Contacts of the strand formed by residues 219 - 226 (chain B) in PDB entry 1UIR
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 219 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B ARG* 4.3 2.5 - - - +
217B PHE* 4.2 0.5 - - - +
218B ARG* 1.3 122.0 + - + +
220B VAL* 1.3 63.2 + - - +
221B ARG* 4.3 0.7 - - + +
238B LEU 3.9 0.5 - - - +
239B ALA* 3.3 4.7 - - - +
240B SER 2.9 43.5 + - - +
241B ASP 3.6 15.3 - - - -
242B ALA 4.8 0.4 - - - -
243B PHE* 3.4 31.0 - - - +
244B ASP* 3.6 26.7 - - + +
245B PRO* 3.5 10.5 - - + +
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Residues in contact with VAL 220 (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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210B HIS* 3.5 34.3 - - + +
213B VAL* 3.9 15.0 - - + +
214B ARG* 3.4 58.6 + - + +
217B PHE* 3.8 14.6 - - + +
219B TYR* 1.3 79.5 - - - +
221B ARG* 1.3 75.4 + - - +
237B LEU* 3.9 20.0 - - + -
238B LEU 3.5 3.8 - - - +
239B ALA* 4.4 0.7 - - + -
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Residues in contact with ARG 221 (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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210B HIS* 4.4 0.2 - - - -
219B TYR* 5.7 0.4 - - + +
220B VAL* 1.3 81.9 + - - +
222B SER* 1.3 62.1 + - - +
237B LEU* 3.3 4.5 - - - -
238B LEU 2.9 35.5 + - - -
244B ASP* 2.9 43.9 + - - +
245B PRO* 3.8 15.3 - - + -
246B ALA* 3.6 24.6 - - + +
276B PHE* 4.0 12.5 - - + -
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Residues in contact with SER 222 (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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206B HIS* 3.1 30.7 + - - -
210B HIS* 2.7 32.3 + - - -
221B ARG* 1.3 75.8 - - - +
223B TYR* 1.3 62.9 + - - +
236B PHE 3.3 6.7 + - - -
237B LEU* 4.0 1.0 - - - +
276B PHE* 3.8 13.0 - - - +
278B LEU* 3.8 20.5 - - - +
282B LEU* 5.7 1.1 - - - -
286B LEU* 3.7 19.2 - - - +
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Residues in contact with TYR 223 (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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66B THR* 2.7 40.2 + - + -
67B LEU* 3.4 14.0 + - - -
70B PRO* 3.5 11.9 - - + +
193B MET 4.8 1.6 + - - -
206B HIS* 4.8 0.6 + - - -
222B SER* 1.3 75.7 - - - +
224B LYS* 1.3 65.0 + - - +
235B GLY* 3.6 1.6 - - - -
236B PHE* 2.7 55.7 + - + +
237B LEU* 3.6 27.8 + - - -
238B LEU* 3.7 15.0 - - + +
275B MET* 3.3 46.0 - - + +
276B PHE* 3.4 28.0 - + + -
278B LEU* 4.4 2.2 - - - -
282B LEU* 6.3 0.2 - - - -
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Residues in contact with LYS 224 (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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225A ASN* 4.9 1.2 + - - -
226A HIS* 5.8 2.6 - - - +
271A TYR* 3.0 27.6 + - - -
198B ILE* 3.8 13.2 - - + -
223B TYR* 1.3 77.4 - - - +
225B ASN* 1.3 65.6 + - - +
233B ASN* 3.8 24.4 + - - +
234B PHE 3.2 14.8 - - - +
236B PHE* 4.4 2.9 - - - -
275B MET* 3.2 31.5 + - - +
277B VAL 4.6 5.1 + - - +
278B LEU* 4.4 3.8 - - + -
279B PRO* 3.6 30.3 - - - -
282B LEU* 3.9 20.0 - - + -
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Residues in contact with ASN 225 (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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224A LYS* 4.9 2.4 - - - +
233A ASN* 5.9 0.6 - - - +
62B ILE* 3.8 3.6 - - - +
66B THR* 2.9 38.7 + - + +
224B LYS* 1.3 79.1 + - - +
226B HIS* 1.3 77.6 + - - +
227B ILE* 3.6 5.2 + - + +
233B ASN* 3.3 5.8 - - - +
234B PHE* 2.9 29.2 + - - +
236B PHE* 4.4 2.8 - - + -
266B HIS* 3.0 23.0 + - - -
271B TYR* 2.7 28.2 + - - -
275B MET* 4.0 9.0 - - - +
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Residues in contact with HIS 226 (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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198A ILE 5.6 2.0 - - - -
199A LEU* 5.8 2.5 - - + -
224A LYS* 6.1 0.4 - - - +
226A HIS* 3.0 38.8 - + + -
231A PHE 4.5 0.2 - - - -
232A LEU* 3.9 8.1 - - + -
233A ASN* 3.7 50.4 + - + +
62B ILE* 4.1 4.9 - - - +
225B ASN* 1.3 83.7 + - - +
227B ILE* 1.3 65.9 + - - +
228B PRO* 3.3 39.1 - - + +
231B PHE* 3.8 10.5 - + - -
232B LEU 3.6 22.0 + - - -
233B ASN* 3.4 9.6 - - - +
266B HIS* 5.5 0.9 + - - -
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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