Contacts of the strand formed by residues 194 - 200 (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 THR 194 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167C THR 2.6 11.6 + - - -
168C HIS* 3.2 30.9 + - + -
169C PHE 2.9 24.1 + - - +
192C PRO* 6.1 0.7 - - - +
193C VAL* 1.3 69.4 - - - +
195C ILE* 1.3 64.5 + - - +
196C VAL* 3.6 5.3 + - + +
227C ASP* 4.2 17.2 + - + -
228C GLU* 3.9 24.2 - - - +
266C VAL* 6.1 0.2 - - + -
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Residues in contact with ILE 195 (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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169C PHE* 3.5 15.5 - - + +
179C ILE* 3.5 34.3 - - + -
183C SER* 3.1 35.4 - - - +
186C MET* 4.3 6.1 - - + -
187C ARG* 4.0 9.9 - - + +
193C VAL* 3.4 33.6 + - + +
194C THR* 1.3 70.3 - - - +
196C VAL* 1.3 59.6 + - - +
225C LEU 3.4 18.6 - - - +
226C VAL* 4.1 5.1 - - + +
227C ASP* 2.8 37.5 + - - +
228C GLU* 3.1 5.5 + - - +
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Residues in contact with VAL 196 (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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168C HIS* 4.9 3.1 - - + -
169C PHE 2.7 22.1 + - - +
170C VAL* 3.1 48.4 - - + +
171C SER 3.3 2.6 + - - -
179C ILE* 3.7 5.1 - - - +
194C THR* 3.6 14.4 - - + +
195C ILE* 1.3 74.9 - - - +
197C GLY* 1.3 69.2 + - - +
198C LEU* 4.6 4.0 - - + -
228C GLU* 3.2 37.0 - - + +
230C LEU* 4.1 17.0 - - + -
266C VAL* 4.7 15.0 - - + -
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Residues in contact with GLY 197 (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 3.1 13.0 - - - -
173C MET* 3.4 21.3 - - - -
179C ILE* 4.3 3.2 - - - +
196C VAL* 1.3 74.1 - - - +
198C LEU* 1.3 78.4 + - - +
226C VAL* 4.3 2.8 - - - +
228C GLU 2.8 10.2 + - - -
230C LEU* 3.0 17.2 + - - +
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Residues in contact with LEU 198 (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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170C VAL* 4.1 10.3 - - + -
171C SER 3.2 4.8 + - - -
172C SER* 3.7 14.6 - - - +
173C MET* 3.0 34.2 + - - +
196C VAL* 4.6 6.3 - - + -
197C GLY* 1.3 89.8 - - - +
199C GLN* 1.3 60.7 + - - +
209C ILE* 4.8 1.6 - - - +
230C LEU* 3.2 29.4 - - + +
231C ASP 5.0 3.4 - - - +
232C ILE* 4.4 13.2 - - + -
258C GLY 2.8 39.0 - - - +
259C ALA* 3.3 15.0 - - - +
262C GLY* 3.7 19.1 - - - -
265C ARG* 5.3 0.2 - - - +
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Residues in contact with GLN 199 (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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173C MET* 3.0 42.0 + - - +
174C GLY 5.3 0.2 + - - -
176C THR* 4.9 5.7 + - - -
198C LEU* 1.3 79.3 - - - +
200C PRO* 1.3 73.6 - - + +
201C GLU 3.2 0.9 + - - -
209C ILE* 4.6 1.3 - - - -
210C ARG 2.7 33.4 + - - +
211C ARG* 4.1 22.5 - - + +
212C TRP* 5.1 4.9 - - - +
229C VAL* 3.4 17.9 - - + +
230C LEU 2.9 8.6 + - - +
231C ASP* 3.0 16.1 - - - +
232C ILE* 3.2 10.4 + - - +
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Residues in contact with PRO 200 (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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199C GLN* 1.3 89.9 - - + +
201C GLU* 1.3 64.2 + - - +
202C GLU* 3.6 11.4 + - - +
204C SER* 3.8 15.5 - - - +
206C ILE* 3.8 24.2 - - + +
209C ILE* 3.6 38.6 - - + +
210C ARG* 3.7 15.3 - - + +
211C ARG* 4.6 7.0 - - - +
231C ASP* 3.5 1.7 - - - +
232C ILE* 3.0 16.7 - - + +
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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