Contacts of the helix formed by residues 197 - 216 (chain A) in PDB entry 3A03
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 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A ALA* 3.7 1.6 - - - -
196A MET* 1.3 78.4 - - - +
198A ASP* 1.3 65.3 + - - +
199A ALA* 3.7 7.4 + - - +
200A GLN* 2.9 49.8 + - - +
201A VAL* 3.2 21.3 + - - +
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Residues in contact with ASP 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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187A ARG* 4.9 8.3 + - + +
188A ALA* 3.5 34.9 - - - +
191A ALA* 3.5 12.7 - - - +
196A MET 5.1 0.2 - - - +
197A THR* 1.3 73.0 - - - +
199A ALA* 1.3 57.9 + - - +
201A VAL* 3.2 5.6 + - - +
202A LYS* 3.0 27.4 + - - +
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Residues in contact with ALA 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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197A THR* 3.2 5.9 + - - +
198A ASP* 1.3 78.4 - - - +
200A GLN* 1.3 58.6 + - + +
202A LYS* 3.3 9.3 + - - +
203A THR* 2.9 36.3 + - - +
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Residues in contact with GLN 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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164A PHE* 3.9 25.5 - - + -
196A MET* 3.5 24.4 - - + +
197A THR* 2.9 50.4 + - - +
199A ALA* 1.3 78.0 - - + +
201A VAL* 1.3 56.2 + - - +
203A THR* 3.9 5.2 - - - +
204A TRP* 3.0 30.1 + - - +
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Residues in contact with VAL 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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172A LEU* 4.7 4.0 - - + -
187A ARG* 4.0 29.2 - - + +
190A LEU* 4.2 10.1 - - + -
191A ALA* 3.7 28.9 - - + +
196A MET* 3.9 22.9 - - + -
197A THR 3.2 13.3 + - - +
198A ASP 3.2 6.9 + - - +
200A GLN* 1.3 72.1 - - - +
202A LYS* 1.3 68.0 + - - +
204A TRP* 3.3 3.3 + - - +
205A PHE* 3.0 45.7 + - + -
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Residues in contact with LYS 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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187A ARG* 3.7 43.7 - - - +
198A ASP 3.0 13.1 + - - +
199A ALA* 3.3 12.3 + - - +
201A VAL* 1.3 78.3 - - - +
203A THR* 1.3 61.4 + - - +
205A PHE* 3.4 3.8 + - - +
206A GLN* 3.1 47.4 + - + +
209A ARG* 5.0 1.0 + - - +
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Residues in contact with THR 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 ALA* 2.9 19.3 + - - +
200A GLN* 3.9 5.4 - - - -
202A LYS* 1.3 72.3 - - - +
204A TRP* 1.3 68.0 + - - +
206A GLN* 3.2 18.3 + - - +
207A ASN* 2.9 41.4 + - - +
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Residues in contact with TRP 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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164A PHE* 4.0 23.6 - + + -
169A VAL* 4.5 13.2 - - + +
172A LEU* 3.6 64.4 - - + +
173A GLU* 3.7 27.4 - - + -
176A PHE* 4.2 3.6 - - + -
200A GLN 3.0 19.4 + - - +
201A VAL* 3.3 6.7 + - - +
203A THR* 1.3 78.3 - - - +
205A PHE* 1.3 83.5 + + - +
207A ASN* 3.3 8.2 + - + +
208A ARG* 2.8 58.4 + - + +
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Residues in contact with PHE 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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1A NA 3.7 10.8 - - - -
172A LEU* 4.0 16.2 - - + -
175A ARG* 4.0 13.7 - - + -
176A PHE* 3.9 18.4 - + + -
179A GLN 3.6 12.1 - - - -
180A LYS 3.7 17.5 - - - -
182A LEU* 3.4 42.4 - - + -
187A ARG* 5.6 0.7 - - - -
190A LEU* 4.0 13.5 - - + -
201A VAL* 3.0 33.1 + - + +
202A LYS* 3.9 3.1 - - - +
204A TRP* 1.3 90.9 - + - +
206A GLN* 1.3 62.3 + - - +
208A ARG* 3.8 1.8 - - - +
209A ARG* 2.9 46.7 + - - +
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Residues in contact with GLN 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 LYS* 3.1 43.4 + - + +
203A THR* 3.2 22.7 + - - +
