Contacts of the strand formed by residues 199 - 206 (chain A) in PDB entry 2OQ1
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 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A PRO* 4.1 0.3 - - - +
194A ARG* 3.0 57.9 + - - +
196A GLU* 2.6 32.5 + - + +
197A GLN* 4.5 2.6 - - - +
198A GLY* 1.3 86.0 + - - +
200A TYR* 1.3 69.1 + - - +
214A LEU* 4.1 3.1 - - + -
215A ILE 3.2 6.5 - - - -
216A SER* 4.3 14.4 - - - -
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Residues in contact with TYR 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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160A HIS* 4.7 7.0 + - - -
166A TYR* 4.1 10.5 - + - -
191A LEU* 3.8 17.7 - - + -
192A ARG 3.4 8.1 - - - +
193A PRO* 3.6 28.9 - - + -
194A ARG* 3.7 6.7 - - - -
197A GLN* 3.6 17.7 + - - -
198A GLY* 4.0 19.0 - - - -
199A THR* 1.3 76.3 - - - +
201A ALA* 1.3 63.4 + - - +
214A LEU* 3.6 9.2 - - - +
215A ILE* 2.8 42.2 + - + +
217A GLN* 5.4 1.8 + - - -
223A TYR* 3.9 21.8 + + - -
234A LEU* 3.7 39.1 - - + +
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Residues in contact with ALA 201 (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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191A LEU* 3.5 8.6 - - - +
192A ARG* 2.8 72.0 + - + +
194A ARG* 4.1 4.7 - - + +
200A TYR* 1.3 75.8 - - - +
202A LEU* 1.3 60.8 + - - +
203A SER* 3.9 1.9 + - - +
212A HIS* 5.3 0.2 - - + -
213A TYR 3.2 10.1 - - - +
215A ILE* 4.6 0.4 - - - +
304B PTR 4.1 14.6 - - + -
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Residues in contact with LEU 202 (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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189A PHE* 3.9 26.2 - - + -
190A LEU 3.7 11.9 - - - +
191A LEU* 3.9 14.8 - - + -
201A ALA* 1.3 71.4 - - - +
203A SER* 1.3 64.8 + - - +
204A LEU* 4.1 3.4 - - + -
211A TYR 3.6 1.4 - - - +
212A HIS* 3.2 4.0 - - - -
213A TYR* 2.8 44.7 + - + +
215A ILE* 4.1 8.6 - - + +
225A ILE* 4.5 5.6 - - + -
237A LEU* 4.4 7.6 - - + -
238A VAL* 5.5 0.9 - - + -
241A LEU* 3.9 28.5 - - + -
248A LEU* 4.3 13.2 - - + -
252A LEU* 4.1 22.9 - - + -
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Residues in contact with SER 203 (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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175A ALA* 4.5 2.0 - - - -
179A LEU* 3.6 20.0 - - - +
189A PHE* 3.2 3.2 - - - +
190A LEU* 3.0 46.4 + - - +
192A ARG* 3.1 22.1 + - - -
201A ALA 3.9 0.2 - - - -
202A LEU* 1.3 74.8 - - - +
204A LEU* 1.3 59.5 + - - +
211A TYR 3.2 4.9 - - - -
212A HIS* 2.9 30.2 + - - -
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Residues in contact with LEU 204 (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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179A LEU* 3.9 4.9 - - - +
187A GLY* 4.8 6.3 - - - +
188A LYS 3.1 14.6 - - - +
189A PHE* 3.7 11.2 - - + -
202A LEU* 4.6 5.8 - - + +
203A SER* 1.3 76.5 - - - +
205A ILE* 1.3 73.5 + - - +
206A TYR* 4.2 3.4 - - + -
209A THR 3.8 0.2 - - - +
210A VAL* 3.3 1.7 - - - -
211A TYR* 2.8 38.3 + - + +
213A TYR* 3.5 35.2 - - + -
248A LEU* 4.9 4.5 - - + -
249A ILE* 3.9 25.4 - - + -
250A TYR* 4.7 11.0 - - + +
251A CYS 6.0 0.2 - - - +
252A LEU* 4.4 18.8 - - + -
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Residues in contact with ILE 205 (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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179A LEU* 3.8 18.1 - - + +
180A TYR* 3.8 17.5 - - + -
184A GLN* 3.4 50.9 - - + +
185A THR 3.6 7.4 - - - +
186A ASP* 3.7 2.1 - - - -
187A GLY* 3.1 26.2 + - - -
188A LYS* 2.9 39.8 + - + +
204A LEU* 1.3 74.2 - - - +
206A TYR* 1.3 64.4 + - - +
208A LYS* 4.1 4.7 - - - +
209A THR 3.3 18.6 - - - +
210A VAL* 4.3 6.7 - - + -
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Residues in contact with TYR 206 (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 ASP* 3.5 24.0 - - + -
204A LEU* 4.1 4.2 + - + -
205A ILE* 1.3 76.4 - - - +
207A GLY* 1.3 70.5 + - - +
209A THR* 2.8 24.8 + - - +
211A TYR* 3.6 22.4 + - + -
249A ILE* 3.5 44.6 + - + -
250A TYR* 3.8 38.4 - + + -
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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