Contacts of the strand formed by residues 202 - 207 (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 ALA 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A VAL 3.3 3.6 + - - +
169A LEU* 3.5 21.3 - - + -
170A SER 3.0 22.5 + - - -
200A ALA* 3.3 6.5 - - - +
201A ASP* 1.3 82.0 - - - +
203A CYS* 1.3 61.5 + - - +
260A LEU* 3.9 20.9 - - + -
264A VAL* 4.3 8.3 - - + -
270A HIS* 3.3 18.4 - - - +
272A LEU* 4.3 8.1 - - + -
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Residues in contact with CYS 203 (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 0.9 - - - -
170A SER* 3.2 25.4 - - - -
172A ALA* 3.8 20.2 - - - -
196A LEU* 3.8 15.3 - - + +
202A ALA* 1.3 74.7 - - - +
204A LEU* 1.3 58.6 + - - +
205A ILE* 3.8 3.3 + - - -
270A HIS* 3.0 8.7 + - + -
271A PHE* 3.3 42.2 - - + -
272A LEU* 2.7 32.0 + - - -
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Residues in contact with LEU 204 (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* 4.1 14.9 - - + +
170A SER 2.7 12.5 + - - +
171A CYS* 3.4 17.8 - - - -
172A ALA 2.9 25.8 + - - -
203A CYS* 1.3 70.2 - - - +
205A ILE* 1.3 79.5 + - - +
206A PHE* 3.6 28.9 - - + -
237A LEU* 4.6 5.6 - - + -
240A ILE* 4.7 10.3 - - + -
272A LEU* 3.6 17.0 - - + +
273A MET 3.9 0.2 - - - -
274A CYS* 3.8 26.5 - - + +
373A LEU* 3.7 27.6 - - + -
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Residues in contact with ILE 205 (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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172A ALA* 3.5 7.9 - - + +
174A LEU* 3.4 48.2 - - + -
193A LEU* 4.9 1.3 - - + -
203A CYS* 3.8 1.7 + - - -
204A LEU* 1.3 87.1 - - - +
206A PHE* 1.3 66.3 + - - +
207A ASP* 4.5 2.2 - - + +
271A PHE* 3.6 35.2 - - + -
272A LEU 3.0 14.1 + - - +
273A MET* 4.6 4.4 - - + -
274A CYS* 4.7 2.4 + - - -
306A PHE 4.2 4.5 - - - +
307A ALA* 4.5 19.1 - - + -
379A ILE* 4.0 23.8 - - + -
382A VAL* 5.0 2.7 - - + -
383A LEU* 4.4 11.7 - - + -
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Residues in contact with PHE 206 (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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171A CYS* 4.0 19.7 - - + -
172A ALA 2.8 16.0 + - - +
173A VAL* 3.3 11.3 - - + +
174A LEU* 2.8 25.8 + - - -
204A LEU* 3.6 38.1 - - + -
205A ILE* 1.3 77.0 - - - +
207A ASP* 1.3 63.3 + - - +
208A ASN 3.4 1.4 + - - -
211A LEU* 4.2 11.9 - - + -
233A ILE* 3.8 39.5 - - + -
236A ALA* 4.1 8.7 - - + -
237A LEU* 4.2 11.7 - - + -
274A CYS* 3.7 19.7 - - - -
306A PHE* 3.7 28.0 - + + -
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Residues in contact with ASP 207 (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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174A LEU* 4.3 14.1 - - + +
175A PRO 4.4 2.1 - - - +
205A ILE* 4.1 1.0 - - + +
206A PHE* 1.3 71.2 - - - +
208A ASN* 1.3 69.6 + - - +
209A GLU* 3.2 11.2 + - - -
210A ALA* 3.2 4.6 + - + +
211A LEU* 3.2 22.8 + - - +
306A PHE 2.9 7.3 + - - -
307A ALA* 3.6 23.1 - - + -
308A ALA* 3.0 19.6 + - - +
382A VAL* 3.8 10.7 - - + +
385A ARG* 2.7 45.5 + - - -
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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