Contacts of the strand formed by residues 168 - 174 (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 VAL 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137B ILE* 3.4 13.7 - - + +
139B VAL* 4.5 5.2 - - + -
156B ILE* 4.3 31.9 - - + -
159B LEU* 3.7 34.8 - - + -
160B LYS* 3.8 21.3 - - + -
166B ILE* 3.8 4.5 - - + +
167B PRO* 1.3 78.6 - - - +
169B LEU* 1.3 66.5 + - - +
170B SER 4.1 0.8 + - - +
200B ALA* 4.0 2.9 - - - -
201B ASP* 2.6 42.6 + - - +
202B ALA 3.5 2.4 + - - +
260B LEU* 5.0 1.1 - - - -
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Residues in contact with LEU 169 (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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137B ILE 3.0 9.2 + - - +
138B ILE* 3.4 17.5 - - + +
139B VAL* 2.9 25.3 + - - +
167B PRO 4.2 0.8 - - - -
168B VAL* 1.3 75.7 - - - +
170B SER* 1.3 78.6 + - - +
171B CYS* 3.9 16.9 + - - -
202B ALA* 3.5 26.7 - - + +
203B CYS 4.5 0.2 - - - -
204B LEU* 4.0 16.4 - - + +
240B ILE* 5.7 9.2 - - + -
256B LEU* 4.0 34.9 - - + +
259B LEU* 6.1 0.9 - - + -
260B LEU* 4.5 11.7 - - + -
272B LEU* 5.1 4.3 - - + -
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Residues in contact with SER 170 (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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139B VAL* 3.6 7.0 - - - -
141B HIS* 2.9 24.8 + - - -
156B ILE* 4.3 8.3 - - - -
168B VAL 4.1 0.8 + - - -
169B LEU* 1.3 76.5 - - - +
171B CYS* 1.3 54.8 + - - +
172B ALA* 3.7 2.4 - - - +
196B LEU* 3.2 29.0 - - - +
200B ALA* 4.4 3.7 - - - +
202B ALA 2.9 14.7 + - - -
203B CYS* 3.3 11.7 - - - -
204B LEU 2.7 32.4 + - - -
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Residues in contact with CYS 171 (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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138B ILE* 4.2 6.1 - - - -
139B VAL 2.8 9.5 + - - +
140B LEU* 3.7 23.2 - - + +
141B HIS* 3.1 27.5 + - - +
169B LEU* 3.9 22.4 + - - -
170B SER* 1.3 76.0 - - - +
172B ALA* 1.3 59.0 + - - +
173B VAL* 5.3 1.5 - - - +
204B LEU* 3.4 15.9 - - - -
206B PHE* 4.0 16.4 - - + -
237B LEU* 3.8 25.1 - - + -
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Residues in contact with ALA 172 (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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141B HIS* 3.2 12.1 - - - +
143B ILE* 4.2 20.9 - - + -
170B SER* 3.7 14.6 - - - +
171B CYS* 1.3 73.9 - - - +
173B VAL* 1.3 63.5 + - - +
174B LEU* 3.8 4.3 + - + +
196B LEU* 4.3 4.0 - - + -
203B CYS* 3.8 16.2 - - - -
204B LEU 2.9 8.3 + - - -
205B ILE* 3.5 6.2 - - + +
206B PHE* 2.9 26.1 + - - -
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Residues in contact with VAL 173 (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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18B ILE* 3.8 28.7 - - + -
141B HIS 2.8 18.5 + - - +
142B ALA* 3.5 14.9 - - + +
143B ILE* 3.0 29.6 + - - +
144B GLY 4.4 0.2 + - - -
171B CYS 5.3 1.6 - - - +
172B ALA* 1.3 73.2 - - - +
174B LEU* 1.3 63.0 + - - +
175B PRO* 4.3 0.7 - - - +
206B PHE* 3.2 16.6 - - + +
208B ASN* 3.2 38.4 - - - +
233B ILE* 4.2 10.5 - - + -
1433B GTP 3.9 11.3 - - + +
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Residues in contact with LEU 174 (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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143B ILE* 3.4 33.0 - - + -
172B ALA* 4.2 9.6 - - + +
173B VAL* 1.3 77.4 - - - +
175B PRO* 1.3 71.2 - - + +
189B THR* 4.4 7.0 - - + -
193B LEU* 5.4 4.0 - - + -
205B ILE* 4.0 29.6 - - + -
206B PHE 2.9 13.1 + - - +
207B ASP* 4.3 8.3 - - - +
208B ASN* 3.1 31.2 + - - +
382B VAL* 3.6 31.0 - - + -
383B LEU* 5.2 7.4 - - + -
385B ARG* 4.7 2.0 - - - +
386B ILE* 5.0 9.6 - - + -
1433B GTP 5.0 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