Contacts of the helix formed by residues 198 - 210 (chain A) in PDB entry 1P0I
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 SER 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A GLY* 4.4 0.4 - - - -
197A GLU* 1.3 86.2 - - - +
199A ALA* 1.3 60.4 + - - -
201A ALA* 2.8 20.0 + - - +
202A ALA 2.8 10.4 + - - -
223A GLN 2.9 13.1 + - - -
224A SER 3.1 14.1 + - - -
225A GLY* 3.9 1.0 - - - -
231A TRP* 3.7 9.4 - - - -
398A PHE* 3.8 2.3 - - - -
438A HIS* 2.8 18.3 + - - -
605A GOL 4.2 1.1 - - - -
606A BUA 2.2 41.8 - - - +
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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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114A TYR 4.4 0.7 - - - -
115A GLY* 3.8 1.3 - - - -
116A GLY 4.0 3.8 - - - +
117A GLY* 3.5 5.2 - - - +
118A PHE* 3.5 46.5 - - + +
146A TYR* 4.9 2.0 - - - +
197A GLU 3.2 0.2 + - - -
198A SER* 1.3 79.2 - - - +
200A GLY* 1.3 57.9 + - - +
202A ALA* 3.7 1.6 - - - -
203A SER* 2.9 32.4 + - - -
231A TRP* 3.8 13.6 - - + -
606A BUA 2.8 16.1 + - - +
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Residues in contact with GLY 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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113A ILE* 3.2 31.4 - - - +
114A TYR 3.3 9.6 - - - -
115A GLY* 3.3 5.3 - - - -
196A GLY 3.9 1.1 - - - -
197A GLU 2.7 15.2 + - - -
199A ALA* 1.3 79.6 - - - +
201A ALA* 1.3 55.1 + - - -
203A SER* 3.3 4.0 + - - -
204A VAL* 3.0 30.0 + - - +
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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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196A GLY 3.5 14.1 - - - +
197A GLU 3.4 5.1 - - - +
198A SER 2.8 12.1 + - - +
200A GLY* 1.3 69.3 - - - +
202A ALA* 1.3 65.0 + - - +
204A VAL* 3.1 9.0 + - - +
205A SER* 2.9 23.6 + - - -
222A LEU* 3.9 7.7 - - - +
223A GLN 3.4 33.7 - - - +
225A GLY* 3.3 22.0 - - - +
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Residues in contact with ALA 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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118A PHE* 4.0 9.4 - - + -
198A SER 2.8 11.8 + - - +
199A ALA 3.6 7.6 - - - +
201A ALA* 1.3 76.2 - - - +
203A SER* 1.3 62.6 + - - +
205A SER* 2.7 24.9 + - - -
206A LEU* 3.0 17.3 + - + +
225A GLY 4.0 1.0 - - - -
226A SER 3.8 17.9 - - - +
227A PHE* 4.1 1.8 - - - +
231A TRP* 3.9 24.2 - - + -
232A ALA* 4.2 5.8 - - + -
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Residues in contact with SER 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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113A ILE* 3.9 5.3 - - - +
118A PHE* 3.3 15.9 - - - -
146A TYR* 4.6 1.0 + - - -
168A LEU* 3.9 10.7 - - - +
171A GLN* 3.2 38.1 + - - -
199A ALA 2.9 20.2 + - - -
200A GLY* 3.3 10.5 - - - -
201A ALA 3.1 0.2 - - - -
202A ALA* 1.3 73.6 - - - +
204A VAL* 1.3 66.8 + - - +
206A LEU* 3.0 15.1 + - - +
207A HIS* 3.0 19.9 + - - -
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Residues in contact with VAL 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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113A ILE* 4.1 9.6 - - + -
194A LEU* 3.9 26.3 - - + +
195A PHE 3.9 3.4 - - - -
196A GLY 3.9 21.3 - - - +
200A GLY 3.0 18.4 + - - +
201A ALA* 3.1 10.1 + - - +
203A SER* 1.3 75.5 - - - +
205A SER* 1.3 64.2 + - - +
207A HIS* 3.1 21.3 + - - +
