Contacts of the strand formed by residues 193 - 199 (chain A) in PDB entry 3BUC
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 ARG 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A TYR* 3.7 14.8 + - - +
163A ASP 3.3 18.4 + - - -
164A GLY* 3.6 14.1 + - - -
166A ASP 2.7 29.3 + - - -
191A ALA* 3.5 3.7 + - + +
192A SER* 1.3 80.6 - - - +
194A ASP* 1.3 62.8 + - - +
195A PHE 3.6 0.2 + - - -
217A PRO* 4.3 2.5 - - - -
218A LEU* 2.8 35.3 + - - +
238A LEU* 3.8 27.3 + - + +
239A PRO 2.9 30.3 + - - -
241A ARG* 4.0 10.4 - - - +
244A VAL* 3.9 27.1 - - + +
248A ARG* 3.6 30.2 - - + +
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Residues in contact with ASP 194 (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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193A ARG* 1.3 75.0 - - - +
195A PHE* 1.3 60.6 - - - +
196A VAL* 4.9 4.5 - - + -
215A ARG* 5.7 6.4 - - + +
216A LEU 3.6 5.3 + - - +
217A PRO* 3.9 23.0 - - - +
238A LEU* 3.1 17.8 - - - +
239A PRO* 3.3 18.3 - - + +
241A ARG* 2.7 49.0 + - + +
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Residues in contact with PHE 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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186A SER* 5.8 0.4 - - - -
193A ARG 3.6 0.2 + - - -
194A ASP* 1.3 73.4 - - - +
196A VAL* 1.3 62.2 + - - +
197A PHE* 3.5 38.6 - + - -
214A VAL 4.0 0.5 - - - +
215A ARG* 3.3 4.2 - - - +
216A LEU* 2.9 44.1 + - + +
218A LEU* 3.8 28.5 - - + -
224A LEU* 3.7 17.7 - - + -
226A MET* 4.3 11.0 - - + -
236A HIS* 3.5 36.3 - + + -
237A SER 3.6 14.6 - - - -
238A LEU* 4.1 6.1 - - + -
259A AKG 3.6 31.2 - - + -
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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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170A GLU* 5.3 1.2 - - - +
194A ASP* 4.8 4.3 - - + -
195A PHE* 1.3 80.3 - - - +
197A PHE* 1.3 68.3 + - - +
198A ARG* 4.0 11.1 + - + +
213A VAL* 3.5 30.5 - - + -
214A VAL 3.6 2.0 - - - +
215A ARG* 3.9 20.9 - - + +
236A HIS* 3.1 7.7 - - - -
237A SER* 3.0 44.1 + - - +
239A PRO* 3.9 25.6 - - + -
241A ARG* 4.9 2.9 - - - +
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Residues in contact with PHE 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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60A ILE* 5.0 3.6 - - + -
65A LEU* 4.3 12.3 - - + -
67A SER* 4.0 22.2 - - - -
195A PHE* 3.5 34.5 - + - -
196A VAL* 1.3 72.8 - - - +
198A ARG* 1.3 59.7 + - - +
213A VAL* 3.5 7.1 - - - +
214A VAL* 2.7 58.5 + - + +
216A LEU* 4.5 11.4 - - + -
224A LEU* 4.4 8.3 - - + -
226A MET* 4.2 13.5 - - + -
230A THR* 3.9 19.7 - - + -
234A TRP* 3.6 27.6 - - + -
235A TYR 3.4 9.9 - - - -
236A HIS* 4.1 12.3 - - + -
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Residues in contact with ARG 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 GLU* 3.2 40.6 + - - +
196A VAL* 4.0 9.4 + - + +
197A PHE* 1.3 75.3 - - - +
199A HIS* 1.3 62.4 + - - +
202A SER* 3.4 16.4 - - - +
203A ARG* 3.5 23.4 - - - +
213A VAL* 3.9 24.4 - - + +
234A TRP* 3.3 5.2 - - - -
235A TYR* 2.8 38.3 + - - +
3C G 5.0 2.8 - - - +
4C C 2.7 43.0 + - - +
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Residues in contact with HIS 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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63A GLU* 4.1 15.9 + - - +
198A ARG* 1.3 77.9 - - - +
200A LYS* 1.3 70.7 + - + +
201A ASP* 3.1 44.8 + - - +
202A SER* 2.4 31.5 + - - +
203A ARG* 3.9 3.1 - - - +
209A ARG* 3.9 19.4 + - - -
211A VAL* 4.1 23.6 - - + +
212A ALA 4.8 2.2 + - - -
233A HIS* 4.1 13.0 + - - +
234A TRP* 3.3 54.5 - + + -
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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