Contacts of the strand formed by residues 168 - 172 (chain C) in PDB entry 2BHT
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 HIS 168 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C ILE* 3.5 11.6 - - - +
167C THR* 1.3 114.0 + - - +
169C PHE* 1.3 60.2 + - - +
170C VAL* 5.2 0.4 - - + -
193C VAL* 4.3 0.2 - - - -
194C THR* 3.2 37.9 + - + +
196C VAL* 4.9 5.8 - - + -
266C VAL* 4.4 22.7 - - + -
270C ASN* 4.0 27.0 + - + -
273C ALA* 3.8 17.6 - - + +
274C VAL 3.8 2.2 + - - -
275C VAL* 4.3 19.6 + - + +
276C VAL 3.2 23.7 + - - -
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Residues in contact with PHE 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C ILE* 4.1 9.6 - - + -
166C ILE* 4.1 11.0 - - + -
168C HIS* 1.3 73.7 - - - +
170C VAL* 1.3 66.8 + - - +
171C SER* 3.9 15.0 - - - -
178C THR* 4.5 1.8 - - + -
179C ILE* 4.2 20.3 - - + +
182C VAL* 3.3 50.5 - - + -
183C SER 4.9 0.7 - - - -
186C MET* 5.1 0.2 - - + -
193C VAL* 4.0 2.1 - - + +
194C THR 2.9 9.7 + - - -
195C ILE* 3.5 17.4 - - + -
196C VAL* 2.7 34.1 + - - +
276C VAL* 3.3 20.6 - - + -
278C ILE* 3.2 43.3 - - + -
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Residues in contact with VAL 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C HIS* 5.2 0.9 - - + -
169C PHE* 1.3 92.3 - - - +
171C SER* 1.3 69.8 + - - +
196C VAL* 3.1 27.1 - - + +
198C LEU* 4.1 20.6 - - + -
259C ALA* 3.6 26.2 - - + +
262C GLY 5.0 0.4 - - - -
263C ALA* 3.9 23.6 - - + +
266C VAL* 4.7 5.4 - - + -
275C VAL* 4.3 14.1 - - + -
276C VAL 3.0 14.5 + - - +
277C ALA* 4.4 5.8 - - + -
278C ILE 3.7 8.9 + - - -
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Residues in contact with SER 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C PHE* 3.9 9.9 - - - -
170C VAL* 1.3 85.4 - - - +
172C SER* 1.3 70.2 + - - +
173C MET* 3.6 4.7 - - - +
178C THR* 4.0 11.2 - - - +
179C ILE* 3.3 42.1 + - - +
196C VAL 3.3 2.6 + - - -
197C GLY* 3.1 22.9 - - - -
198C LEU 3.2 2.6 + - - -
259C ALA* 5.5 1.6 - - - -
278C ILE* 5.1 8.8 - - - +
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Residues in contact with SER 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C SER* 1.3 78.5 + - - +
173C MET* 1.3 59.4 + - - +
178C THR* 5.5 0.3 - - - -
198C LEU* 3.7 21.5 - - - +
209C ILE* 3.5 28.4 - - - +
255C SER* 3.3 26.6 + - - -
258C GLY 4.2 0.7 - - - -
259C ALA* 3.6 17.2 + - - +
280C CYS* 4.9 6.8 - - - -
320C PLP 3.4 21.6 + - - +
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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
------------------------------------------------------------
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