Contacts of the strand formed by residues 229 - 237 (chain B) in PDB entry 3IEU
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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190B GLN* 3.6 25.1 + - - -
221B PHE* 3.9 24.7 - + - -
222B VAL 3.3 14.6 - - - +
223B SER* 3.7 19.5 - - - +
224B ASN* 3.5 9.2 + - - +
227B GLY 5.2 2.0 - - - -
228B GLY* 1.3 75.3 - - - -
230B ASP* 1.3 61.8 + - - +
231B ILE* 4.2 11.4 - - + -
269B PHE* 4.1 28.0 - + + -
271B ALA* 3.9 27.8 - - + -
272B PRO 2.7 15.7 + - - +
273B VAL* 3.5 9.5 + - + -
274B HIS* 2.9 26.1 + - - +
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Residues in contact with ASP 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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220B ARG* 3.6 32.8 + - - +
221B PHE* 3.8 0.2 - - - -
222B VAL* 2.8 44.2 + - + +
224B ASN* 5.5 6.7 - - + +
229B TYR* 1.3 74.2 - - - +
231B ILE* 1.3 63.2 + - - +
232B ASN* 4.0 10.4 - - - +
274B HIS* 3.4 27.6 + - + +
276B GLU* 5.1 0.7 - - - +
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Residues in contact with ILE 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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194B ALA* 4.8 0.4 - - + -
218B ILE* 3.9 28.9 - - + -
220B ARG 3.3 7.6 - - - +
221B PHE* 3.7 33.0 - - + -
229B TYR* 4.5 7.0 - - + -
230B ASP* 1.3 80.8 + - - +
232B ASN* 1.3 68.7 + - - +
265B MET* 3.7 25.6 - - - -
269B PHE* 4.2 9.0 - - + -
273B VAL* 3.9 15.3 - - + -
274B HIS 2.9 13.7 + - - +
275B LEU* 3.5 20.3 - - + +
276B GLU 3.0 24.4 + - - -
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Residues in contact with ASN 232 (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* 3.7 4.3 - - - +
219B GLU* 3.1 40.8 + - + +
220B ARG* 2.9 41.3 + - + +
230B ASP* 4.0 8.8 - - - +
231B ILE* 1.3 82.8 - - - +
233B GLY* 1.3 61.7 + - - +
276B GLU* 3.4 34.3 + - - +
278B TRP* 4.8 7.2 - - + +
293B ARG* 5.8 0.4 - - - +
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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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198B ILE* 4.4 13.5 - - - -
217B GLU 3.9 4.7 - - - -
218B ILE* 4.7 3.1 - - - -
219B GLU* 5.2 0.7 - - - -
231B ILE 4.0 1.0 + - - -
232B ASN* 1.3 73.8 - - - +
234B LEU* 1.3 59.6 + - - +
235B ILE* 4.2 0.9 - - - -
275B LEU* 4.5 1.6 - - - +
276B GLU 2.6 16.5 + - - +
277B LEU* 3.3 17.9 - - - +
278B TRP* 2.9 30.2 + - - -
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Residues in contact with LEU 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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38B ARG* 5.9 4.3 - - - +
198B ILE* 5.4 1.2 - - - +
215B THR 3.9 0.9 - - - +
216B VAL* 3.8 3.1 - - - -
217B GLU* 2.9 52.5 + - + +
219B GLU* 3.1 34.8 - - + +
233B GLY* 1.3 73.9 - - - +
235B ILE* 1.3 60.3 + - - +
236B LEU* 3.9 26.1 + - + +
278B TRP* 3.5 16.2 - - + +
280B LYS* 4.0 17.7 - - + +
285B TRP* 3.7 31.9 - - + -
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Residues in contact with ILE 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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198B ILE* 4.2 14.8 - - + -
202B LEU* 4.0 42.0 - - + -
214B VAL* 4.1 12.6 - - + -
215B THR 3.7 3.4 - - - +
216B VAL* 4.8 3.1 - - + +
234B LEU* 1.3 73.7 - - - +
236B LEU* 1.3 60.7 + - - +
237B VAL* 4.6 5.2 - - + -
246B VAL* 4.6 10.1 - - + -
254B ILE* 4.0 27.1 - - + -
257B ILE* 5.0 0.7 - - + -
277B LEU* 4.3 18.6 - - + -
278B TRP 2.7 13.8 + - - +
279B VAL* 3.3 17.2 - - + +
280B LYS 2.8 27.2 + - - +
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Residues in contact with LEU 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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36B THR* 4.9 1.8 - - - +
38B ARG* 5.9 4.7 - - - +
213B SER 3.8 1.7 - - - +
214B VAL* 3.4 7.8 - - - +
215B THR* 2.8 57.3 + - - +
217B GLU* 4.1 24.0 - - + +
234B LEU* 4.2 21.3 - - + +
235B ILE* 1.3 75.1 - - - +
237B VAL* 1.3 62.2 + - - +
280B LYS* 3.3 43.7 - - + +
282B LYS* 4.2 23.2 - - + -
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Residues in contact with VAL 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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211B PRO* 5.3 1.1 - - + -
213B SER 4.4 3.6 - - - -
214B VAL* 4.6 15.3 - - + +
235B ILE* 4.6 5.2 - - + -
236B LEU* 1.3 79.7 - - - +
238B GLU* 1.3 61.3 + - - +
239B ARG 3.6 18.4 - - - +
242B GLN* 4.0 14.8 - - + +
243B LYS* 3.9 20.9 - - + +
246B VAL* 4.3 24.0 - - + -
279B VAL* 4.6 8.5 - - + -
280B LYS 3.0 12.5 + - - +
281B VAL* 3.4 5.1 - - - -
282B LYS* 2.9 29.6 + - - +
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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