Contacts of the strand formed by residues 202 - 207 (chain B) 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 ALA 202 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B VAL 3.5 2.8 + - - -
169B LEU* 3.5 9.3 - - + -
170B SER 2.9 24.6 + - - -
200B ALA* 3.2 8.0 - - - +
201B ASP* 1.3 81.0 - - - +
203B CYS* 1.3 61.6 + - - +
260B LEU* 3.8 29.4 - - + -
264B VAL* 4.2 11.0 - - + -
270B HIS* 3.4 16.6 - - - +
272B LEU* 4.5 6.5 - - + -
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Residues in contact with CYS 203 (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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169B LEU* 4.5 0.7 - - - -
170B SER* 3.3 27.8 - - - -
172B ALA* 3.8 19.7 - - - -
196B LEU* 4.1 15.3 - - + +
202B ALA* 1.3 75.4 - - - +
204B LEU* 1.3 64.1 + - - +
205B ILE* 3.7 4.2 + - - -
270B HIS* 2.9 10.4 + - - +
271B PHE* 3.4 40.3 - - + -
272B LEU* 2.9 26.7 + - - -
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Residues in contact with LEU 204 (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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169B LEU* 4.0 13.1 - - + +
170B SER 2.7 13.5 + - - +
171B CYS* 3.4 15.3 - - - -
172B ALA 2.9 26.9 + - - -
203B CYS* 1.3 70.8 - - - +
205B ILE* 1.3 78.5 + - - +
206B PHE* 3.7 25.6 - - + -
237B LEU* 4.9 0.2 - - + -
240B ILE* 3.7 26.5 - - + -
272B LEU* 3.7 20.2 - - + +
273B MET 3.7 19.7 - - - -
274B CYS* 3.9 11.7 - - + +
373B LEU* 3.9 13.2 - - + -
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Residues in contact with ILE 205 (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 ALA* 3.5 4.0 - - + +
174B LEU* 4.0 38.8 - - + -
193B LEU* 6.0 0.2 - - + -
203B CYS* 4.5 6.3 - - - -
204B LEU* 1.3 89.1 - - - +
206B PHE* 1.3 64.7 + - - +
207B ASP* 4.6 3.1 - - + -
271B PHE* 4.2 26.0 - - + -
272B LEU 3.1 17.1 + - - +
273B MET* 3.8 23.4 - - + -
274B CYS 4.8 0.5 + - - -
306B PHE* 4.1 8.9 - - - +
307B ALA* 4.0 17.3 - - + -
379B ILE* 4.1 17.7 - - + -
382B VAL* 4.2 8.5 - - + -
383B LEU* 5.8 2.5 - - + -
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Residues in contact with PHE 206 (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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171B CYS* 4.0 22.4 - - + -
172B ALA 2.9 14.4 + - - +
173B VAL* 3.2 11.7 - - + +
174B LEU* 2.9 26.0 + - - -
204B LEU* 3.7 37.9 - - + -
205B ILE* 1.3 77.4 - - - +
207B ASP* 1.3 62.7 + - - +
208B ASN 3.4 1.4 + - - -
211B LEU* 4.4 4.9 - - + -
233B ILE* 3.8 48.5 - - + -
236B ALA* 4.2 11.4 - - + -
237B LEU* 4.1 11.2 - - + -
274B CYS* 3.7 19.3 - - - -
306B PHE* 3.7 26.2 - + - -
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Residues in contact with ASP 207 (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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174B LEU* 4.2 8.0 - - + +
205B ILE* 4.0 7.4 - - + -
206B PHE* 1.3 70.4 - - - +
208B ASN* 1.3 65.9 + - - +
209B GLU* 3.1 14.4 + - - +
210B ALA* 3.0 11.5 + - - +
211B LEU* 3.1 15.7 + - - +
306B PHE 3.0 20.2 + - - +
307B ALA* 3.6 11.4 - - + -
308B ALA* 3.0 19.2 + - - +
382B VAL* 3.7 11.6 - - + +
385B ARG* 2.8 45.6 + - - -
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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