Contacts of the strand formed by residues 227 - 235 (chain F) in PDB entry 1II4
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 GLY 227 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193F LYS* 5.4 0.7 - - - -
194F ASN* 3.6 11.9 - - - -
225F ASP 3.4 1.5 + - - -
226F LYS* 1.3 79.1 - - - +
228F ASN* 1.3 66.4 + - - -
229F TYR* 3.4 10.7 - - - -
245F HIS* 3.6 1.3 - - - -
246F LEU 2.8 31.9 + - - +
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Residues in contact with ASN 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F LEU 3.4 0.2 - - - +
193F LYS* 3.2 5.7 - - - +
194F ASN* 2.7 49.4 + - - +
195F GLY 5.5 0.2 - - - +
227F GLY* 1.3 76.3 - - - -
229F TYR* 1.3 62.8 + - - +
230F THR* 4.1 2.9 + - - +
243F THR* 3.9 19.4 - - + +
244F TYR 3.4 2.1 + - - -
245F HIS* 3.7 24.2 - - - +
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Residues in contact with TYR 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177F PHE* 3.8 30.5 - + + -
191F TRP* 4.5 8.7 - - + -
192F LEU 3.1 11.4 - - - +
193F LYS* 3.6 26.6 + - + +
198F PHE* 3.8 17.8 - + - -
216F LEU* 4.1 11.7 - - + -
218F MET* 3.5 27.3 - - + +
225F ASP* 2.3 41.6 + - - +
227F GLY 3.4 20.2 - - - -
228F ASN* 1.3 73.8 - - - +
230F THR* 1.3 61.3 + - - +
231F CYS 4.3 0.3 + - - -
242F HIS 3.9 0.5 - - - +
243F THR* 3.4 1.1 - - - -
244F TYR* 2.7 46.1 + - + +
246F LEU* 3.6 14.6 - - + -
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Residues in contact with THR 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F ARG 3.6 0.3 - - - +
191F TRP* 3.1 8.5 - - - -
192F LEU* 2.6 56.1 + - + +
195F GLY* 5.0 5.9 + - - -
228F ASN* 4.8 3.1 + - - +
229F TYR* 1.3 76.2 + - - +
231F CYS* 1.3 67.6 + - - +
232F VAL* 3.9 8.0 + - + -
241F ASN* 3.9 20.4 - - + +
242F HIS 3.3 15.0 - - - +
243F THR* 2.9 25.1 + - - +
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Residues in contact with CYS 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156F TRP* 3.7 9.2 - - - -
179F CYS* 2.6 48.0 - - + -
189F MET* 4.1 6.3 - - + -
190F ARG 3.4 5.2 - - - -
191F TRP* 3.6 22.7 - - + -
230F THR* 1.3 74.2 - - - +
232F VAL* 1.3 61.2 + - - +
241F ASN* 3.1 20.8 - - - +
242F HIS* 3.0 28.0 + - - -
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Residues in contact with VAL 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188F THR 3.6 0.9 - - - +
189F MET* 3.4 4.1 - - - +
190F ARG* 2.8 62.1 + - + +
192F LEU* 4.0 29.8 - - + -
230F THR* 4.2 5.4 - - + -
231F CYS* 1.3 78.6 - - - +
233F VAL* 1.3 61.6 + - - +
234F GLU* 3.3 25.7 + - - +
239F SER* 4.0 8.1 - - - +
240F ILE 3.7 4.9 - - - +
241F ASN* 4.0 13.9 - - + -
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Residues in contact with VAL 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F PRO* 4.0 6.0 - - + +
156F TRP* 3.4 34.1 - - + -
181F ALA* 3.9 12.8 - - + -
187F PRO* 3.3 31.2 - - + -
188F THR 3.1 9.9 - - - +
189F MET* 4.2 22.2 - - + -
214F TRP* 4.2 4.5 - - + -
231F CYS 4.9 0.2 - - - -
232F VAL* 1.3 78.4 - - - +
234F GLU* 1.3 68.7 + - - +
239F SER* 3.3 1.7 + - - -
240F ILE* 2.9 39.4 + - + +
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Residues in contact with GLU 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F PRO* 3.5 4.3 - - - -
187F PRO* 2.9 7.7 - - - +
188F THR* 2.7 51.1 + - - +
190F ARG* 3.3 33.7 + - - -
232F VAL* 3.3 11.4 - - - +
233F VAL* 1.3 78.9 - - - +
235F ASN* 1.3 62.2 + - - +
238F GLY 3.3 13.9 - - - +
239F SER* 2.8 26.8 + - - +
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Residues in contact with ASN 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F ARG 2.9 26.6 + - - -
153F ALA 3.7 0.2 - - - -
154F PRO* 3.3 25.3 - - - +
183F GLY* 4.1 2.0 - - - -
184F ASN 4.0 3.0 - - - +
185F PRO* 3.2 35.1 + - + +
186F MET 4.8 1.1 - - - +
187F PRO* 4.1 4.2 - - + +
234F GLU* 1.3 76.5 - - - +
236F GLU* 1.3 60.5 + - - +
237F TYR* 2.7 39.3 + - - +
238F GLY 3.0 18.7 + - - +
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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