Contacts of the strand formed by residues 271 - 277 (chain B) in PDB entry 3THW
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 271 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220B TYR* 4.2 11.0 - + - -
224B GLU* 3.5 38.4 + - + +
227B TYR* 4.6 13.2 - + - -
228B ILE* 3.6 38.6 - - + -
250B PHE* 4.3 17.3 - + + -
251B GLY* 3.4 28.0 - - - +
267B LEU* 3.2 9.5 - - - +
268B ASP 3.1 28.2 + - - +
270B ASN* 1.3 87.3 - - + +
272B MET* 1.3 64.1 + - - +
273B THR* 4.5 1.3 + - - +
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Residues in contact with MET 272 (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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250B PHE* 3.4 1.0 - - - -
251B GLY* 2.7 40.0 + - - +
254B ALA* 3.2 9.1 - - + +
255B GLU* 4.3 27.6 - - + +
265B CYS* 3.0 43.3 - - + +
266B HIS* 3.4 6.3 - - - +
267B LEU* 4.0 27.6 - - + -
271B PHE* 1.3 74.7 - - - +
273B THR* 1.3 63.4 + - - +
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Residues in contact with THR 273 (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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248B ARG* 3.1 42.7 + - - +
249B PHE 3.2 6.5 - - - +
250B PHE* 3.2 26.9 - - - -
254B ALA* 3.7 2.7 - - - -
264B TYR 3.8 0.3 - - - +
265B CYS* 3.1 18.7 - - - -
266B HIS* 2.9 34.2 + - - +
268B ASP* 4.9 11.3 + - - +
271B PHE* 4.5 2.9 + - - +
272B MET* 1.3 75.0 + - - +
274B ALA* 1.3 68.7 + - - +
275B SER* 4.3 3.4 - - - +
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Residues in contact with ALA 274 (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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248B ARG* 3.6 4.0 - - - -
249B PHE* 3.1 39.8 + - + -
254B ALA* 3.7 10.6 - - + +
263B ILE* 3.6 22.4 - - + -
264B TYR 3.2 22.0 - - - +
265B CYS* 4.2 7.6 - - + -
273B THR* 1.3 75.0 - - - +
275B SER* 1.3 67.8 + - - +
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Residues in contact with SER 275 (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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246B LYS* 3.7 32.8 - - - +
247B TYR 3.5 5.2 - - - -
248B ARG* 3.9 16.5 - - - -
249B PHE* 5.2 0.2 - - - -
263B ILE* 4.3 10.3 - - - +
264B TYR 4.7 1.4 + - - -
273B THR* 4.3 4.2 - - - +
274B ALA* 1.3 79.7 + - - +
276B ILE* 1.3 72.4 + - - +
277B PRO* 4.8 0.7 - - - +
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Residues in contact with ILE 276 (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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240B CYS* 5.3 0.9 - - - -
246B LYS* 3.1 5.8 - - - +
247B TYR* 2.7 56.8 + - + +
249B PHE* 4.1 21.5 - - + -
261B LEU* 5.0 0.2 - - + -
263B ILE* 4.1 23.1 - - + -
275B SER* 1.3 81.2 - - - +
277B PRO* 1.3 73.0 - - + +
280B ARG 4.6 4.9 - - - +
281B LEU* 4.6 14.6 - - + -
284B HIS* 3.9 48.5 - - + +
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Residues in contact with PRO 277 (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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245B TYR* 4.0 4.5 - - + +
246B LYS* 3.9 15.9 - - + +
247B TYR* 4.9 0.2 - - - -
275B SER 4.8 0.7 - - - +
276B ILE* 1.3 90.6 - - + +
278B THR* 1.3 55.5 + - - +
279B HIS* 3.6 22.4 - - + +
280B ARG* 2.7 55.6 + - + +
281B LEU* 3.7 0.9 + - - -
284B HIS* 5.8 1.1 - - - +
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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