Contacts of the strand formed by residues 194 - 200 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A THR* 2.7 18.2 + - - -
168A HIS* 3.2 34.0 - - + +
169A PHE 3.0 22.5 + - - -
192A PRO* 5.3 2.4 + - - +
193A VAL* 1.3 70.5 - - - +
195A ILE* 1.3 62.7 + - - +
196A VAL* 3.6 8.9 + - + -
227A ASP* 4.2 25.1 - - + +
228A GLU* 6.5 0.2 - - + -
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Residues in contact with ILE 195 (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 PHE* 3.5 24.2 - - + +
179A ILE* 3.3 30.3 - - + +
182A VAL* 5.0 0.2 - - + -
183A SER* 3.3 39.3 - - - +
186A MET* 4.8 11.9 - - + -
187A ARG* 6.1 2.9 - - - +
193A VAL* 3.9 11.9 - - + +
194A THR* 1.3 72.5 - - - +
196A VAL* 1.3 60.2 + - - +
197A GLY 4.3 0.2 + - - -
225A LEU 2.8 33.9 - - - +
226A VAL* 4.0 4.7 - - + -
227A ASP* 3.4 30.2 + - - +
228A GLU 4.0 1.9 + - - +
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Residues in contact with VAL 196 (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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168A HIS* 4.1 26.2 - - + -
169A PHE 2.6 16.2 + - - +
170A VAL* 4.2 11.9 - - + -
171A SER* 2.8 24.4 + - - -
179A ILE* 3.8 6.7 - - - +
194A THR* 4.2 9.4 - - + +
195A ILE* 1.3 78.5 - - - +
197A GLY* 1.3 61.8 + - - +
198A LEU* 4.0 7.9 - - + -
228A GLU* 3.9 21.3 - - + +
230A LEU* 3.3 33.9 - - + -
266A VAL* 4.5 9.9 - - + -
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Residues in contact with GLY 197 (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 SER 3.2 9.2 - - - -
173A MET* 4.2 5.2 - - - -
179A ILE* 3.3 19.0 - - - +
196A VAL* 1.3 77.0 - - - +
198A LEU* 1.3 57.6 + - - +
228A GLU 3.2 9.2 + - - -
229A VAL* 3.1 10.1 - - - +
230A LEU 2.6 33.6 + - - -
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Residues in contact with LEU 198 (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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170A VAL* 3.3 36.1 - - + -
171A SER 2.8 13.7 + - - +
172A SER* 4.4 7.9 - - - +
173A MET* 3.1 29.5 + - - +
196A VAL* 4.0 1.3 - - + -
197A GLY* 1.3 79.1 - - - -
199A GLN* 1.3 62.9 + - - +
209A ILE* 3.8 6.7 - - + +
230A LEU* 3.3 37.7 - - + -
232A ILE* 3.4 30.1 - - + -
258A GLY 4.1 0.2 - - - +
259A ALA* 3.3 31.6 - - + +
262A GLY* 4.2 3.1 - - - -
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Residues in contact with GLN 199 (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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173A MET* 4.3 21.5 - - + +
198A LEU* 1.3 80.0 - - - +
200A PRO* 1.3 75.0 - - + +
209A ILE* 4.1 2.9 - - - -
210A ARG 3.5 22.5 + - - +
211A ARG* 3.4 36.2 + - + +
212A TRP* 4.6 2.4 - - - +
229A VAL* 4.1 20.1 - - + +
230A LEU 2.9 10.0 + - - +
231A ASP* 3.4 10.1 - - - +
232A ILE* 2.8 28.6 + - - -
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Residues in contact with PRO 200 (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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199A GLN* 1.3 95.0 - - + +
201A GLU* 1.3 67.1 + - - +
204A SER* 2.9 29.6 - - - +
206A ILE* 4.6 8.5 - - + +
209A ILE* 3.3 33.8 - - + +
210A ARG* 4.1 10.5 - - - -
211A ARG* 4.0 24.5 - - + +
231A ASP* 4.1 6.8 - - - +
232A ILE 3.4 8.7 - - - +
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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