Contacts of the helix formed by residues 202 - 217 (chain A) in PDB entry 3IPA
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 LEU 202 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ASN* 3.5 36.1 - - - +
18A PHE* 5.8 0.2 - - + -
77A PHE* 4.1 6.3 - - + -
78A ASN* 3.6 13.5 - - - +
146A ASP* 4.1 11.6 + - - +
150A TYR* 3.7 26.7 - - + -
177A VAL* 6.0 5.4 - - + -
199A TRP* 2.9 21.2 + - - +
201A GLY* 1.3 73.6 - - - -
203A HIS* 1.3 65.2 + - - +
204A THR* 3.4 4.0 + - - +
205A GLU* 3.8 11.3 + - - +
206A ALA* 3.2 8.7 + - - +
227A GLY* 3.7 20.6 - - - +
228A ILE* 4.0 2.7 - - - -
500A ALA* 4.1 16.8 - - + +
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Residues in contact with HIS 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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14A PRO 3.1 23.7 + - - -
15A ASN* 3.6 13.1 + - - -
17A ALA* 5.5 2.7 - - + +
18A PHE* 3.5 26.6 - + + -
202A LEU* 1.3 76.4 - - - +
204A THR* 1.3 75.5 + - - +
206A ALA* 4.1 0.9 - - - -
207A GLY* 2.8 27.7 + - - -
227A GLY 3.3 12.7 + - - +
228A ILE* 3.9 19.7 - - - +
230A SER* 5.0 2.4 - - - -
232A GLU* 3.7 32.8 - - + +
233A LEU* 3.5 24.1 + - + +
236A ILE* 4.1 11.4 - - + +
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Residues in contact with THR 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO* 3.7 25.3 + - + +
15A ASN* 4.7 0.9 + - - -
180A LYS* 3.7 26.2 - - - +
202A LEU* 3.4 2.1 - - - +
203A HIS* 1.3 100.0 + - - +
205A GLU* 1.3 77.6 + - - +
207A GLY* 3.4 0.9 + - - -
208A LEU* 3.1 30.1 + - + +
236A ILE* 3.9 18.7 - - + +
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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
----------------------------------------------------------
14A PRO* 6.2 0.2 - - - +
146A ASP* 5.2 1.4 - - + +
175A VAL* 5.0 1.6 - - + -
176A ASN 4.6 4.9 - - - +
177A VAL* 3.7 20.0 - - - +
178A GLY* 3.0 29.5 + - - +
179A ASP 4.2 7.4 - - - +
180A LYS* 4.9 0.9 + - - -
182A PHE* 4.0 21.1 - - + -
199A TRP* 3.3 30.2 - - + -
202A LEU* 3.8 13.9 + - - +
204A THR* 1.3 90.6 + - - +
206A ALA* 1.3 66.3 + - - +
208A LEU* 3.3 9.2 + - + +
209A ILE* 2.9 30.5 + - - +
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Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A TRP* 3.5 23.6 - - + +
202A LEU 3.2 20.4 + - - +
203A HIS 3.7 3.6 - - - +
204A THR 3.3 0.2 - - - -
205A GLU* 1.3 76.9 - - - +
207A GLY* 1.3 56.9 + - - +
209A ILE* 3.3 6.9 + - - +
210A ILE* 2.9 34.1 + - - +
222A LEU* 4.2 13.0 - - + +
228A ILE* 3.9 15.0 - - + -
233A LEU* 3.9 8.3 - - + -
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Residues in contact with GLY 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 HIS 2.8 20.7 + - - -
206A ALA* 1.3 73.4 - - - +
208A LEU* 1.3 56.0 + - - +
211A ARG* 3.0 30.3 + - - +
233A LEU* 3.6 13.9 - - - +
236A ILE* 3.6 17.7 - - - +
237A ALA* 3.7 15.9 - - - +
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Residues in contact with LEU 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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179A ASP 4.1 3.1 - - - +
180A LYS* 3.8 52.0 - - + +
182A PHE* 3.8 14.8 - - + -
204A THR* 3.1 22.6 + - + +
205A GLU* 3.3 6.9 + - + +
207A GLY* 1.3 75.9 - - - +
209A ILE* 1.3 59.3 + - - +
211A ARG* 3.5 6.5 + - - +
212A GLN* 2.9 50.9 + - - +
236A ILE* 3.7 14.6 - - + +
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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
----------------------------------------------------------
144A ILE* 5.0 8.1 - - + -
182A PHE* 3.9 35.0 - - + -
185A LEU* 5.3 3.4 - - + -
