Contacts of the helix formed by residues 196 - 210 (chain A) in PDB entry 4OQZ
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 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A VAL* 5.5 2.0 - - - -
190A ALA* 5.0 0.8 - - - +
194A GLY 4.9 4.5 - - - +
195A LEU* 1.3 76.4 - - - +
197A ALA* 1.3 62.6 + - - +
198A ALA* 3.4 9.4 + - - +
199A ASP* 2.6 48.6 + - - +
200A ILE* 3.5 12.3 + - - +
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Residues in contact with ALA 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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183A TYR* 2.9 25.5 + - + +
187A VAL* 3.8 32.4 - - + +
196A THR* 1.3 74.0 - - - +
198A ALA* 1.4 52.1 + - - +
200A ILE* 3.4 4.2 + - - +
201A ALA* 2.8 30.0 + - - +
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Residues in contact with ALA 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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196A THR* 3.4 7.9 + - - +
197A ALA* 1.4 75.6 - - - +
199A ASP* 1.3 63.3 + - - +
201A ALA* 3.8 10.7 - - - +
202A PRO* 3.4 17.7 - - - +
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Residues in contact with ASP 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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194A GLY 4.5 2.1 - - - +
195A LEU* 3.7 27.2 - - + +
196A THR* 2.6 50.0 + - - +
197A ALA 3.2 0.2 - - - -
198A ALA* 1.3 79.3 - - - +
200A ILE* 1.3 58.5 + - + +
202A PRO* 3.4 13.9 - - - +
203A TYR* 3.7 15.6 - - - -
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Residues in contact with ILE 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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183A TYR* 4.1 8.5 - - + -
186A ALA* 3.5 44.9 - - + +
187A VAL* 3.6 15.5 - - + +
190A ALA* 3.9 21.3 - - + -
195A LEU* 4.5 14.1 - - + -
196A THR 3.5 9.6 + - - +
197A ALA 3.5 12.3 - - - +
199A ASP* 1.3 76.6 - - + +
201A ALA* 1.4 65.2 + - - +
202A PRO* 3.4 2.0 - - - -
203A TYR* 3.1 16.2 + - + +
204A VAL* 3.0 26.9 + - + +
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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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183A TYR* 4.1 15.7 - - + +
197A ALA 2.8 18.7 + - - +
198A ALA* 3.9 11.2 - - - +
199A ASP 3.5 0.2 - - - -
200A ILE* 1.4 77.1 - - - +
202A PRO* 1.4 67.2 - - + +
204A VAL* 3.9 1.4 - - - +
205A SER* 2.8 32.4 + - - +
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Residues in contact with PRO 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 ALA 3.4 12.6 - - - +
199A ASP 3.4 17.9 - - - +
200A ILE 3.4 1.3 - - - -
201A ALA* 1.4 91.0 - - + +
203A TYR* 1.3 61.9 + - + +
205A SER* 3.7 5.4 - - - -
206A GLU* 3.0 31.1 + - - +
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Residues in contact with TYR 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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199A ASP 3.7 23.3 - - - -
200A ILE* 3.1 14.9 + - + +
202A PRO* 1.3 82.6 - - + +
204A VAL* 1.3 60.3 + - + +
206A GLU* 3.5 7.3 + - + +
207A ASN* 2.9 28.3 + - - +
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Residues in contact with VAL 204 (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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182A SER* 6.0 0.2 - - - +
183A TYR* 3.8 40.8 - - + -
186A ALA* 4.6 10.8 - - + -
200A ILE* 3.0 24.9 + - + +
201A ALA 4.0 2.5 - - - +
203A TYR* 1.3 74.2 - - + +
205A SER* 1.3 61.1 + - - +
207A ASN* 3.2 9.4 + - + +
208A PHE* 3.0 54.0 + - + -
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Residues in contact with SER 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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201A ALA* 2.8 24.7 + - - +
202A PRO* 3.7 5.8 - - - -
204A VAL* 1.3 77.2 - - - +
206A GLU* 1.3 51.3 + - - +
208A PHE* 3.4 8.3 + - - +
209A ALA* 2.9 33.9 + - - +
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Residues in contact with GLU 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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202A PRO 3.0 18.7 + - - +
203A TYR* 3.6 7.9 - - + +
205A SER* 1.3 72.9 - - - +
207A ASN* 1.3 65.6 + - - +
209A ALA* 3.4 11.4 + - - +
210A GLY* 3.0 21.5 + - - -
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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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203A TYR 2.9 15.6 + - - +
204A VAL* 3.2 13.3 + - + +
206A GLU* 1.3 76.5 - - - +
208A PHE* 1.3 63.1 + - + +
210A GLY* 3.3 11.3 + - - -
211A MET* 3.3 31.0 + - - +
214A PHE* 6.2 0.2 - - - -
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Residues in contact with PHE 208 (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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179A ALA* 3.7 44.6 - - + -
180A MET* 6.0 3.8 - - - -
182A SER* 3.9 9.9 - - - -
183A TYR* 5.1 3.6 - - + -
204A VAL* 3.0 45.1 + - + -
205A SER* 3.8 8.7 - - - +
207A ASN* 1.3 76.0 - - + +
209A ALA* 1.4 63.0 + - - +
211A MET* 3.2 36.0 + - + +
212A GLY 4.5 1.4 + - - -
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Residues in contact with ALA 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 SER 2.9 18.6 + - - +
206A GLU* 3.6 15.3 - - - +
207A ASN 3.3 0.2 - - - -
208A PHE* 1.4 77.3 - - - +
210A GLY* 1.3 58.1 + - - +
211A MET 3.6 0.7 + - - -
212A GLY* 4.4 5.0 + - - -
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Residues in contact with GLY 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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206A GLU* 3.0 16.4 + - - -
207A ASN 3.3 5.4 + - - -
208A PHE 3.3 0.6 - - - -
209A ALA* 1.3 74.1 - - - +
211A MET* 1.3 61.6 + - - +
212A GLY 3.4 2.0 + - - -
213A GLN* 3.6 18.0 - - - +
214A PHE* 3.6 19.7 - - - -
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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