Contacts of the strand formed by residues 168 - 174 (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 VAL 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A ILE* 3.5 21.1 - - + +
139A VAL* 4.1 13.5 - - + -
156A ILE* 3.8 34.8 - - + -
159A LEU* 4.2 16.6 - - + -
160A LYS* 3.7 25.1 - - + -
166A ILE* 3.9 3.8 - - + +
167A PRO* 1.3 76.6 - - - +
169A LEU* 1.3 63.6 + - - +
170A SER 4.6 0.9 - - - +
200A ALA* 3.9 3.4 - - - -
201A ASP* 2.7 44.3 + - - +
202A ALA 3.3 7.1 + - - +
260A LEU* 4.7 1.8 - - - -
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Residues in contact with LEU 169 (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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137A ILE 3.1 8.8 + - - +
138A ILE* 3.3 17.7 - - + +
139A VAL* 2.8 25.8 + - - +
167A PRO 4.1 1.0 - - - -
168A VAL* 1.3 74.5 - - - +
170A SER* 1.3 69.7 + - - +
171A CYS* 4.0 20.4 - - - -
202A ALA* 3.5 31.4 - - + +
203A CYS 4.6 0.2 - - - -
204A LEU* 4.1 15.9 - - + +
237A LEU* 6.2 0.2 - - + -
240A ILE* 5.4 11.7 - - + -
244A MET* 5.8 0.2 - - + -
256A LEU* 4.2 32.7 - - + +
259A LEU* 6.1 0.7 - - + -
260A LEU* 4.1 12.1 - - + -
272A LEU* 4.6 4.7 - - + -
373A LEU* 6.4 1.1 - - + -
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Residues in contact with SER 170 (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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139A VAL* 3.5 7.0 - - - -
141A HIS* 2.7 26.2 + - - -
156A ILE* 4.9 6.7 - - - -
168A VAL* 4.0 1.6 + - - +
169A LEU* 1.3 72.7 - - - +
171A CYS* 1.3 55.0 + - - +
172A ALA* 3.8 2.3 - - - +
196A LEU* 3.2 28.0 - - - +
200A ALA* 4.5 5.4 - - - -
202A ALA 3.0 13.2 + - - -
203A CYS* 3.2 11.2 - - - -
204A LEU* 2.7 33.6 + - - +
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Residues in contact with CYS 171 (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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138A ILE* 4.0 12.8 - - - -
139A VAL 2.8 8.7 + - - +
140A LEU* 3.6 18.7 - - + +
141A HIS* 3.2 24.8 + - - +
169A LEU* 4.0 24.0 - - - -
170A SER* 1.3 74.1 - - - +
172A ALA* 1.3 59.4 + - - +
173A VAL* 4.0 3.1 + - - +
204A LEU* 3.4 17.3 - - - -
206A PHE* 4.0 15.9 - - + -
237A LEU* 3.8 24.9 - - + -
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Residues in contact with ALA 172 (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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141A HIS* 3.4 9.6 - - - +
143A ILE* 4.4 8.5 - - + -
170A SER* 3.7 15.0 - - - +
171A CYS* 1.3 71.4 - - - +
173A VAL* 1.3 62.7 + - - +
174A LEU* 3.7 11.2 + - + -
196A LEU* 4.2 11.9 - - + -
203A CYS* 3.8 17.5 - - - -
204A LEU 2.9 9.2 + - - +
205A ILE* 3.5 5.6 - - + +
206A PHE* 2.8 26.6 + - - -
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Residues in contact with VAL 173 (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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18A ILE* 3.7 28.7 - - + -
141A HIS 3.0 13.8 + - - +
142A ALA* 3.4 16.2 - - + +
143A ILE* 3.0 25.1 + - - +
144A GLY 4.4 0.7 + - - -
171A CYS 4.8 3.4 - - - +
172A ALA* 1.3 71.9 - - - +
174A LEU* 1.3 63.9 + - - +
175A PRO 4.1 0.2 - - - -
206A PHE* 3.3 13.9 - - + +
208A ASN* 3.4 29.4 - - - +
233A ILE* 4.1 10.3 - - + -
1433A GTP 3.5 21.0 - - + +
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Residues in contact with LEU 174 (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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143A ILE* 3.5 31.2 - - + -
172A ALA* 4.2 3.8 - - + +
173A VAL* 1.3 77.9 - - - +
175A PRO* 1.3 71.1 - - + +
189A THR* 4.5 5.6 - - + -
193A LEU* 5.1 2.0 - - + -
205A ILE* 3.4 47.1 - - + -
206A PHE 2.8 12.7 + - - +
207A ASP* 4.3 11.2 - - - +
208A ASN* 3.1 29.7 + - - +
382A VAL* 3.7 28.3 - - + -
383A LEU* 5.7 0.4 - - + -
385A ARG* 5.0 0.9 - - - +
386A ILE* 4.0 13.5 - - + -
1433A GTP 6.1 0.7 - - - -
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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