Contacts of the helix formed by residues 204 - 217 (chain A) in PDB entry 5PAH
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 TYR 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A ALA 3.9 0.4 + - - -
203A CYS* 1.3 71.5 - - - +
205A GLU* 1.4 78.9 + - + +
206A TYR 3.2 0.3 + - - -
207A ASN* 3.2 9.5 + - + +
208A HIS* 2.9 57.7 + + + +
336A GLN* 2.6 34.9 + - + +
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Residues in contact with GLU 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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203A CYS* 3.7 16.2 - - - +
204A TYR* 1.4 98.4 + - + +
206A TYR* 1.3 61.4 + - - +
208A HIS* 3.6 6.9 + - - +
209A ILE* 3.4 23.6 + - - +
292A PRO 4.8 3.1 - - - +
293A LEU* 4.4 8.5 - - + -
296A ASP* 3.5 39.7 - - + +
336A GLN* 4.3 1.7 - - - +
392A PHE* 3.8 21.8 - - + -
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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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198A TYR* 3.3 42.1 + + + -
202A ALA* 3.8 20.2 - - + -
203A CYS* 3.0 22.1 + - - +
205A GLU* 1.3 78.1 - - - +
207A ASN* 1.3 64.2 + - - +
209A ILE* 3.3 10.3 + - - +
210A PHE* 3.0 54.2 + + + +
288A LEU* 2.7 32.8 + - - -
289A GLY 4.6 0.4 - - - -
292A PRO* 3.6 22.5 - - + +
293A LEU* 3.7 14.1 - - + +
348A LEU* 3.5 28.0 - - + -
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Residues in contact with ASN 207 (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 TYR* 3.0 44.8 + - - +
199A LYS* 3.8 13.4 + - - +
202A ALA* 3.2 21.4 + - - -
203A CYS 3.3 4.9 + - - -
204A TYR* 3.2 10.8 + - + +
206A TYR* 1.3 76.9 - - - +
208A HIS* 1.3 64.4 + - - +
210A PHE* 4.1 4.9 - - - +
211A PRO* 3.1 21.8 - - - +
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Residues in contact with HIS 208 (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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204A TYR* 2.9 49.9 + + + +
205A GLU* 3.7 7.4 - - - +
207A ASN* 1.3 77.6 - - - +
209A ILE* 1.3 77.0 + - + +
211A PRO* 3.7 7.6 - - - +
212A LEU* 4.7 12.7 - - + +
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Residues in contact with ILE 209 (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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205A GLU 3.4 10.2 + - - +
206A TYR 3.3 10.7 + - - +
208A HIS* 1.3 94.6 - - + +
210A PHE* 1.3 69.4 + - - +
211A PRO 3.3 1.8 - - - -
212A LEU* 2.9 36.0 + - + +
213A LEU* 3.2 15.2 + - + +
233A PHE* 4.1 18.2 - - + -
237A CYS* 4.6 5.6 - - - -
292A PRO* 3.7 36.1 - - + +
295A SER* 3.7 30.3 - - - +
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Residues in contact with PHE 210 (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 PHE* 3.9 28.3 - + - -
195A LYS* 4.3 15.5 - - + -
198A TYR* 4.4 12.3 - + + -
206A TYR* 3.0 54.9 + + + +
207A ASN* 4.1 7.0 - - - +
209A ILE* 1.3 77.9 - - - +
211A PRO* 1.4 69.6 - - + +
213A LEU* 3.0 16.7 + - + +
214A GLU* 3.0 50.4 + - + +
219A PHE* 4.3 13.2 - + - -
288A LEU* 4.2 12.8 - - + -
292A PRO* 4.7 0.9 - - + -
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Residues in contact with PRO 211 (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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207A ASN 3.1 18.4 - - - +
208A HIS 3.7 7.2 - - - +
209A ILE 3.5 3.6 - - - -
210A PHE* 1.4 91.8 - - + +
212A LEU* 1.3 57.9 + - + +
214A GLU* 3.2 18.6 + - - +
215A LYS* 2.9 48.6 + - - +
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Residues in contact with LEU 212 (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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208A HIS* 4.7 11.9 - - + +
209A ILE* 2.9 29.5 + - + +
211A PRO* 1.3 80.2 - - + +
213A LEU* 1.3 56.6 + - - +
215A LYS* 4.5 14.1 - - + +
216A TYR* 2.8 59.3 + - + +
233A PHE* 4.0 22.3 - - + -
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Residues in contact with LEU 213 (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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209A ILE* 3.2 19.1 + - + +
210A PHE* 3.0 13.9 + - + +
212A LEU* 1.3 72.2 - - - +
214A GLU* 1.3 63.3 + - - +
217A CYS* 2.9 39.2 + - - +
218A GLY 3.3 0.2 + - - -
219A PHE* 3.3 48.0 + - + -
230A VAL* 5.4 1.1 - - + -
233A PHE* 3.7 33.0 - - + -
291A VAL* 4.3 10.5 - - + -
292A PRO* 3.6 38.6 - - + -
295A SER* 5.1 0.9 - - - +
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Residues in contact with GLU 214 (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 PHE* 4.6 1.6 - - - -
195A LYS* 3.0 33.2 + - - -
210A PHE* 3.0 35.0 + - + +
211A PRO* 3.5 24.6 - - + +
213A LEU* 1.3 78.2 - - - +
215A LYS* 1.3 64.1 + - + +
218A GLY* 3.8 11.1 + - - -
219A PHE* 3.4 30.1 + - + +
220A HIS* 6.0 0.3 - - - +
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Residues in contact with LYS 215 (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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211A PRO* 2.9 36.9 + - - +
212A LEU* 4.7 14.7 - - + +
214A GLU* 1.3 81.2 - - + +
216A TYR* 1.3 81.2 + - + +
218A GLY 4.7 1.2 + - - -
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Residues in contact with TYR 216 (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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212A LEU* 2.8 56.3 + - + +
215A LYS* 1.3 90.1 - - + +
217A CYS* 1.3 61.4 + - - +
218A GLY 3.5 0.7 - - - -
229A ASP* 5.2 4.9 - - - +
233A PHE* 4.4 22.7 - + + -
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Residues in contact with CYS 217 (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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213A LEU* 2.9 25.4 + - - +
216A TYR* 1.3 82.4 - - - +
218A GLY* 1.3 64.6 + - - +
219A PHE* 3.4 17.9 - - + -
223A ASN* 4.7 0.5 + - - -
225A PRO* 3.4 19.6 - - - +
226A GLN 5.0 0.7 + - - -
229A ASP* 3.9 21.1 - - + +
230A VAL* 4.1 12.0 - - + +
233A PHE* 3.6 39.3 - - - -
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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