186A ILE* 3.9 12.5 - - + +
189A MET* 5.0 5.2 - - + -
197A ILE* 4.0 24.7 - - + -
199A TRP* 3.9 34.8 - - + -
205A GLU 2.9 22.8 + - - +
206A ALA* 3.6 4.0 - - - +
208A LEU* 1.3 72.9 - - - +
210A ILE* 1.3 60.5 + - - +
213A ALA* 2.8 30.5 + - - +
222A LEU* 3.9 18.6 - - + -
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Residues in contact with ILE 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 ALA 2.9 25.0 + - - +
207A GLY 3.8 3.8 - - - +
209A ILE* 1.3 77.4 - - - +
211A ARG* 1.3 63.5 + - - +
213A ALA* 3.8 4.2 - - - +
214A ALA* 3.2 22.2 + - - +
222A LEU* 3.9 25.8 - - + -
233A LEU* 4.5 9.6 - - + -
237A ALA* 3.8 10.5 - - + -
240A ALA* 3.4 35.7 - - + +
241A VAL* 4.4 10.5 - - + -
244A THR* 3.3 33.9 - - + +
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Residues in contact with ARG 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 GLY 3.0 17.5 + - - +
208A LEU* 3.9 7.4 - - - +
210A ILE* 1.3 78.0 - - - +
212A GLN* 1.3 64.8 + - + +
214A ALA* 3.3 5.0 + - - +
215A ASP* 3.1 22.9 + - + +
235A SER 4.8 1.2 + - - -
236A ILE* 3.2 25.8 + - - +
237A ALA 3.4 27.1 + - - +
238A GLY* 3.7 0.6 - - - -
240A ALA* 4.7 3.4 - - - -
357A SO4 2.8 44.3 + - - -
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Residues in contact with GLN 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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180A LYS 2.7 25.4 + - - -
181A ASP* 3.9 4.0 - - - +
182A PHE* 2.9 31.3 + - - -
183A SER* 3.7 7.4 + - - -
186A ILE* 3.4 13.7 - - + -
208A LEU* 2.9 40.3 + - + +
211A ARG* 1.3 76.1 - - + +
213A ALA* 1.3 60.9 + - - +
215A ASP* 3.3 7.2 + - + +
216A GLN* 2.9 39.7 + - - +
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Residues in contact with ALA 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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186A ILE* 3.4 17.4 - - + +
197A ILE* 4.9 9.0 - - + -
209A ILE 2.8 20.5 + - - +
210A ILE* 3.8 5.2 - - - +
212A GLN* 1.3 75.6 - - - +
214A ALA* 1.3 62.9 + - - +
216A GLN 3.3 0.9 + - - -
217A GLY 3.1 4.5 + - - -
218A LEU* 2.9 54.5 + - + +
220A ALA 5.5 4.3 - - - +
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Residues in contact with ALA 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 ILE 3.2 11.0 + - - +
211A ARG 3.6 8.5 - - - +
213A ALA* 1.3 78.9 - - - +
215A ASP* 1.3 62.6 + - - +
217A GLY* 3.3 12.1 + - - -
218A LEU 4.5 3.8 + - - +
240A ALA* 3.8 22.2 - - + -
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Residues in contact with ASP 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 ARG* 3.1 17.7 + - + +
212A GLN* 3.3 8.5 + - - +
214A ALA* 1.3 77.6 - - - +
216A GLN* 1.3 65.7 + - - +
217A GLY 3.3 0.7 + - - -
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Residues in contact with GLN 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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183A SER* 3.2 51.1 + - - +
186A ILE* 3.6 37.5 - - + +
187A SER* 3.4 13.2 + - - -
190A LYS* 3.1 23.1 + - + +
212A GLN* 2.9 21.1 + - + +
213A ALA 4.1 0.4 - - - +
215A ASP* 1.3 82.3 - - + +
217A GLY* 1.3 59.1 + - - +
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Residues in contact with GLY 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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190A LYS* 3.3 17.4 + - - -
213A ALA 3.1 3.5 + - - -
214A ALA* 3.3 7.7 + - - -
215A ASP 3.3 5.1 + - - -
216A GLN* 1.3 80.3 - - - +
218A LEU* 1.3 61.8 + - - +
219A LYS* 3.5 5.0 + - - +
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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