Contacts of the strand formed by residues 233 - 242 (chain B) in PDB entry 5AJI
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 ILE 233 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190B ILE 3.6 0.9 - - - +
191B GLY* 3.2 3.1 - - - -
192B VAL* 2.8 41.7 + - + +
193B ALA 4.6 1.3 - - - +
194B TYR* 3.2 56.8 - - + +
196B SER* 6.1 0.4 - - - -
198B ILE* 5.8 2.9 - - + -
225B LEU* 3.4 16.4 - - + -
227B GLU 3.7 3.1 - - - -
228B LEU* 4.1 16.4 - - + -
232B SER* 1.3 72.3 - - - +
234B ASN* 1.3 61.1 + - - +
235B PHE* 3.1 35.9 - - + -
258C LYS* 3.9 15.5 - - - +
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Residues in contact with ASN 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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189B ILE* 4.2 20.1 - - + +
190B ILE 3.3 4.7 - - - +
191B GLY* 3.4 7.9 - - - -
225B LEU* 3.8 1.4 - - - +
226B ASN* 2.8 35.3 + - + +
227B GLU* 2.9 55.2 + - + +
229B GLY* 4.5 4.2 - - - -
232B SER* 2.8 31.7 + - - -
233B ILE* 1.3 73.7 - - - +
235B PHE* 1.3 56.6 + - - +
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Residues in contact with PHE 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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188B PHE 3.6 0.7 - - - +
189B ILE* 3.3 5.9 - - - -
190B ILE* 2.7 44.4 + - + +
192B VAL* 3.7 16.2 - - + -
196B SER* 5.7 0.4 - - - -
198B ILE* 4.2 21.1 - - + -
201B VAL* 3.4 38.6 - - + -
202B LYS* 4.1 20.6 - - + -
205B LEU* 4.2 18.8 - - + -
224B ARG 3.2 19.7 - - - +
225B LEU* 3.5 22.9 - - + -
226B ASN* 4.5 0.7 - - - -
233B ILE* 3.1 30.5 - - + -
234B ASN* 1.3 72.8 - - - +
236B VAL* 1.3 60.5 + - - +
237B VAL* 5.0 0.2 - - - -
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Residues in contact with VAL 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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187B GLU* 3.8 15.3 - - + -
188B PHE 3.4 8.7 - - - +
189B ILE* 4.3 7.2 - - + -
222B THR* 3.9 5.8 - - + +
223B VAL* 3.4 1.7 - - - +
224B ARG* 2.9 41.4 + - + +
226B ASN* 3.9 30.9 - - + +
235B PHE* 1.3 74.3 - - - +
237B VAL* 1.3 66.8 + - - +
238B ARG* 3.6 31.4 - - + +
251C TRP* 4.1 22.0 - - + +
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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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187B GLU* 3.3 4.2 - - - -
188B PHE* 2.8 59.8 + - + +
190B ILE* 4.7 8.5 - - + -
205B LEU* 3.8 37.2 - - + -
209B ILE* 4.1 25.6 - - + -
222B THR 3.2 9.0 - - - +
223B VAL* 4.1 12.1 - - + -
235B PHE 4.9 0.9 - - - +
236B VAL* 1.3 80.7 - - - +
238B ARG* 1.3 63.3 + - - +
239B VAL* 4.3 7.0 - - + -
253B VAL* 5.9 0.7 - - + -
257B ILE* 5.6 1.6 - - + -
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Residues in contact with ARG 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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185B ARG* 3.8 31.3 - - - +
186B ASN 3.3 2.5 - - - -
187B GLU* 2.7 40.1 + - + -
220B GLU* 3.4 28.5 + - - +
221B MET* 3.4 3.6 + - - -
222B THR* 2.9 35.6 + - - -
226B ASN* 5.2 6.1 + - - +
236B VAL* 3.6 18.9 - - + +
237B VAL* 1.3 78.4 - - - +
239B VAL* 1.3 65.7 + - - +
247C GLN* 4.3 9.1 + - - +
251C TRP* 3.8 29.5 - - - -
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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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185B ARG* 4.1 2.8 - - - +
186B ASN* 3.1 30.9 + - + +
188B PHE* 3.8 29.6 - - + -
209B ILE* 3.7 35.4 - - + -
215B ILE* 3.8 35.2 - - + -
220B GLU 4.0 4.0 - - - -
221B MET* 4.2 7.0 - - + -
237B VAL* 4.3 4.7 - - + -
238B ARG* 1.3 81.9 - - - +
240B TRP* 1.3 65.8 + - - +
241B SER* 4.0 3.0 + - - -
249B VAL* 5.4 1.3 - - + -
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Residues in contact with TRP 240 (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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183B VAL* 3.7 28.5 - - + -
184B ARG* 3.3 27.8 - - - -
185B ARG* 3.5 20.7 - - + +
215B ILE* 3.5 4.6 - - - +
216B LEU* 2.9 28.4 + - + -
219B ARG* 3.8 43.3 - - + +
220B GLU* 3.2 47.4 + - + +
239B VAL* 1.3 72.7 - - - +
241B SER* 1.3 66.5 + - - +
156C ARG* 5.5 6.5 - - - -
157C THR 5.2 0.9 - - - -
158C ALA 3.4 26.5 - - - -
160C GLY* 4.0 16.4 - - - -
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Residues in contact with SER 241 (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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183B VAL* 3.4 3.2 - - - +
184B ARG 2.9 28.9 + - - +
186B ASN* 4.0 9.2 + - - -
214B ARG 3.3 15.8 + - - -
215B ILE* 4.4 1.7 - - - +
216B LEU* 3.5 13.5 - - - -
239B VAL 4.0 2.3 + - - -
240B TRP* 1.3 77.8 + - - +
242B ASN* 1.3 68.8 + - - +
245B ASP* 4.1 1.8 - - - -
246B LEU* 4.5 8.8 - - - +
249B VAL* 3.8 31.8 - - - +
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Residues in contact with ASN 242 (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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182B PRO* 3.4 9.8 - - - +
183B VAL* 4.0 13.2 - - - +
214B ARG 4.4 0.8 + - - -
216B LEU* 3.9 17.1 - - - +
241B SER* 1.3 75.1 - - - +
243B SER* 1.3 67.5 + - - +
244B GLY* 4.4 4.9 - - - +
245B ASP* 2.8 35.1 + - - +
246B LEU* 3.1 11.4 + - - +
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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