Contacts of the strand formed by residues 228 - 233 (chain B) in PDB entry 4CY1
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 228 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222B PHE* 3.4 9.9 - - - -
223B SER* 2.9 41.5 + - - +
225B ASN* 4.1 12.7 + - - -
226B GLY 4.4 0.5 - - - -
227B LYS* 1.3 107.5 - - + +
229B ILE* 1.3 65.2 + - - +
240B LEU* 3.5 35.4 - - + -
241B TRP 3.2 13.0 - - - +
242B ASP* 4.8 2.7 - - + -
243B TYR* 3.8 3.3 - - - -
249B LEU* 3.4 34.5 - - + -
266B PHE* 4.7 3.1 - + - -
288B LEU* 5.4 9.0 - - + +
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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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187B VAL* 4.2 17.5 - - + -
195B CYS* 4.3 6.1 - - + -
197B ILE* 4.5 0.7 - - + -
209B LEU* 3.2 32.8 - - + -
220B VAL* 3.8 21.1 - - + -
221B LYS 3.2 10.3 - - - +
222B PHE* 3.5 38.8 - - + +
223B SER 4.5 0.2 - - - +
228B TYR* 1.3 75.6 - - - +
230B LEU* 1.3 59.7 + - - +
231B ALA* 4.1 0.8 + - + -
239B LYS 3.7 0.9 - - - +
240B LEU* 3.6 3.9 - - - +
241B TRP* 2.9 47.1 + - + +
243B TYR* 3.7 13.4 - - + -
266B PHE* 4.6 0.4 - - - -
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Residues in contact with LEU 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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219B PHE* 4.4 3.4 - - + -
220B VAL* 3.1 5.4 - - - -
221B LYS* 2.8 35.7 + - + +
229B ILE* 1.3 72.3 - - - +
231B ALA* 1.3 60.5 + - - +
232B ALA 4.4 0.2 + - - -
238B LEU* 4.2 22.4 - - + -
239B LYS 3.5 20.2 - - - +
240B LEU* 4.4 4.0 - - + +
252B TYR* 4.4 8.1 - - + -
264B ALA* 3.7 28.0 - - + +
265B ASN 4.1 13.2 - - - +
266B PHE* 3.5 23.5 - - + -
274B ILE* 4.1 33.2 - - + -
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Residues in contact with ALA 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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195B CYS* 3.9 27.6 - - - -
217B VAL* 4.3 4.5 - - + -
219B PHE 3.3 6.3 - - - +
220B VAL* 4.1 3.8 - - + -
229B ILE* 4.0 0.9 - - + -
230B LEU* 1.3 75.2 - - - +
232B ALA* 1.3 59.7 + - - +
233B THR* 4.2 4.0 + - + +
237B THR 4.0 0.7 - - - +
238B LEU* 3.4 5.4 - - - -
239B LYS* 2.8 42.8 + - + +
241B TRP* 4.3 17.5 - - + +
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Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B VAL* 3.3 9.4 - - - +
218B SER* 2.8 36.3 + - - +
219B PHE* 2.8 24.0 + - + -
230B LEU 4.4 0.2 + - - -
231B ALA* 1.3 72.6 - - - +
233B THR* 1.3 61.2 + - - +
237B THR 3.6 5.6 - - - +
238B LEU* 3.5 20.6 - - + +
257B ASN* 4.2 13.2 - - - +
262B ILE 4.6 4.7 - - - +
264B ALA* 5.5 0.2 - - + -
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Residues in contact with THR 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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215B PRO* 3.7 26.5 - - + +
216B PRO 3.2 13.7 - - - +
217B VAL* 3.9 14.1 - - + -
218B SER* 4.1 4.5 - - - -
231B ALA* 5.3 4.2 + - + +
232B ALA* 1.3 78.6 - - - +
234B LEU* 1.3 58.9 + - - +
235B ASP* 2.7 31.4 + - - +
236B ASN 3.5 6.2 + - - -
237B THR 2.9 18.6 + - - +
239B LYS* 3.5 19.3 + - - +
257B ASN* 3.7 7.4 + - - +
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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