Contacts of the helix formed by residues 210 - 226 (chain A) in PDB entry 1P45
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 GLU 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A ILE* 5.0 6.5 - - + -
208A GLY 3.0 0.8 + - - -
209A GLU* 1.4 83.8 - - - +
211A ALA* 1.3 69.8 + - - +
212A GLY 3.2 1.1 - - - +
213A ALA* 3.0 26.4 + - - +
214A GLN* 3.2 18.6 + - + +
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Residues in contact with ALA 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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104A GLY* 6.0 0.4 - - - -
105A ILE* 3.9 36.4 - - + +
202A ILE* 6.0 0.2 - - - -
207A LEU* 3.2 39.5 - - + +
208A GLY* 3.5 1.6 + - - -
210A GLU* 1.3 79.7 - - - +
212A GLY* 1.3 60.9 + - - +
213A ALA 3.1 0.3 + - - -
214A GLN* 3.4 5.7 + - - +
215A ILE* 3.0 34.4 + - + +
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Residues in contact with GLY 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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202A ILE* 3.9 21.7 + - - +
203A VAL* 4.9 10.7 - - - +
205A GLY* 5.4 1.6 - - - -
207A LEU* 5.1 1.2 - - - +
208A GLY 2.9 20.2 + - - +
209A GLU 5.3 0.4 - - - -
210A GLU 3.2 0.2 - - - -
211A ALA* 1.3 71.1 - - - +
213A ALA* 1.3 56.2 + - - +
215A ILE* 4.0 10.0 + - - +
216A GLN* 3.2 24.9 + - - +
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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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209A GLU 4.9 4.8 + - - +
210A GLU* 3.0 32.3 + - - +
212A GLY* 1.3 73.0 - - - +
214A GLN* 1.3 71.2 + - - +
216A GLN* 2.7 17.9 + - - +
217A LEU* 3.0 24.4 + - + +
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Residues in contact with GLN 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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105A ILE* 6.5 0.7 - - + -
156A PRO* 3.6 38.2 - - + +
157A ALA* 6.0 0.9 - - + -
210A GLU* 3.2 13.6 + - + +
211A ALA* 3.7 9.4 - - - +
213A ALA* 1.3 78.0 - - - +
215A ILE* 1.3 64.6 + - + +
216A GLN 3.1 0.3 + - - -
217A LEU* 3.3 22.4 + - + +
218A LEU* 3.2 26.5 + - - +
177B ARG* 5.3 1.0 + - - -
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Residues in contact with ILE 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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104A GLY* 5.3 4.9 - - - -
157A ALA* 4.0 21.1 - - + -
202A ILE* 3.4 25.8 - - + -
203A VAL* 4.6 4.3 - - + +
207A LEU* 5.4 1.8 - - + -
211A ALA* 3.0 36.5 + - + +
212A GLY 4.2 5.2 - - - +
213A ALA 3.2 0.6 - - - -
214A GLN* 1.3 79.3 - - + +
216A GLN* 1.3 57.9 + - - +
218A LEU* 4.0 7.9 - - - +
219A GLU* 2.7 53.4 + - - +
450A TCL 3.1 44.6 - - + +
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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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195A ARG* 4.8 10.1 - - - +
203A VAL* 4.9 10.5 - - + +
212A GLY 3.2 17.9 + - - +
213A ALA* 2.7 17.0 + - - +
215A ILE* 1.3 73.6 - - + +
217A LEU* 1.3 62.5 + - + +
219A GLU* 3.5 17.4 + - - +
220A GLU* 2.8 55.5 + - - +
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Residues in contact with LEU 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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213A ALA* 3.0 27.4 + - + +
214A GLN* 3.5 32.5 - - - +
216A GLN* 1.3 79.9 - - + +
218A LEU* 1.3 60.7 + - - +
220A GLU* 3.4 14.3 + - - +
221A GLY* 3.5 10.2 + - - -
224A GLN* 4.9 1.6 - - - +
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Residues in contact with LEU 218 (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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155A MET* 4.5 20.9 - - + -
156A PRO* 3.8 33.4 - - + +
157A ALA* 4.6 4.9 - - + -
214A GLN* 3.2 21.0 + - - +
215A ILE* 4.0 4.9 - - - +
217A LEU* 1.3 75.0 - - - +
219A GLU* 1.3 66.3 - - - +
220A GLU 3.4 0.5 + - - -
221A GLY* 3.5 8.0 + - - -
222A TRP* 3.5 31.2 + - + -
225A ARG* 4.8 2.4 + - - +
450A TCL 3.5 37.2 - - + -