208A LEU* 3.2 10.9 + - - +
220A ALA* 3.5 31.2 - - + -
221A ILE 3.9 4.9 - - - +
222A LEU* 3.9 14.4 - - + -
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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 2.9 12.4 + - - -
202A ALA* 2.7 18.9 + - - -
204A VAL* 1.3 78.5 - - - +
206A LEU* 1.3 59.1 + - - +
208A LEU* 3.2 26.6 + - - +
209A LEU* 3.4 12.0 + - - +
222A LEU* 3.7 19.7 - - - -
227A PHE* 2.8 39.8 + - - -
405A PHE* 4.1 9.5 - - - -
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Residues in contact with LEU 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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118A PHE* 5.0 1.1 - - + -
168A LEU* 3.9 14.6 - - + -
202A ALA* 3.0 18.8 + - + +
203A SER* 3.0 9.2 + - - +
205A SER* 1.3 74.7 - - - +
207A HIS* 1.3 60.9 + - - +
209A LEU* 3.0 16.5 + - + +
210A SER* 2.9 28.4 + - - -
227A PHE* 3.5 31.6 - - + -
232A ALA 5.2 1.1 - - - +
233A VAL* 5.0 2.9 - - + -
292A PRO* 3.8 35.9 - - + -
298A PHE* 3.8 16.5 - - + -
299A LEU* 4.5 22.8 - - + +
303A PRO* 4.5 3.8 - - + -
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Residues in contact with HIS 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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113A ILE* 4.0 12.9 - - + +
168A LEU* 4.0 11.5 - - - +
171A GLN* 2.8 34.2 + - + +
172A GLN* 4.1 7.6 - - - -
175A LEU* 4.0 8.7 - - + +
194A LEU* 3.9 20.6 - - + -
203A SER 3.0 28.5 + - - -
204A VAL* 3.1 9.6 + - - +
206A LEU* 1.3 73.6 - - - +
208A LEU* 1.3 65.0 + - - +
209A LEU 3.3 0.3 + - - -
210A SER 3.5 9.5 + - - +
213A SER* 2.9 38.2 + - - -
214A HIS* 4.6 1.6 + - - -
217A PHE* 3.6 14.2 - - + -
298A PHE* 3.6 24.3 - + - -
313A LYS* 5.2 0.3 - - - +
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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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204A VAL 3.2 11.4 + - - +
205A SER* 3.2 17.4 + - - +
206A LEU 3.1 0.6 - - - -
207A HIS* 1.3 79.7 - - - +
209A LEU* 1.3 59.9 + - + +
210A SER 5.1 0.5 - - - +
217A PHE* 3.7 25.8 - - + -
220A ALA* 4.2 13.7 - - + -
222A LEU* 4.8 2.7 - - + -
312A PHE* 3.5 4.8 - - + -
313A LYS* 2.9 41.5 + - + +
315A THR* 3.9 24.0 - - + -
317A ILE* 4.0 13.0 - - + -
405A PHE* 3.9 21.3 - - + -
409A PHE* 3.9 22.9 - - + -
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Residues in contact with LEU 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 3.7 11.9 - - - +
206A LEU* 3.0 14.3 + - + +
208A LEU* 1.3 81.1 - - + +
210A SER* 1.3 58.2 + - - +
211A PRO* 3.2 14.4 - - - +
227A PHE* 3.7 24.9 - - + -
298A PHE 5.2 0.2 - - - -
299A LEU* 4.5 7.8 - - + +
303A PRO* 3.5 40.6 - - + +
306A LEU* 4.0 23.8 - - + +
307A LEU* 4.9 1.8 - - + +
311A GLN 3.7 14.5 - - - +
312A PHE* 3.6 29.5 - - + -
405A PHE* 5.8 1.3 - - + -
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Residues in contact with SER 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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172A GLN* 4.0 2.9 + - - -
206A LEU 2.9 14.9 + - - -
207A HIS 3.5 5.4 + - - +
208A LEU 5.1 0.6 - - - +
209A LEU* 1.3 75.6 - - - +
211A PRO* 1.3 70.3 - - - +
212A GLY* 3.8 7.3 + - - -
213A SER* 2.9 19.7 + - - -
214A HIS* 3.3 8.7 + - - +
297A ASP 4.8 0.5 + - - -
298A PHE* 2.7 56.2 + - - -
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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