Contacts of the helix formed by residues 197 - 212 (chain A) in PDB entry 5AJI
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 ASP 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A ASP 3.8 1.4 + - - -
196A SER* 1.3 70.9 - - - +
198A ILE* 1.3 65.2 + - - +
199A ASP* 3.0 22.7 + - - +
200A GLN* 3.7 30.8 + - + +
201A VAL* 3.0 27.2 + - - +
266A ILE* 6.1 0.2 - - - +
259B ARG* 5.0 4.5 + - - -
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Residues in contact with ILE 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 SER* 3.3 8.5 + - - +
197A ASP* 1.3 74.4 + - - +
199A ASP* 1.3 62.2 + - - +
201A VAL* 3.6 1.9 + - - +
202A LYS* 3.2 35.7 + - + +
225A LEU* 4.5 18.8 - - + -
233A ILE* 5.8 3.1 - - + -
235A PHE* 4.2 22.0 - - + -
255B GLU* 3.8 22.9 - - + +
258B LYS* 3.9 34.5 - - + +
259B ARG* 3.7 34.5 - - + +
262B ASP* 5.3 0.7 - - - +
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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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197A ASP* 3.0 13.9 + - - +
198A ILE* 1.3 76.3 - - - +
200A GLN* 1.3 59.6 + - - +
202A LYS* 3.5 11.2 + - - +
203A GLN* 2.9 29.7 + - - +
255B GLU* 4.3 1.6 - - - +
259B ARG* 2.5 36.4 + - - +
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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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197A ASP* 3.2 31.0 + - + +
199A ASP* 1.3 75.5 - - - +
201A VAL* 1.3 68.4 + - - +
203A GLN* 3.1 7.5 + - + +
204A ILE* 2.9 36.7 + - + +
264A ALA* 3.9 26.5 + - - +
266A ILE* 4.0 20.3 - - + +
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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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192A VAL* 4.3 4.9 - - + -
196A SER* 3.8 21.5 - - - -
197A ASP 3.0 20.1 + - - +
198A ILE 3.8 3.6 - - - +
200A GLN* 1.3 78.6 - - - +
202A LYS* 1.3 62.4 + - - +
204A ILE* 3.4 2.4 + - - +
205A LEU* 3.0 34.7 + - + +
235A PHE* 3.4 41.3 - - + -
261A PHE* 4.0 13.6 - - + -
266A ILE* 3.8 26.5 - - + -
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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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198A ILE* 3.2 28.1 + - + +
199A ASP* 3.7 10.6 + - - +
201A VAL* 1.3 80.2 - - - +
203A GLN* 1.3 56.8 + - - +
205A LEU* 3.4 1.4 + - - +
206A THR* 2.8 36.8 + - - +
223A VAL* 4.0 34.5 - - + +
224A ARG* 4.5 12.3 - - - +
225A LEU 4.5 11.0 - - - +
235A PHE* 4.1 12.3 - - + -
255B GLU* 2.8 33.6 + - - -
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Residues in contact with GLN 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 2.9 18.1 + - - +
200A GLN* 3.1 8.0 + - + +
202A LYS* 1.3 76.2 - - - +
204A ILE* 1.3 60.3 + - + +
206A THR* 3.2 10.7 + - - +
207A ASN* 2.8 55.4 + - - +
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Residues in contact with ILE 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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200A GLN* 2.9 26.6 + - + +
201A VAL 3.7 3.1 - - - +
203A GLN* 1.3 77.9 - - + +
205A LEU* 1.3 64.1 + - - +
207A ASN* 3.1 13.2 + - - +
208A ILE* 3.0 26.9 + - + +
260A GLU* 3.8 28.3 - - + +
261A PHE* 3.6 18.8 - - + -
264A ALA* 3.6 24.0 - - + -
266A ILE* 3.4 31.4 - - + -
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Residues in contact with LEU 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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190A ILE* 4.8 4.9 - - + -
201A VAL* 3.0 35.5 + - + +
202A LYS 3.7 3.4 - - - +
204A ILE* 1.3 75.9 - - - +
206A THR* 1.3 62.1 + - - +
208A ILE* 3.2 8.5 + - + +
209A ILE* 3.1 27.5 + - + +
223A VAL* 3.8 18.8 - - + -
235A PHE* 4.2 13.9 - - + -
237A VAL* 3.8 27.6 - - + -
257A ILE* 3.7 37.7 - - + -
261A PHE* 3.8 19.5 - - + -
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Residues in contact with THR 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* 2.8 22.3 + - - +
203A GLN* 3.6 13.0 - - - +
205A LEU* 1.3 76.1 - - - +
207A ASN* 1.3 58.5 + - - +
209A ILE* 3.3 12.2 + - + +
210A GLN* 2.8 55.5 + - + +
223A VAL* 3.9 17.5 - - - +
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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 GLN* 2.8 48.9 + - - +
204A ILE* 3.1 11.6 + - - +
206A THR* 1.3 77.9 - - - +
208A ILE* 1.3 63.7 + - + +
210A GLN* 3.7 7.3 - - - +
211A SER* 3.1 26.0 + - - -
256A ARG* 4.4 2.8 + - - +
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Residues in contact with ILE 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 ILE* 3.0 29.5 + - + +
205A LEU* 3.5 10.3 - - + +
207A ASN* 1.3 77.7 - - + +
209A ILE* 1.3 61.7 + - + +
211A SER* 3.1 15.8 + - - -
212A GLU* 3.3 8.1 + - - +
253A VAL* 4.0 29.2 - - + +
256A ARG* 3.3 46.8 + - + +
257A ILE* 3.9 27.6 - - + +
260A GLU* 3.7 30.3 - - + +
261A PHE* 5.1 0.2 - - + -
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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 LEU* 3.1 11.8 + - + +
206A THR* 3.3 18.4 - - + +
208A ILE* 1.3 81.5 - - + +
210A GLN* 1.3 64.7 + - + +
212A GLU 3.7 7.3 - - - +
215A ILE* 3.8 32.6 - - + +
217A LYS* 3.3 16.8 - - - -
221A MET* 4.1 23.0 - - + +
223A VAL* 3.6 27.8 - - + -
237A VAL* 4.1 18.8 - - + -
239A VAL* 3.7 21.5 - - + -
253A VAL* 4.7 8.7 - - + -
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Residues in contact with GLN 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 THR* 2.8 41.9 + - + +
207A ASN* 3.7 8.7 - - - +
209A ILE* 1.3 79.1 - - + +
211A SER* 1.3 57.6 + - - +
213A ASP* 4.9 0.7 - - - +
217A LYS* 3.0 38.9 + - - +
221A MET* 3.7 27.0 - - - +
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Residues in contact with SER 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 10.8 + - - -
208A ILE 3.1 1.7 + - - -
210A GLN* 1.3 73.9 - - - +
212A GLU* 1.3 59.6 + - - +
213A ASP* 3.2 16.3 + - - +
256A ARG* 2.7 44.0 + - - -
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Residues in contact with GLU 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 ILE 3.3 14.8 + - - +
209A ILE 4.1 0.4 - - - +
210A GLN 3.3 1.4 - - - -
211A SER* 1.3 76.7 - - - +
213A ASP* 1.3 62.4 + - - +
214A ARG* 2.9 53.0 + - - +
215A ILE* 3.3 40.1 + - + +
217A LYS* 3.1 19.2 + - - -
249A VAL* 4.3 10.3 - - + -
252A ASP* 4.6 8.0 - - - +
253A VAL* 4.4 9.5 - - + +
256A ARG* 4.5 12.6 + - - +
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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