Contacts of the strand formed by residues 237 - 242 (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 THR 237 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B ALA 4.0 0.3 - - - +
232B ALA* 3.6 2.6 - - - +
233B THR* 2.9 34.5 + - - +
235B ASP* 2.9 33.8 + - - -
236B ASN* 1.3 76.3 + - - +
238B LEU* 1.3 66.5 + - - +
239B LYS* 3.7 20.0 - - + +
251B THR* 3.3 32.1 - - + -
252B TYR 3.8 2.2 - - - -
253B THR* 4.2 7.6 - - + +
255B HIS* 3.8 4.2 + - - -
257B ASN* 5.5 0.2 + - - -
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B PHE* 5.8 0.2 - - + -
230B LEU* 4.2 10.8 - - + -
231B ALA 3.4 5.8 - - - +
232B ALA* 3.5 30.5 - - + +
237B THR* 1.3 76.5 - - - +
239B LYS* 1.3 63.2 + - - +
251B THR* 3.4 4.0 - - - -
252B TYR* 2.8 47.9 + - + +
255B HIS* 4.0 8.9 - - - +
264B ALA* 3.8 19.7 - - + -
274B ILE* 4.1 12.8 - - + -
276B SER* 3.8 17.7 - - - +
286B TRP* 3.7 35.2 - - + -
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Residues in contact with LYS 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ASP* 3.3 27.4 + - - +
215B PRO* 5.1 4.4 - - - +
230B LEU* 3.5 7.4 - - - -
231B ALA* 2.8 38.4 + - + +
233B THR* 3.5 28.7 + - + +
235B ASP* 4.4 7.5 + - - -
237B THR* 3.7 19.2 - - + +
238B LEU* 1.3 81.4 - - - +
240B LEU* 1.3 61.6 + - - +
241B TRP* 3.5 25.3 - - + +
248B CYS* 3.8 18.8 - - - -
250B LYS 3.4 6.1 - - - +
251B THR* 4.2 9.2 - - - +
252B TYR* 4.9 0.2 - - - -
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Residues in contact with LEU 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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228B TYR* 3.5 48.9 - - + -
229B ILE 3.6 4.0 - - - +
230B LEU* 4.6 5.2 - - + -
239B LYS* 1.3 72.1 - - - +
241B TRP* 1.3 54.1 + - - +
248B CYS* 3.7 2.4 - - - -
249B LEU* 2.8 37.6 + - + -
250B LYS* 3.0 43.4 + - + +
252B TYR* 4.0 17.1 - - + +
266B PHE* 3.5 30.7 - - + -
274B ILE* 5.2 0.4 - - + -
288B LEU* 4.3 14.6 - - + -
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Residues in contact with TRP 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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195B CYS* 5.9 1.3 - - - -
209B LEU* 4.0 31.9 - - + -
210B ILE 4.0 11.7 - - - -
211B ASP* 3.8 47.1 - - + -
228B TYR* 3.2 10.7 - - - +
229B ILE* 2.9 47.4 + - + -
231B ALA* 4.3 16.0 - - + +
239B LYS* 3.5 35.3 - - + +
240B LEU* 1.3 76.1 - - - +
242B ASP* 1.3 62.4 + - - +
243B TYR 3.5 0.2 + - - -
246B GLY 3.8 20.0 - - - -
247B LYS* 3.4 22.7 - - - -
248B CYS* 4.0 15.3 - - + -
249B LEU* 4.4 4.0 - - - -
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Residues in contact with ASP 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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227B LYS 4.4 11.8 - - - +
228B TYR* 4.9 1.4 - - - -
241B TRP* 1.3 69.1 - - - +
243B TYR* 1.3 58.3 + - - +
244B SER* 3.1 21.7 + - - -
245B LYS* 3.1 37.6 + - + +
246B GLY* 2.8 24.4 + - - -
247B LYS* 2.8 20.7 + - + +
249B LEU* 3.9 26.7 - - + +
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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