Contacts of the strand formed by residues 218 - 226 (chain B) in PDB entry 1O94
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 ALA 218 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B ILE* 3.3 47.3 - - + +
17B PRO* 3.7 7.9 - - + +
18B LYS* 3.9 5.4 - - + +
164B ASP 2.8 13.3 + - - +
165B ILE* 3.4 7.7 - - + -
166B VAL 2.8 31.2 + - - +
217B CYS* 1.3 72.1 - - - +
219B ILE* 1.3 58.4 + - - +
220B ALA 3.8 0.8 + - - -
252B ASP* 3.6 9.4 - - + +
253B MET* 5.3 1.6 - - + -
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Residues in contact with ILE 219 (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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166B VAL* 3.3 10.1 - - + +
168B VAL* 5.2 1.3 - - + -
206B LEU* 3.8 37.0 - - + +
209B VAL* 4.2 14.4 - - + -
210B LYS* 3.9 25.6 - - + -
213B VAL* 3.9 19.5 - - + -
214B GLY* 3.9 15.5 - - - -
217B CYS 3.6 15.0 - - - +
218B ALA* 1.3 74.3 - - - +
220B ALA* 1.3 62.7 + - - +
250B LEU 4.1 11.7 - - - +
251B VAL* 3.8 0.9 - - - -
252B ASP* 2.8 50.4 + - - +
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Residues in contact with ALA 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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165B ILE* 3.9 16.8 - - + -
166B VAL 2.8 7.1 + - - +
167B TYR* 3.2 33.6 - - + -
168B VAL* 3.0 22.5 + - - +
206B LEU* 5.2 0.2 - - - -
218B ALA 3.8 1.2 + - - -
219B ILE* 1.3 78.9 - - - +
221B THR* 1.3 63.8 + - - +
251B VAL* 5.6 0.7 - - - -
253B MET* 3.5 24.9 - - + +
255B ASP* 5.6 0.4 - - + -
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Residues in contact with THR 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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167B TYR* 3.8 4.7 - - - -
168B VAL* 2.6 21.1 + - - +
202B TRP* 3.0 29.5 + - + +
206B LEU* 4.2 12.1 - - + -
220B ALA* 1.3 79.6 - - - +
222B ARG* 1.3 59.6 + - - +
223B PHE 4.1 0.2 + - - -
251B VAL* 3.8 15.5 - - + +
253B MET 3.2 7.3 + - - +
254B TRP* 3.3 35.7 - - + -
255B ASP* 3.0 25.6 + - - +
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Residues in contact with ARG 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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27B VAL* 3.6 18.0 - - - +
28B PRO* 3.8 5.4 + - - -
103B GLU* 3.7 14.6 - - - -
167B TYR* 3.8 12.7 - - + -
168B VAL 3.3 4.8 + - - -
169B TYR* 4.1 15.0 - - + -
170B GLY* 2.8 30.6 + - - -
171B ALA* 3.9 13.0 - - + -
172B HIS* 3.8 5.7 - - - -
202B TRP* 3.6 3.7 - - - -
221B THR* 1.3 75.7 + - - +
223B PHE* 1.3 59.6 + - - +
255B ASP* 2.7 39.7 + - - +
256B ILE 5.0 0.2 + - - -
257B THR* 3.3 19.9 - - + +
297B VAL* 3.6 9.7 - - - +
1730B FMN 2.8 76.5 + - - -
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Residues in contact with PHE 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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170B GLY 3.5 3.4 - - - -
171B ALA* 4.2 0.2 - - - -
177B LEU* 3.8 5.2 - - + -
180B LEU* 3.6 32.8 - - + -
202B TRP* 3.3 22.4 - + + -
222B ARG* 1.3 77.1 - - - +
224B GLY* 1.3 75.0 + - - +
225B VAL* 3.0 31.8 + - + -
234B ILE* 4.5 3.8 - - + -
240B GLY* 3.5 33.2 - - - -
243B PHE* 3.8 12.1 - + + -
244B VAL* 4.1 6.1 - - + -
254B TRP* 4.1 28.5 - + + -
255B ASP 3.0 5.5 + - - -
256B ILE* 3.6 13.3 - - + +
257B THR* 2.9 25.9 + - - -
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Residues in contact with GLY 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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170B GLY 3.3 11.0 + - - -
171B ALA* 3.7 8.2 - - - +
177B LEU* 4.0 10.5 - - - +
223B PHE* 1.3 85.6 - - - +
225B VAL* 1.3 60.3 + - - -
226B ASP* 3.1 11.0 + - - -
227B THR* 4.8 1.0 + - - -
234B ILE* 4.1 5.9 - - - +
257B THR* 3.3 19.1 - - - -
258B ILE* 4.7 2.9 - - - -
259B GLY 4.8 9.4 - - - -
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Residues in contact with VAL 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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223B PHE* 3.0 34.9 + - + -
224B GLY* 1.3 70.9 - - - -
226B ASP* 1.3 59.4 + - + +
234B ILE* 3.4 11.5 - - - +
236B ALA* 3.2 26.8 + - + -
240B GLY* 3.9 16.9 - - - +
241B GLN* 4.5 2.5 - - + +
256B ILE* 3.5 28.9 - - + -
257B THR 3.0 9.7 + - - +
258B ILE* 4.4 8.5 - - + -
282B TRP* 4.2 19.1 - - + +
285B LEU* 5.8 1.1 - - + -
286B VAL* 4.0 17.0 - - + -
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Residues in contact with ASP 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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616A TYR* 4.5 4.0 - - - -
224B GLY 3.1 4.1 - - - -
225B VAL* 1.3 81.9 - - + +
227B THR* 1.3 60.7 + - - +
228B VAL* 2.7 32.4 + - - +
229B TYR 4.4 0.9 + - - -
230B GLY 5.1 1.9 + - - -
234B ILE 3.3 12.3 - - - +
235B GLU* 3.5 8.4 - - - +
236B ALA* 3.0 21.0 + - + +
257B THR 4.1 0.4 + - - -
258B ILE* 3.3 10.8 - - + +
259B GLY 2.9 21.8 + - - +
282B TRP* 3.4 37.5 + - + -
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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