Contacts of the helix formed by residues 191 - 203 (chain A) in PDB entry 2XAR
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 SER 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A CYS 5.1 5.4 - - - -
173A PHE 5.6 1.3 - - - -
174A LEU* 3.6 15.4 - - - +
189A SER 4.0 0.8 + - - -
190A VAL* 1.3 79.0 - - - +
192A ARG* 1.3 65.3 + - - +
193A PHE* 3.8 8.8 + - - +
194A LYS* 3.3 20.8 + - - +
195A MET* 3.1 20.6 + - - +
213A ASP* 3.3 24.4 + - - -
214A PRO* 4.3 3.3 - - - +
215A LEU* 4.1 19.7 - - - +
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Residues in contact with ARG 192 (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 CYS* 5.5 15.3 + - + +
173A PHE 5.7 1.8 + - - -
175A PRO* 6.1 2.4 - - - +
190A VAL 3.6 1.0 + - - -
191A SER* 1.3 72.0 - - - +
193A PHE* 1.3 55.6 + - - +
195A MET* 3.7 14.2 - - + +
196A HIS* 2.8 56.6 + - + +
315A ILE* 5.3 2.2 - - - +
360A TYR* 5.8 1.4 + - - -
419A TYR* 4.8 9.3 + - - +
422A LEU* 3.8 25.4 - - - +
423A ASP* 2.9 45.5 + - - +
426A ILE* 4.6 13.1 - - - +
500A IHP 4.9 14.3 + - - +
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Residues in contact with PHE 193 (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 LYS* 4.0 25.4 - - + -
171A CYS 5.1 3.4 + - - +
191A SER* 3.1 3.0 - - - +
192A ARG* 1.3 81.8 - - - +
194A LYS* 1.3 59.7 + - + +
196A HIS* 3.7 6.5 - - + +
197A GLN* 3.1 66.6 + - + +
200A LYS* 5.8 5.3 - - - -
210A SER* 4.2 10.8 - - - -
212A TYR* 3.3 43.5 - + - -
214A PRO* 3.6 29.2 - - + -
238A ASN* 6.0 0.4 - - - -
239A ASN* 3.7 31.9 - - - -
500A IHP 6.1 0.7 - - - -
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Residues in contact with LYS 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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190A VAL* 3.8 22.9 - - + -
191A SER* 3.3 16.1 + - - +
193A PHE* 1.3 81.9 - - + +
195A MET* 1.3 64.8 + - - +
197A GLN* 3.4 18.4 + - - +
198A LEU* 3.8 6.9 + - - +
209A GLU* 3.7 25.7 + - - +
212A TYR 5.7 3.1 - - - +
213A ASP* 5.3 12.1 - - + +
430A TYR* 4.7 13.2 + - + +
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Residues in contact with MET 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 LEU 4.5 4.9 - - - +
187A LYS* 3.9 31.6 - - + +
190A VAL* 3.6 33.7 - - + +
191A SER 3.1 13.1 + - - +
192A ARG* 3.7 13.2 - - + +
194A LYS* 1.3 74.1 - - - +
196A HIS* 1.3 64.9 + - - +
198A LEU* 3.2 18.5 + - - +
199A LEU* 3.7 3.3 + - - +
423A ASP* 5.8 0.7 - - - +
426A ILE* 3.6 24.7 - - + +
427A ILE* 3.7 24.5 - - + -
429A PHE* 5.5 1.2 - - - -
430A TYR* 3.6 38.0 - - + +
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Residues in contact with HIS 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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192A ARG* 2.8 37.9 + - + +
193A PHE* 3.7 7.4 - - + +
195A MET* 1.3 72.9 - - - +
197A GLN* 1.3 57.0 + - - +
199A LEU* 3.0 9.0 + - + +
200A LYS* 3.0 71.5 + - + +
205A GLU* 5.2 2.7 - - - -
422A LEU* 4.1 16.8 - - + +
426A ILE* 3.1 41.4 - - + +
500A IHP 3.6 25.2 + - - -
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Residues in contact with GLN 197 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A PHE* 3.1 49.2 + - + +
194A LYS* 3.5 12.6 - - - +
195A MET 3.2 0.6 - - - -
196A HIS* 1.3 77.0 - - - +
198A LEU* 1.3 57.2 + - - +
