Contacts of the strand formed by residues 225 - 238 (chain A) in PDB entry 5OAQ
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 TRP 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A ARG* 3.3 44.7 - - + +
218A SER 4.1 2.0 - - - +
219A VAL 3.3 16.2 - - - -
220A ALA* 3.6 19.3 - - + -
224A LEU* 1.3 75.3 - - - +
226A MET* 1.3 80.8 + - - +
227A LEU* 3.5 46.0 - - + +
320A TYR* 3.0 9.4 - - - -
321A GLU* 2.9 61.7 + - + +
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Residues in contact with MET 226 (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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219A VAL* 2.8 33.8 + - + +
225A TRP* 1.3 84.4 + - - +
227A LEU* 1.3 59.8 + - - +
228A GLU 3.5 16.6 - - - +
229A PHE* 3.8 34.8 - - + -
250A ILE* 4.2 22.6 - - + +
319A GLN 3.5 4.3 - - - +
320A TYR* 3.4 32.3 - - + -
397A GLN* 4.0 10.3 - - - -
409A LEU* 3.9 10.1 - - + +
411A ILE* 4.0 12.6 - - + -
413A TYR* 3.6 18.4 - - + +
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Residues in contact with LEU 227 (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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225A TRP* 3.5 47.0 - - + +
226A MET* 1.3 73.0 - - - +
228A GLU* 1.3 62.0 + - + +
250A ILE* 4.0 5.1 - - - +
251A GLY* 3.4 22.0 + - - +
319A GLN* 2.9 22.7 + - + +
320A TYR* 3.6 7.6 - - - +
321A GLU* 3.5 48.7 - - + +
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Residues in contact with GLU 228 (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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226A MET* 3.5 9.0 - - - +
227A LEU* 1.3 82.4 - - + +
229A PHE* 1.3 63.0 + - - +
230A SER* 3.3 23.8 + - - -
250A ILE* 3.3 11.0 - - - +
251A GLY* 4.9 4.5 - - - -
317A SER* 3.0 23.5 - - - +
318A SER* 3.1 18.5 + - - -
319A GLN* 3.1 33.3 + - + +
360A ARG* 2.9 32.1 + - - +
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Residues in contact with PHE 229 (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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226A MET* 3.8 22.2 - - + -
228A GLU* 1.3 76.2 - - - +
230A SER* 1.3 67.2 + - - +
248A VAL* 4.2 12.3 - - + -
249A HIS* 3.2 2.8 - - - -
250A ILE* 2.8 40.3 + - + +
298A PHE* 4.0 33.0 - + - -
316A VAL* 4.0 24.0 - - + -
317A SER 3.3 6.5 - - - -
318A SER* 4.2 10.5 - - - -
332A THR* 6.3 2.2 - - + -
397A GLN* 3.6 21.8 - - - -
413A TYR* 3.6 22.4 - + - -
502A MYR 4.2 23.8 - - + -
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Residues in contact with SER 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A GLU* 3.3 14.1 + - - -
229A PHE* 1.3 80.9 - - - +
231A ALA* 1.3 59.1 + - - +
232A PHE* 4.0 13.7 - - - -
246A LEU* 4.3 15.7 - - - +
248A VAL 3.3 13.0 - - - -
249A HIS* 4.0 10.1 - - - -
250A ILE 5.5 0.2 - - - -
315A GLY 3.9 0.2 - - - +
316A VAL* 3.1 9.1 - - - +
317A SER* 2.8 39.1 + - - -
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Residues in contact with ALA 231 (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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229A PHE* 5.1 0.2 - - + -
230A SER* 1.3 72.1 - - - +
232A PHE* 1.3 61.4 + - - +
246A LEU* 3.6 1.7 - - - +
247A PHE* 2.8 30.9 + - + -
248A VAL* 3.2 30.4 + - + +
315A GLY 3.3 8.5 - - - +
316A VAL* 4.3 8.3 - - + +
366A LEU* 5.5 3.4 - - + -
502A MYR 3.9 31.6 - - + -
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Residues in contact with PHE 232 (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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230A SER* 4.0 14.6 - - - -
231A ALA* 1.3 76.1 - - - +
233A LEU* 1.3 61.5 + - - +
234A GLU* 4.1 11.9 - - + -
244A LYS* 3.9 27.8 - - + -
245A HIS 3.1 14.6 - - - +
246A LEU* 3.6 14.6 - - + -
247A PHE* 3.6 11.0 - - - -
313A PHE* 4.0 21.8 - + - -
314A TYR* 3.4 4.0 - - - +
315A GLY* 2.8 56.0 + - - +
316A VAL 3.9 1.1 - - - -
317A SER* 3.7 22.2 - - - -
363A ARG* 3.9 35.2 - - + -
366A LEU* 5.5 1.3 - - - +
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Residues in contact with LEU 233 (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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232A PHE* 1.3 75.6 - - - +
234A GLU* 1.3 66.1 + - - +
235A GLN* 3.9 23.4 - - + +
243A ASN 3.7 1.6 - - - +
244A LYS* 3.4 1.4 - - - -
245A HIS* 2.8 39.0 + - + +
247A PHE* 3.6 17.4 - - + -
304A THR* 3.9 25.4 - - + +
305A ASN 4.1 13.7 - - - +
312A SER* 3.6 33.2 - - - +
313A PHE 3.5 6.5 - - - +
314A TYR* 3.9 28.3 - - + +
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Residues in contact with GLU 234 (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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232A PHE* 4.1 13.2 - - + -
233A LEU* 1.3 73.0 - - - +
235A GLN* 1.3 63.6 + - - +
236A GLN 4.2 0.2 + - - -
242A TYR* 3.9 39.6 - - + +
243A ASN 3.3 9.0 - - - +
244A LYS* 4.3 13.4 + - + +
311A SER 3.7 0.7 - - - +
312A SER* 3.4 3.1 - - - -
313A PHE* 2.7 51.0 + - + +
363A ARG* 2.7 44.1 + - - -
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Residues in contact with GLN 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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233A LEU* 3.9 17.7 - - + +
234A GLU* 1.3 75.7 - - - +
236A GLN* 1.3 61.7 + - - +
237A GLN 3.4 3.3 + - - +
242A TYR* 3.3 3.9 - - - -
243A ASN* 2.7 53.2 + - + +
245A HIS* 5.9 0.5 - - - +
304A THR* 4.0 6.9 + - - -
305A ASN* 3.3 49.3 + - - +
311A SER* 3.3 7.9 - - - +
312A SER* 3.6 23.4 + - - +
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Residues in contact with GLN 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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234A GLU* 4.2 1.0 - - - +
235A GLN* 1.3 69.1 - - - +
237A GLN* 1.3 67.6 + - - +
238A ASP* 3.3 16.3 - - - +
239A PRO* 3.3 30.9 - - - +
241A THR 3.6 3.8 - - - -
242A TYR* 3.6 34.5 + - + -
311A SER* 2.9 40.6 + - - +
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Residues in contact with GLN 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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235A GLN* 3.4 3.8 + - - +
236A GLN* 1.3 74.9 - - - +
238A ASP* 1.3 68.6 + - - +
241A THR* 2.8 34.2 + - + +
243A ASN* 2.9 34.4 + - - +
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Residues in contact with ASP 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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236A GLN* 3.3 13.1 - - - +
237A GLN* 1.3 85.6 + - - +
239A PRO* 1.4 71.4 - - + +
240A ASP* 2.8 22.0 + - - +
241A THR* 2.7 43.4 + - - +
242A TYR* 4.4 0.2 - - - -
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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