Contacts of the strand formed by residues 227 - 232 (chain B) in PDB entry 3K74
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 PHE 227 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B ARG* 4.2 0.2 - - - -
207B VAL* 3.6 26.9 - - + -
208B SER* 4.5 3.6 - - - +
219B TYR* 3.3 16.8 - - + -
223B VAL* 3.0 39.8 + - + +
225B GLY 4.9 3.5 + - - -
226B ARG* 1.3 111.7 + - + +
228B THR* 1.3 63.5 + - - +
240B LEU* 3.9 15.5 - - + -
241B GLN 3.0 8.1 - - - +
242B MET* 2.8 50.9 - - + -
243B ASN 4.3 2.5 - - - -
245B LEU* 4.2 2.5 - - + -
249B ASP* 3.9 15.3 - - - -
253B TYR* 4.1 7.6 - + - -
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Residues in contact with THR 228 (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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219B TYR* 3.4 9.6 - - - +
226B ARG 5.2 0.9 + - - -
227B PHE* 1.3 76.0 + - - +
229B ILE* 1.3 72.5 + - - +
230B SER* 4.1 6.5 + - - -
239B TYR 3.9 0.3 - - - +
240B LEU* 3.5 4.5 - - - -
241B GLN* 2.9 52.3 + - - +
243B ASN* 5.7 1.7 + - - -
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Residues in contact with ILE 229 (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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193B MET 4.0 4.0 - - - +
195B TRP* 3.6 24.0 - - + +
208B SER* 3.8 13.0 - - - +
209B MET* 3.6 37.2 - - - +
210B ILE* 3.6 32.8 - - + +
217B THR* 3.7 15.2 - - + +
219B TYR* 3.0 28.6 + - + +
228B THR* 1.3 81.4 - - - +
230B SER* 1.3 65.3 - - - +
238B LEU* 4.1 6.5 - - + -
239B TYR 3.5 13.0 - - - +
240B LEU* 4.4 1.8 - - + -
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Residues in contact with SER 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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178B ARG* 4.0 8.8 + - - -
210B ILE* 3.7 10.8 - - - -
228B THR* 5.1 7.4 + - - -
229B ILE* 1.3 76.9 - - - +
231B ARG* 1.3 63.6 + - - +
238B LEU* 3.3 8.3 - - - +
239B TYR* 2.8 49.9 + - - +
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Residues in contact with ARG 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B PHE* 2.9 44.9 + - + -
191B TYR 2.9 23.0 + - - -
193B MET* 3.6 17.3 - - - +
210B ILE* 3.5 23.6 + - + +
211B ASN 2.9 31.0 + - - -
212B PRO 3.4 14.3 + - - +
213B GLY 5.1 0.2 - - - -
214B GLY* 3.9 13.7 - - - -
230B SER* 1.3 81.8 - - - +
232B ASP* 1.3 60.8 + - - +
233B ASN* 2.9 21.1 + - - +
237B THR 3.3 11.9 - - - +
238B LEU* 4.0 8.5 - - + -
239B TYR* 4.3 5.2 - - - -
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Residues in contact with ASP 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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188B PHE* 4.0 0.6 - - - -
231B ARG* 1.3 74.8 - - - +
233B ASN* 1.3 59.4 + - - +
234B ALA* 3.0 21.5 + - - +
235B LYS* 3.2 40.7 + - + +
236B ASN 2.8 25.1 + - - -
237B THR 2.8 15.6 + - - +
239B TYR* 4.0 18.2 + - + +
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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