200A LYS* 3.8 22.1 - - - +
201A LEU* 3.0 31.4 + - - +
206A ILE* 3.0 21.3 - - - +
209A GLU* 4.1 16.4 - - + +
210A SER* 2.8 33.7 + - - +
237A GLN* 2.7 23.9 + - - -
238A ASN* 5.9 0.2 + - - -
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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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194A LYS 3.8 5.6 + - - +
195A MET 3.2 9.9 + - - +
196A HIS 3.2 0.6 - - - -
197A GLN* 1.3 80.7 - - - +
199A LEU* 1.3 55.9 + - - +
201A LEU* 4.1 16.9 - - + +
202A GLU* 3.2 26.2 + - - +
209A GLU* 4.3 20.4 - - - +
429A PHE* 3.4 19.9 - - + -
430A TYR* 3.7 31.4 - - + -
433A LYS* 4.8 19.1 - - + -
434A GLN* 4.8 8.3 - - - +
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Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A MET 3.7 3.0 + - - +
196A HIS* 3.0 14.4 + - + +
198A LEU* 1.3 76.9 - - - +
200A LYS* 1.3 56.0 + - + +
201A LEU 3.3 0.2 - - - -
202A GLU* 3.0 2.7 + - + +
203A TYR* 2.8 66.3 + - + -
205A GLU* 5.6 0.2 - - - -
422A LEU* 4.9 6.5 - - + -
425A LYS* 4.0 32.1 - - + +
426A ILE* 3.4 32.8 - - + -
429A PHE* 4.0 34.9 - - + -
312B LYS* 5.8 0.2 - - - +
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Residues in contact with LYS 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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193A PHE* 5.8 5.2 - - - -
196A HIS* 3.0 48.6 + - + +
197A GLN* 3.8 28.5 - - - +
199A LEU* 1.3 74.8 - - - +
201A LEU* 1.3 60.4 + - - +
203A TYR 3.0 7.1 + - - -
204A ILE 3.1 0.2 + - - -
205A GLU* 2.8 58.9 + - + +
206A ILE* 3.6 22.2 - - + +
237A GLN* 5.1 0.2 - - - +
238A ASN* 4.5 6.9 + - - -
256A SER* 5.7 1.0 + - - -
500A IHP 2.9 40.1 + - - -
178B ARG* 5.2 4.2 - - - +
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Residues in contact with LEU 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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197A GLN 3.0 17.5 + - - +
198A LEU* 4.1 18.6 - - + +
200A LYS* 1.3 76.2 - - - +
202A GLU* 1.3 62.0 + - - +
204A ILE* 3.5 13.2 + - - +
206A ILE* 3.4 29.2 - - + +
207A SER 3.5 23.8 - - - +
208A GLU* 3.7 8.1 - - - +
209A GLU* 4.2 21.8 - - + +
352B GLU* 5.1 3.1 - - - +
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Residues in contact with GLU 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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198A LEU 3.2 19.3 + - - +
199A LEU* 3.0 9.1 + - - +
201A LEU* 1.3 79.1 - - - +
203A TYR* 1.3 63.6 + - + +
204A ILE* 3.2 16.8 + - - +
429A PHE* 3.6 31.8 - - + -
433A LYS* 4.6 8.4 + - - -
312B LYS* 3.8 33.7 + - + +
313B LEU* 4.7 2.9 - - - +
352B GLU* 4.5 16.3 - - - +
355B LYS* 4.3 20.3 - - - +
356B ILE* 6.1 0.5 - - - +
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Residues in contact with TYR 203 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A LEU* 2.8 57.6 + - + +
200A LYS 3.0 0.6 + - - -
202A GLU* 1.3 76.2 - - + +
204A ILE* 1.3 73.3 + - - +
205A GLU* 3.2 28.4 + - + +
425A LYS* 3.2 32.0 + - - -
176B THR* 4.7 12.8 - - + -
177B SER* 5.9 3.4 - - - -
178B ARG* 4.7 3.1 - - - +
179B PHE* 4.1 11.8 - - - -
309B LYS* 4.5 6.2 + - - +
312B LYS* 3.1 62.3 + - + +
313B LEU* 4.3 7.8 - - + +
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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