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Residues in contact with GLU 219 (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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193A PRO* 4.4 10.1 - - + +
195A ARG* 3.7 6.6 + - - -
199A MET* 3.7 9.2 - - + +
202A ILE* 4.6 0.2 - - - +
203A VAL* 3.3 24.7 - - - +
215A ILE* 2.7 37.3 + - - +
216A GLN* 3.5 12.9 + - - +
218A LEU* 1.3 81.6 - - - +
220A GLU* 1.3 59.5 + - - +
221A GLY 3.3 0.9 + - - -
222A TRP* 3.7 18.5 + - - +
223A ASP* 4.9 0.5 + - - +
230A TRP* 5.6 1.0 - - - -
232A MET* 3.2 49.8 - - + +
450A TCL 4.1 15.0 - - + -
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Residues in contact with GLU 220 (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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216A GLN* 2.8 43.5 + - + +
217A LEU* 3.9 8.7 - - - +
218A LEU 3.2 0.8 - - - -
219A GLU* 1.3 76.9 - - - +
221A GLY* 1.3 59.2 + - - +
222A TRP 3.4 1.2 + - - -
223A ASP* 3.8 11.7 + - - +
224A GLN* 3.3 30.2 + - + +
232A MET* 6.1 0.7 - - - -
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Residues in contact with GLY 221 (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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217A LEU 3.5 7.4 + - - -
218A LEU 3.5 5.4 + - - -
219A GLU 3.2 1.0 - - - -
220A GLU* 1.3 76.9 - - - +
222A TRP* 1.3 60.3 + - - +
223A ASP 3.4 0.9 - - - -
224A GLN* 3.1 23.1 - - - +
225A ARG* 3.1 42.3 + - - +
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Residues in contact with TRP 222 (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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149A PHE* 3.1 43.1 - + - -
150A ASP* 5.8 8.1 - - + -
155A MET* 5.2 5.6 - - + -
191A ALA 5.0 1.1 - - - -
192A GLY* 3.8 13.3 - - - -
193A PRO* 3.6 25.1 - - + -
218A LEU* 3.5 36.1 - - + -
219A GLU 3.7 10.6 + - - +
221A GLY* 1.3 77.0 - - - +
223A ASP* 1.3 59.6 + - - +
225A ARG* 3.2 29.1 + - - +
226A ALA* 2.9 33.1 + - - +
230A TRP* 4.0 16.2 - + + -
261A ASP* 3.7 33.8 + - - +
264A ALA* 3.7 14.7 - - + +
265A HIS* 6.4 0.9 - - + -
450A TCL 4.0 9.2 - - + -
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Residues in contact with ASP 223 (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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219A GLU 4.9 0.4 + - - +
220A GLU 3.8 9.9 + - - +
221A GLY 3.4 0.4 - - - -
222A TRP* 1.3 76.2 - - - +
224A GLN* 1.3 69.7 + - + +
226A ALA 3.2 17.5 + - - +
229A GLY* 3.2 11.1 - - - -
230A TRP* 3.1 45.0 + - + +
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Residues in contact with GLN 224 (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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217A LEU 4.9 1.9 - - - +
220A GLU* 3.3 32.4 + - + +
221A GLY* 3.1 22.8 + - - +
222A TRP 3.3 0.6 - - - -
223A ASP* 1.3 80.2 - - + +
225A ARG* 1.3 59.5 + - + +
226A ALA 4.5 1.6 - - - +
269A LEU* 4.2 9.7 - - - +
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Residues in contact with ARG 225 (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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218A LEU* 4.8 2.8 + - - +
221A GLY 3.1 34.4 + - - +
222A TRP* 3.8 34.8 - - - +
223A ASP 3.2 0.4 - - - -
224A GLN* 1.3 74.7 - - + +
226A ALA* 1.3 62.9 + - - +
227A PRO* 3.3 11.1 - - - +
264A ALA* 3.1 41.9 + - + +
265A HIS* 4.2 5.3 - - - +
267A GLN* 3.5 26.8 + - + +
268A LEU 3.6 27.6 - - - +
269A LEU* 4.2 17.0 - - + +
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Residues in contact with ALA 226 (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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222A TRP 2.9 18.0 + - - +
223A ASP 3.2 9.3 + - - +
224A GLN 4.5 1.8 - - - +
225A ARG* 1.3 75.2 - - - +
227A PRO* 1.3 74.6 - - - +
228A ILE 2.9 2.2 + - - -
229A GLY 3.0 31.2 + - - +
230A TRP* 4.1 5.4 - - + +
261A ASP 4.3 0.2 - - - +
262A GLY 3.6 17.3 - - - +
264A ALA* 4.1 6.5 - - + -
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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