Contacts of the helix formed by residues 220 - 232 (chain A) in PDB entry 2PU1
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 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A LYS* 4.2 9.2 - - - -
198A TYR* 2.7 39.6 + - - +
214A PRO 5.4 0.2 - - - +
215A ILE* 3.8 18.6 - - + +
216A LYS 5.1 0.7 + - - -
217A ASP* 3.3 30.8 + - - +
219A ASN* 1.3 75.3 - - - +
221A PRO* 1.4 69.2 - - + +
222A LEU 3.2 0.9 + - - -
223A PRO* 3.4 13.5 - - - +
224A ILE* 3.6 13.0 - - + +
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Residues in contact with PRO 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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151A ILE* 3.7 37.6 - - + +
161A LEU* 4.0 8.3 - - + -
166A PHE* 3.6 34.8 - - + -
215A ILE* 4.2 6.9 - - + -
217A ASP 3.6 9.6 - - - +
218A ILE 3.4 15.5 - - - +
219A ASN 3.4 0.7 - - - -
220A GLU* 1.4 89.9 - - + +
222A LEU* 1.3 61.5 + - - +
223A PRO 3.6 0.2 - - - -
224A ILE* 3.2 9.2 + - + +
225A LEU* 3.1 24.2 + - - +
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Residues in contact with LEU 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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166A PHE* 3.8 25.6 - - + -
219A ASN* 3.2 9.3 + - + +
221A PRO* 1.3 73.5 - - - +
223A PRO* 1.3 75.5 - - + +
225A LEU* 3.1 17.5 + - + +
226A MET* 3.1 15.6 + - - +
240A ILE* 4.0 33.3 - - + +
242A MET* 4.2 4.5 - - - -
281A TRP* 3.6 38.8 - - + +
285A TYR* 3.6 38.4 - - + -
287A ILE* 4.0 5.8 - - + -
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Residues in contact with PRO 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 ASN 3.5 9.6 - - - +
220A GLU* 3.4 14.1 - - - +
222A LEU* 1.3 87.6 - - - +
224A ILE* 1.3 58.4 + - + +
226A MET* 3.3 6.0 + - + +
227A GLU* 2.9 30.0 + - - +
285A TYR* 3.4 27.8 - - + +
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Residues in contact with ILE 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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151A ILE* 4.0 7.6 - - + -
190A LEU* 3.4 25.3 - - + +
193A ILE* 4.0 17.1 - - + +
194A ILE* 4.4 5.6 - - + -
197A LYS* 4.1 16.2 - - + -
198A TYR* 3.2 39.3 - - + +
215A ILE* 4.2 9.6 - - + -
220A GLU 3.6 17.5 - - - +
221A PRO* 3.2 8.5 + - + +
222A LEU 3.1 0.8 - - - -
223A PRO* 1.3 78.3 - - + +
225A LEU* 1.3 57.5 + - - +
227A GLU* 3.3 11.8 + - - +
228A ALA* 3.0 27.9 + - - +
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Residues in contact with LEU 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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150A VAL* 3.6 27.8 - - + -
151A ILE* 3.7 21.3 - - + -
166A PHE* 4.1 22.0 - - + -
167A MET 4.1 12.8 - - - +
168A ILE* 4.0 22.0 - - + -
186A VAL* 4.8 1.1 - - + +
190A LEU* 4.2 7.2 - - + -
221A PRO 3.1 16.4 + - - +
222A LEU* 3.1 14.0 + - + +
224A ILE* 1.3 76.6 - - - +
226A MET* 1.3 56.0 - - - +
228A ALA* 3.3 6.0 + - + +
229A ILE* 3.0 34.9 + - + +
240A ILE* 4.3 21.8 - - + -
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Residues in contact with MET 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 LEU 3.1 13.1 + - - +
223A PRO* 3.3 7.4 + - + +
225A LEU* 1.3 75.0 - - - +
227A GLU* 1.3 61.6 + - - +
229A ILE* 3.4 19.7 + - + +
230A GLU* 3.0 24.3 + - - +
238A PHE 5.8 0.7 - - - +
240A ILE* 3.8 23.8 - - - -
285A TYR* 3.6 20.6 - - + -
286A PRO* 3.7 30.7 - - + -
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Residues in contact with GLU 227 (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 ILE* 3.5 35.6 - - + +
197A LYS* 6.2 0.5 - - - +
223A PRO 2.9 17.0 + - - +
224A ILE* 3.6 10.2 - - - +
225A LEU 3.3 0.2 - - - -
226A MET* 1.3 77.2 - - - +
228A ALA* 1.3 56.8 + - - +
230A GLU* 3.3 8.8 + - + +
231A GLU* 2.8 35.7 + - + +
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Residues in contact with ALA 228 (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 VAL* 3.7 15.5 - - + +
189A SER* 3.8 4.9 - - - -
190A LEU* 3.7 38.4 - - + +
193A ILE* 3.4 11.1 - - + +
224A ILE 3.0 13.3 + - - +
225A LEU* 3.3 8.5 + - + +
227A GLU* 1.3 71.5 - - - +
229A ILE* 1.3 67.2 + - - +
231A GLU* 4.4 0.2 - - - -
232A ALA* 3.0 27.4 + - - +
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Residues in contact with ILE 229 (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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168A ILE* 4.3 13.0 - - + -
186A VAL* 3.9 21.1 - - + -
225A LEU* 3.0 27.7 + - + +
226A MET* 3.6 25.8 - - + +
228A ALA* 1.3 78.2 - - - +
230A GLU* 1.3 59.3 + - - +
232A ALA* 3.6 1.0 + - - +
233A GLY 3.6 1.9 + - - -
234A HIS* 3.0 51.9 + - - +
235A ARG* 4.0 5.8 - - - +
236A GLY 4.5 2.9 - - - +
238A PHE* 3.5 41.1 - - + +
239A ALA 5.3 0.2 - - - +
240A ILE* 5.1 5.2 - - + -
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Residues in contact with GLU 230 (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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226A MET 3.0 13.1 + - - +
227A GLU* 3.5 11.7 - - + +
229A ILE* 1.3 78.1 - - - +
231A GLU* 1.3 58.6 + - + +
233A GLY* 3.0 21.5 + - - -
235A ARG* 3.0 62.1 + - + +
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Residues in contact with GLU 231 (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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189A SER* 3.9 24.9 + - - +
192A GLY* 5.9 0.7 - - - -
193A ILE* 3.5 26.1 + - + +
227A GLU* 2.8 25.7 + - + +
228A ALA 3.9 3.4 - - - +
230A GLU* 1.3 76.2 - - - +
232A ALA* 1.3 57.5 + - - +
233A GLY* 3.0 5.1 + - - -
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Residues in contact with ALA 232 (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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185A GLU* 3.8 11.7 - - + +
186A VAL* 3.7 31.9 - - + +
189A SER* 3.5 16.6 + - - +
228A ALA 3.0 16.9 + - - +
229A ILE 4.0 0.9 - - - +
230A GLU 3.3 0.2 - - - -
231A GLU* 1.3 76.9 - - - +
233A GLY* 1.3 59.9 + - - +
234A HIS* 3.5 18.6 + - + -
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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