Contacts of the strand formed by residues 229 - 239 (chain B) in PDB entry 5M5X
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 229 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222B PHE* 3.2 34.5 - - + +
223B ALA* 5.2 3.4 - - - +
225B ARG* 3.3 36.4 + - + +
226B GLY* 3.5 12.0 - - - -
227B ALA* 3.1 33.0 - - + +
228B SER* 1.3 80.8 - - - +
230B SER* 1.3 62.4 + - - +
251B HIS* 4.8 12.1 - + + -
252B TYR 4.1 4.3 - - - +
253B LEU* 3.4 23.6 - - + -
254B ASN* 5.6 0.6 - - - +
261B ARG* 2.4 38.6 + - - -
270B LEU* 4.6 7.4 - - - +
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Residues in contact with SER 230 (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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222B PHE* 4.4 12.5 - - - +
229B TYR* 1.3 78.5 - - - +
231B HIS* 1.3 65.3 + - - +
232B TYR* 3.3 20.7 + - - +
252B TYR* 3.1 49.8 + - - +
254B ASN* 3.7 18.5 + - - +
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Residues in contact with HIS 231 (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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218B ILE* 3.4 32.3 - - + +
219B ARG 3.5 18.5 + - - +
220B PRO* 5.8 2.7 - - + -
230B SER* 1.3 75.4 - - - +
232B TYR* 1.3 109.7 + + - +
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Residues in contact with TYR 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ILE 3.7 4.0 - - - -
218B ILE* 3.7 8.2 - - + -
222B PHE* 3.2 20.6 - - - -
230B SER* 3.3 12.8 - - - +
231B HIS* 1.3 119.5 + + - +
233B GLY* 1.3 60.2 + - - +
251B HIS* 5.2 0.7 - - - +
252B TYR* 3.5 52.3 + + + +
381B LEU* 4.6 2.9 - - + -
384B LEU* 3.6 29.4 - - + -
385B VAL* 3.2 44.4 + - + -
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Residues in contact with GLY 233 (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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216B ALA* 3.5 2.8 - - - +
217B ILE* 2.8 32.0 + - - +
218B ILE* 4.4 1.7 - - - +
222B PHE* 3.6 14.6 - - - -
232B TYR* 1.3 81.0 - - - +
234B ILE* 1.3 69.8 + - - +
250B LEU 3.7 7.4 - - - -
251B HIS* 4.7 3.8 - - - +
381B LEU* 4.6 5.1 - - - +
384B LEU* 5.3 2.1 - - - +
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Residues in contact with ILE 234 (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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215B MET 3.4 15.3 - - - +
216B ALA* 3.9 9.4 - - + +
217B ILE* 4.5 0.9 - - - +
222B PHE* 4.8 2.2 - - - -
233B GLY* 1.3 81.8 - - - +
235B GLN* 1.3 64.0 + - - +
236B ILE 5.0 0.2 - - - +
249B VAL* 3.4 6.3 - - - +
250B LEU* 2.7 53.1 + - + +
377B MET* 3.5 53.2 - - + +
380B LYS* 3.7 17.3 - - - +
381B LEU* 3.7 32.8 - - + +
384B LEU* 6.3 0.2 - - + -
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Residues in contact with GLN 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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209B GLN* 5.0 16.6 + - + +
215B MET* 3.0 42.5 + - + +
217B ILE* 4.1 25.6 - - + +
219B ARG* 5.2 6.9 + - - -
222B PHE* 6.1 2.2 - - + -
234B ILE* 1.3 77.2 - - - +
236B ILE* 1.3 67.7 + - - +
237B ARG* 5.8 3.2 - - + +
247B THR* 4.0 26.1 - - - +
248B ASN 3.5 10.1 - - - +
249B VAL* 4.4 16.9 - - + +
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Residues in contact with ILE 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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212B ASN 5.7 0.2 - - - +
213B HIS 3.8 19.3 - - - +
214B PRO* 4.3 1.3 - - + -
215B MET* 4.1 4.3 - - - -
235B GLN* 1.3 76.8 - - - +
237B ARG* 1.3 62.7 + - - +
238B SER* 3.7 21.6 + - - +
247B THR* 4.0 1.2 - - - -
248B ASN* 2.9 53.0 + - + +
250B LEU* 6.0 0.4 - - + -
359B LEU* 4.0 6.7 - - + -
361B HIS* 4.0 4.3 - - + -
373B MET* 3.8 22.9 - - + -
374B LEU* 5.3 4.7 - - + -
377B MET* 3.6 43.1 - - + -
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Residues in contact with ARG 237 (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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208B VAL* 3.9 29.6 - - - +
209B GLN* 3.9 30.3 - - + +
210B ARG 3.7 11.8 + - - +
211B ARG* 3.8 15.7 - - + +
212B ASN 3.5 20.3 + - - -
213B HIS 4.5 0.6 + - - -
215B MET* 4.2 8.0 - - + +
235B GLN* 5.8 4.5 - - + +
236B ILE* 1.3 75.6 - - - +
238B SER* 1.3 63.8 + - - +
239B VAL* 3.7 1.4 + - - +
245B SER* 3.4 27.8 + - - +
246B GLN 3.7 9.2 - - - +
247B THR* 4.7 11.2 - - + +
403B LEU* 5.1 11.9 - - - +
411B MET* 5.8 3.6 - - - -
477B ASP* 3.2 43.4 + - - +
478B LEU* 4.8 4.0 - - - +
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Residues in contact with SER 238 (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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212B ASN* 5.2 0.4 - - - +
236B ILE* 3.7 12.2 + - - +
237B ARG* 1.3 75.9 - - - +
239B VAL* 1.3 58.9 + - - +
245B SER* 3.1 1.9 - - - -
246B GLN* 2.8 58.2 + - - +
248B ASN* 3.5 10.0 + - - -
359B LEU* 3.7 8.1 - - - +
360B VAL 3.9 9.0 - - - -
361B HIS* 3.0 32.3 + - - -
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Residues in contact with VAL 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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211B ARG* 3.3 43.1 - - + +
212B ASN* 3.4 25.1 - - - +
237B ARG 4.6 1.3 - - - +
238B SER* 1.3 75.4 - - - +
240B ARG* 1.3 77.1 + - - +
241B PRO 3.8 0.2 - - - -
243B GLN* 3.8 6.7 - - - -
244B THR 3.1 17.3 - - - +
245B SER* 3.2 22.9 - - - +
360B VAL* 3.9 3.4 - - - -
361B HIS* 3.1 19.8 - - - +
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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