* 3.2 28.0 - - + +
212K PHE* 4.1 4.7 - - + -
296K LEU 3.5 0.7 - - - +
297K LEU* 3.4 7.0 - - - +
298K ILE* 2.9 43.1 + - + +
300K ASN* 6.5 0.7 - - + -
302K GLU* 4.1 10.3 - - + +
303K GLU* 1.3 79.0 - - - +
305K SER* 1.3 67.1 + - - +
306K VAL* 4.2 4.4 + - + -
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Residues in contact with SER 305 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210K ASN* 3.5 5.7 + - - +
211K GLU* 3.5 22.6 + - - +
212K PHE 2.9 26.0 + - - +
285K GLU* 5.2 2.6 + - - -
295K THR* 4.2 12.6 - - - +
296K LEU 3.3 5.8 - - - -
297K LEU* 3.2 20.0 - - - +
303K GLU* 4.5 1.2 + - - +
304K ILE* 1.3 71.8 - - - +
306K VAL* 1.3 65.2 + - - +
307K ASP* 4.2 1.6 - - - -
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Residues in contact with VAL 306 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171K VAL* 3.8 34.8 - - + -
175K VAL* 4.7 6.3 - - + -
212K PHE* 3.2 15.0 - - + +
214K VAL* 4.3 28.9 - - + -
294K VAL 3.5 0.3 - - - +
295K THR* 3.4 1.1 - - - +
296K LEU* 2.8 46.0 + - + +
298K ILE* 4.1 20.0 - - + -
304K ILE* 4.2 2.0 - - + -
305K SER* 1.3 78.8 - - - +
307K ASP* 1.3 65.6 + - - +
308K ILE* 3.5 8.2 + - + +
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Residues in contact with ASP 307 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212K PHE 3.1 7.5 + - - -
213K ASP* 3.1 19.1 - - - +
214K VAL 3.4 22.2 + - - -
288K LYS* 5.9 0.2 + - - -
293K ALA* 3.7 21.0 - - + +
294K VAL 3.8 3.1 - - - -
295K THR* 2.4 36.7 + - - +
305K SER* 4.2 1.6 - - - -
306K VAL* 1.3 70.9 - - - +
308K ILE* 1.3 60.5 + - - +
309K ILE* 3.5 12.2 - - + +
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Residues in contact with ILE 308 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175K VAL* 5.7 1.6 - - + -
178K LEU* 4.2 13.0 - - + -
214K VAL* 3.7 20.2 - - + +
216K PHE* 4.0 29.6 - - + -
266K PHE* 3.7 31.3 - - + -
270K ILE* 4.9 9.9 - - + -
292K PRO 4.6 0.7 - - - +
293K ALA* 3.5 2.6 - - - -
294K VAL* 2.8 44.2 + - + +
296K LEU* 3.8 33.4 - - + -
306K VAL* 4.1 8.7 - - + +
307K ASP* 1.3 73.5 - - - +
309K ILE* 1.3 62.1 + - - +
310K LEU 4.2 0.7 + - - -
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Residues in contact with ILE 309 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213K ASP* 4.4 10.8 - - + +
214K VAL 3.3 10.4 + - - +
215K MET* 3.5 13.6 - - + +
216K PHE 3.1 22.6 + - - -
292K PRO* 5.7 8.3 - - + -
293K ALA* 4.1 15.5 - - + +
307K ASP* 3.5 31.6 - - + +
308K ILE* 1.3 76.9 - - - +
310K LEU* 1.3 73.3 + - - +
348K VAL* 4.6 17.5 - - + -
349K PRO* 4.7 9.9 - - + +
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Residues in contact with LEU 310 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189K PHE* 4.6 21.3 - - + -
192K VAL* 5.1 3.6 - - + -
216K PHE* 3.3 20.0 - - + +
218K LEU* 4.4 18.8 - - + -
262K MET* 5.0 17.9 - - + -
263K LEU* 4.4 20.5 - - + +
266K PHE* 4.0 38.0 - - + -
308K ILE 4.2 1.8 + - - -
309K ILE* 1.3 75.8 - - - +
311K ALA* 1.3 70.0 + - - +
312K LEU* 4.6 14.8 - - + -
349K PRO* 3.2 27.8 - - + +
363K TRP* 5.2 4.2 - - + -
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Residues in contact with ALA 311 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215K MET* 3.5 38.1 - - + -
216K PHE 2.8 11.3 + - - +
217K LYS* 3.0 9.4 - - - -
218K LEU 3.0 23.4 + - - -
309K ILE 3.6 0.2 + - - -
310K LEU* 1.3 76.5 - - - +
312K LEU* 1.3 66.9 + - - +
346K TYR* 4.8 5.8 - - + -
347K LEU 3.4 10.5 - - - +
348K VAL* 3.8 9.6 - - + -
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Residues in contact with LEU 312 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218K LEU* 3.7 13.2 - - + +
220K VAL* 4.0 30.5 - - + -
223K ILE* 5.5 0.7 - - + -
237K VAL* 5.3 8.7 - - + -
248K LEU* 6.5 0.7 - - + -
257K LEU* 4.4 21.8 - - + -
262K MET* 5.2 8.7 - - + -
310K LEU* 4.6 15.9 - - + -
311K ALA* 1.3 75.0 - - - +
313K GLU* 1.3 59.5 + - - +
314K SER 4.3 0.2 - - - -
346K TYR* 3.3 7.2 - - - +
347K LEU* 2.9 55.0 + - + +
363K TRP* 3.5 33.7 - - + -
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Residues in contact with GLU 313 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217K LYS* 4.5 18.0 + - + -
218K LEU 2.7 18.9 + - - +
219K GLU* 2.8 31.9 - - - +
220K VAL* 3.5 25.2 + - - +
312K LEU* 1.3 73.9 - - - +
314K SER* 1.3 66.0 + - - +
315K LYS* 4.1 6.4 - - - +
344K PRO* 3.5 25.8 - - + +
345K PHE 3.7 3.6 - - - +
346K TYR* 3.3 36.2 + - + +
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Residues in contact with SER 314 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219K GLU* 5.6 0.2 - - - -
220K VAL* 4.8 6.4 + - - -
222K ARG 5.8 0.3 + - - -
223K ILE* 3.2 39.7 + - - +
312K LEU 4.3 0.2 - - - -
313K GLU* 1.3 75.6 - - - +
315K LYS* 1.3 62.3 + - - +
316K GLY* 3.5 6.2 + - - -
344K PRO* 3.1 7.8 - - - +
345K PHE* 3.0 58.5 + - - -
347K LEU* 4.9 3.1 - - - -
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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