205A PHE* 1.3 74.8 - - - +
207A ASN* 1.3 66.4 + - - +
209A ARG* 3.2 25.9 + - - +
210A THR* 3.1 24.6 + - - -
217A SO4 4.2 14.6 + - - +
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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 THR* 2.9 39.5 + - - +
204A TRP* 3.7 7.2 - - + +
206A GLN* 1.3 80.1 - - - +
208A ARG* 1.3 62.7 + - - +
210A THR* 3.3 10.4 + - - -
211A LYS* 3.1 21.3 + - - +
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Residues in contact with ARG 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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173A GLU* 2.8 34.4 + - - -
176A PHE* 3.5 42.8 - - + -
204A TRP* 2.8 45.2 + - + +
205A PHE 3.8 4.3 - - - +
206A GLN 3.3 0.2 - - - -
207A ASN* 1.3 74.6 - - - +
209A ARG* 1.3 59.2 + - - +
211A LYS* 3.3 29.5 + - - +
212A TRP* 3.0 41.1 + - - +
215A GLN* 4.9 6.3 + - - -
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Residues in contact with ARG 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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1A NA 3.3 23.8 - - - -
176A PHE* 3.7 9.2 - - + -
180A LYS 2.9 31.7 + - - +
181A TYR* 3.3 40.4 - - - -
202A LYS* 5.0 0.6 + - - +
205A PHE* 2.9 26.8 + - - +
206A GLN* 3.6 26.0 - - - +
208A ARG* 1.3 74.7 - - - +
210A THR* 1.3 59.6 + - - +
212A TRP* 3.2 16.1 + - + +
213A ARG* 2.9 49.3 + - - +
217A SO4 2.8 35.7 + - - -
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Residues in contact with THR 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 GLN 3.1 14.7 + - - -
207A ASN* 3.5 13.2 + - - -
208A ARG 3.3 0.2 - - - -
209A ARG* 1.3 76.7 - - - +
211A LYS* 1.3 62.1 + - - +
213A ARG* 3.3 16.7 + - - +
214A ARG* 3.0 24.3 + - + +
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Residues in contact with LYS 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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173A GLU* 4.7 11.5 + - - -
207A ASN 3.1 14.1 + - - +
208A ARG* 3.6 31.1 - - - +
210A THR* 1.3 75.2 - - - +
212A TRP* 1.3 57.8 + - - +
214A ARG* 3.1 6.6 + - - +
215A GLN* 2.9 70.8 + - + +
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Residues in contact with TRP 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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176A PHE* 3.7 12.8 - + + -
180A LYS* 3.6 45.5 - - + +
181A TYR* 4.7 8.3 - + - -
208A ARG* 3.0 21.7 + - - +
209A ARG* 3.4 32.8 - - + +
211A LYS* 1.3 75.3 - - - +
213A ARG* 1.3 88.4 + - + +
215A GLN* 3.4 4.1 + - - -
216A THR* 2.9 54.6 + - + +
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Residues in contact with ARG 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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181A TYR* 3.0 28.3 + - - -
209A ARG* 2.9 36.6 + - - +
210A THR* 3.6 13.6 + - - +
211A LYS 3.2 0.2 - - - -
212A TRP* 1.3 92.1 - - + +
214A ARG* 1.3 63.5 - - - +
216A THR* 3.2 20.0 - - - +
217A SO4 2.9 37.1 + - - -
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Residues in contact with ARG 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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210A THR* 3.0 15.2 + - + +
211A LYS* 3.1 11.6 + - + +
213A ARG* 1.3 78.1 - - - +
215A GLN* 1.3 65.8 + - + +
216A THR 3.8 1.2 + - - +
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Residues in contact with GLN 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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208A ARG* 4.9 6.2 + - - -
211A LYS* 2.9 53.8 + - + +
212A TRP* 4.2 3.9 - - - +
214A ARG* 1.3 83.7 - - + +
216A THR* 1.3 66.8 + - + +
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Residues in contact with THR 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 TRP* 2.9 44.8 + - + +
213A ARG* 3.2 17.7 + - - +
214A ARG 3.5 1.1 - - - +
215A GLN* 1.3 87.6 - - + +
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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