Contacts of the strand formed by residues 271 - 277 (chain A) in PDB entry 2BTO
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A LEU* 3.8 20.4 - - + -
196A LEU* 3.9 17.9 - - + -
197A ARG* 4.2 7.0 - - - -
203A CYS* 3.3 26.7 - - + -
205A ILE* 3.6 28.5 - - + -
270A HIS* 1.3 99.5 - + - +
272A LEU* 1.3 59.8 + - - +
375A ASN* 3.0 26.2 - - - +
376A ASN 4.7 1.2 + - - -
379A ILE* 4.3 15.8 - - + +
383A LEU* 4.6 4.5 - - + -
423A LEU* 3.4 45.5 - - + -
427A TYR* 2.8 25.3 + + + +
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LEU* 4.6 12.6 - - + -
202A ALA* 4.3 18.8 - - + -
203A CYS 2.7 15.2 + - - +
204A LEU* 4.0 11.7 - - + -
205A ILE* 3.0 31.4 + - - +
260A LEU* 4.7 2.5 - - + -
263A LEU* 4.1 38.1 - - + +
264A VAL* 5.0 1.8 - - + -
270A HIS 4.2 5.6 - - - +
271A PHE* 1.3 83.6 - - - +
273A MET* 1.3 66.6 + - - +
373A LEU* 4.5 12.8 - - + -
374A ALA 3.3 15.7 - - - +
375A ASN* 3.9 22.0 - - + +
379A ILE* 3.8 1.6 - - - +
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Residues in contact with MET 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A LEU* 3.9 4.9 - - - -
205A ILE* 4.6 3.8 - - + -
272A LEU* 1.3 73.0 - - - +
274A CYS* 1.3 64.1 + - - +
305A VAL* 5.2 6.1 - - + -
307A ALA* 4.0 18.8 - - + -
309A CYS* 3.4 27.8 - - - -
311A PRO* 4.0 24.0 - - + -
373A LEU* 3.6 2.6 - - - +
374A ALA* 2.9 39.1 + - + +
376A ASN* 3.5 35.2 - - + +
379A ILE* 3.4 39.0 - - + -
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Residues in contact with CYS 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A LEU* 3.8 10.7 - - + +
205A ILE 4.7 2.0 + - - -
206A PHE* 3.7 30.7 - - - -
236A ALA* 4.2 12.1 - - + -
240A ILE* 4.9 4.9 - - + -
273A MET* 1.3 76.7 - - - +
275A ALA* 1.3 59.3 + - - +
305A VAL* 3.5 6.0 - - - +
306A PHE* 2.8 48.5 + - - +
371A VAL* 5.9 0.9 - - + -
372A LEU* 3.0 14.4 - - - +
373A LEU* 3.7 16.2 - - + -
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Residues in contact with ALA 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A CYS* 1.3 77.0 - - - +
276A PHE* 1.3 61.7 + - - +
299A LEU* 3.5 26.0 - - - +
304A SER* 3.4 20.2 - - - +
305A VAL* 3.8 15.5 - - + -
306A PHE* 4.4 3.8 - - - -
371A VAL* 3.3 8.9 - - - +
372A LEU* 2.8 38.3 + - + +
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Residues in contact with PHE 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A GLU* 3.2 61.5 - - + -
236A ALA* 4.4 1.3 - - + -
239A GLY* 5.7 1.8 - - - -
275A ALA* 1.3 77.6 - - - +
277A ALA* 1.3 77.4 + - - +
278A PRO* 3.5 24.9 - - + -
279A LEU* 3.4 26.0 - - + +
298A SER 5.5 0.2 - - - -
299A LEU* 3.8 4.5 - - - +
304A SER* 4.0 11.0 + - - -
306A PHE* 3.8 22.8 - - + -
365A SER* 5.6 1.3 - - - -
366A HIS* 4.3 7.4 - + - -
369A SER* 3.8 24.7 - - - -
370A MET 3.5 10.1 - - - -
371A VAL* 3.5 22.4 - - + -
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Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A PHE* 1.3 79.4 - - - +
278A PRO* 1.3 70.3 - - + +
279A LEU 4.0 0.9 - - - +
295A MET* 3.8 33.8 - - + +
298A SER* 4.7 6.7 - - - -
299A LEU* 4.0 16.6 - - + +
369A SER* 3.3 3.6 - - - -
370A MET* 2.8 38.4 + - + +
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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