Contacts of the strand formed by residues 234 - 241 (chain B) in PDB entry 4U8T
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 ARG 234 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B SER* 2.9 22.7 + - - -
229B VAL 4.2 0.2 + - - -
232B SER* 3.0 38.7 + - - +
233B GLY* 1.3 79.8 - - - +
235B PHE* 1.3 69.4 + - - +
236B CYS* 5.3 3.7 - - + +
273B ASP* 3.2 40.3 + - - -
274B VAL 3.2 19.5 - - - +
275B HIS* 3.9 23.4 + - + -
276B ASN* 3.5 8.8 + - - +
321B GLN* 5.3 3.5 + - - -
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Residues in contact with PHE 235 (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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182B VAL* 4.1 20.4 - - + -
184B LYS* 5.5 2.0 - - + -
226B LEU* 3.6 42.2 - - + -
227B PHE 3.3 15.9 - - - +
228B SER* 3.7 17.9 - - - -
234B ARG* 1.3 82.8 - - - +
236B CYS* 1.3 61.4 + - - +
237B GLY 3.8 0.4 - - - -
272B ARG 4.4 0.7 - - - -
273B ASP* 3.5 3.1 - - - -
274B VAL 2.9 32.5 + - - +
276B ASN* 4.0 11.0 - - - -
279B LEU* 3.9 21.5 - - + -
292B VAL* 4.1 19.7 - - + -
293B THR* 4.3 20.0 - - + -
295B SER* 5.8 0.2 - - - -
309B ILE* 6.1 1.1 - - + -
313B PHE* 4.1 18.2 - + + -
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Residues in contact with CYS 236 (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 LEU* 4.9 3.4 - - + -
191B VAL* 4.0 17.9 - - - -
227B PHE* 2.8 24.5 + - - -
228B SER* 4.6 1.6 - - - -
229B VAL* 4.4 19.1 - - - -
234B ARG* 5.3 5.2 - - + +
235B PHE* 1.3 75.1 - - - +
237B GLY* 1.3 58.4 + - - +
272B ARG 3.2 28.1 + - - -
273B ASP* 3.7 15.4 - - - +
323B PHE* 3.6 37.0 - - + -
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Residues in contact with GLY 237 (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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226B LEU* 3.7 0.9 - - - -
227B PHE* 2.8 29.0 + - - +
235B PHE 3.8 0.4 - - - -
236B CYS* 1.3 82.0 - - - +
238B VAL* 1.3 66.2 + - - +
268B TRP* 3.9 12.3 - - - -
270B VAL 3.2 14.1 - - - -
272B ARG 3.8 1.2 + - - -
313B PHE* 3.9 14.7 - - - -
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Residues in contact with VAL 238 (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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172B ILE* 5.9 0.7 - - + -
224B TYR* 4.3 16.2 - - + -
225B LEU 3.2 10.8 - - - +
226B LEU* 3.7 15.0 - - + -
237B GLY* 1.3 78.7 - - - +
239B ALA* 1.3 70.4 + - - +
268B TRP* 3.6 4.8 - - - -
269B ILE* 2.8 29.8 + - + -
270B VAL* 2.9 28.8 + - + +
310B LEU* 3.8 22.4 - - + -
313B PHE* 3.7 28.9 - - + -
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Residues in contact with ALA 239 (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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224B TYR* 3.5 2.6 - - - -
225B LEU* 2.7 41.4 + - + +
227B PHE* 4.1 14.3 - - + -
238B VAL* 1.3 79.0 - - - +
240B GLU* 1.3 61.1 + - - +
266B VAL* 4.2 11.9 - - + -
267B ARG 3.3 14.6 - - - +
268B TRP* 3.8 28.3 - - + -
269B ILE* 4.1 0.9 - - - +
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Residues in contact with GLU 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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222B LYS* 3.3 38.6 + - + +
223B ILE 3.4 9.4 - - - +
224B TYR* 3.8 15.8 + - + -
225B LEU* 4.9 1.1 - - - -
239B ALA* 1.3 75.0 - - - +
241B MSE 1.3 67.6 + - - +
266B VAL* 3.0 8.6 - - - +
267B ARG* 2.7 71.6 + - + +
269B ILE* 3.1 35.9 - - + +
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Residues in contact with MSE 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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210B LEU* 3.3 63.0 - - + +
211B SER* 5.8 0.2 - - - -
214B TYR* 3.7 38.4 - - + -
222B LYS* 5.8 1.9 - - - +
223B ILE* 3.2 29.4 + - + +
225B LEU* 3.5 20.6 - - + +
239B ALA 4.4 0.2 + - - -
240B GLU* 1.3 80.3 - - - +
242B SER* 1.3 59.7 + - - +
243B SER 4.1 6.5 - - - +
264B PHE* 4.0 21.8 - - + -
265B LYS 3.5 7.2 - - - +
266B VAL* 4.4 1.3 - - - +
267B ARG* 3.5 12.5 + - - -
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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