Contacts of the helix formed by residues 212 - 221 (chain A) in PDB entry 2Z82
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 PHE 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A LEU* 4.3 19.7 - - + -
187A ARG* 3.3 35.2 - - - -
188A ASN* 3.5 14.4 - - - -
189A TYR* 3.5 43.3 - + + -
207A LEU* 5.4 2.2 - - + +
209A GLU* 5.3 3.7 + - + -
210A SER 3.2 0.4 - - - -
211A ALA* 1.3 94.0 - - + +
213A LEU* 1.3 64.7 + - - +
214A LEU 3.3 2.5 - - - -
215A GLU* 3.7 12.7 + - + +
216A ILE* 3.0 32.7 + - + +
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Residues in contact with LEU 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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205A LEU* 5.3 1.1 - - + -
207A LEU* 4.2 12.6 - - + +
210A SER* 3.0 20.4 + - - +
212A PHE* 1.3 77.7 - - - +
214A LEU* 1.3 58.6 + - - +
216A ILE* 3.4 13.8 + - + +
217A PHE* 2.8 43.3 + - + +
227A LEU* 5.7 2.2 - - + -
229A LEU* 3.9 39.0 - - + -
232A THR* 5.5 0.9 - - + -
234A LEU* 3.7 28.7 - - + -
237A PHE* 4.0 20.9 - - + -
269A LEU* 4.8 9.0 - - + -
272A LEU* 5.7 0.2 - - + -
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Residues in contact with LEU 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 SER 4.5 1.2 + - - -
211A ALA 5.3 2.2 + - - +
212A PHE 3.3 1.0 - - - -
213A LEU* 1.3 78.7 - - - +
215A GLU* 1.3 66.0 + - + +
217A PHE* 3.0 10.7 + - + +
218A ALA 3.0 17.0 + - - -
237A PHE* 4.3 16.8 - - + -
238A GLN 3.7 22.2 - - - +
239A PHE* 5.4 1.1 - - + -
240A SER* 2.8 37.2 - - - +
242A LEU* 3.3 30.3 - - + +
272A LEU* 5.1 9.0 - - + -
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Residues in contact with GLU 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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189A TYR* 4.3 16.6 - - + +
191A SER* 3.5 29.5 + - - -
212A PHE* 3.7 13.6 + - + +
214A LEU* 1.3 76.6 - - + +
216A ILE* 1.3 67.2 + - - +
218A ALA* 2.9 20.2 + - + +
219A ASP* 3.1 19.4 + - - +
242A LEU* 5.4 0.4 - - - -
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Residues in contact with ILE 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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165A ILE* 5.7 3.4 - - + -
186A LEU* 4.9 3.1 - - + -
189A TYR* 3.9 37.9 - - + -
194A LEU* 5.0 8.1 - - + -
203A LEU* 5.5 0.4 - - + -
205A LEU* 3.8 26.0 - - + -
207A LEU* 4.1 28.0 - - + -
212A PHE* 3.0 35.4 + - + +
213A LEU* 3.5 10.1 - - + +
215A GLU* 1.3 75.9 - - - +
217A PHE* 1.3 59.6 + - + +
219A ASP* 3.0 19.4 + - - +
220A ILE* 3.3 24.8 + - + +
227A LEU* 6.3 1.6 - - + -
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Residues in contact with PHE 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 LEU* 2.8 27.8 + - + +
214A LEU* 3.2 15.0 - - + +
216A ILE* 1.3 79.3 - - + +
218A ALA* 1.3 56.4 + - - +
219A ASP 3.5 0.2 + - - -
220A ILE* 3.5 14.7 + - + +
221A LEU* 3.1 48.7 + - + +
227A LEU* 3.7 30.3 - - + -
229A LEU* 6.0 1.8 - - + -
242A LEU* 4.3 4.7 - - + -
251A MET* 4.5 7.6 - - + -
254A LEU* 5.0 10.1 - - + -
256A PHE* 6.5 0.2 - + - -
269A LEU* 6.0 1.6 - - + -
272A LEU* 3.6 48.5 - - + -
275A TYR* 5.6 0.2 - - + -
276A ILE* 4.3 24.0 - - + -
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Residues in contact with ALA 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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195A LYS* 4.4 7.4 + - - -
214A LEU 3.0 5.1 + - - +
215A GLU* 2.9 16.7 + - + +
217A PHE* 1.3 76.9 - - - +
219A ASP* 1.3 63.7 + - - +
220A ILE 3.4 0.6 + - - -
221A LEU* 4.3 9.0 + - - +
242A LEU* 3.4 31.4 - - + -
243A PRO* 5.8 1.3 - - + -
244A VAL* 3.6 31.5 - - + +
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Residues in contact with ASP 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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189A TYR* 2.5 36.8 + - - +
191A SER* 3.8 1.6 - - - -
192A GLN* 2.8 43.0 + - - +
194A LEU* 3.7 7.0 - - + +
195A LYS* 3.6 37.4 - - - +
215A GLU 3.3 7.6 - - - +
216A ILE 3.0 7.3 + - - +
218A ALA* 1.3 84.7 - - - +
220A ILE* 1.3 62.1 + - - +
221A LEU 3.7 0.2 - - - -
222A SER* 5.2 1.9 + - - -
223A SER* 4.3 3.5 + - - -
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Residues in contact with ILE 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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194A LEU* 3.9 21.8 - - + -
200A ILE* 5.0 2.9 - - + -
203A LEU* 3.8 23.6 - - + -
216A ILE* 3.3 22.9 - - + +
217A PHE* 3.7 21.3 - - + +
218A ALA 3.4 0.4 - - - -
219A ASP* 1.3 83.5 - - - +
221A LEU* 1.3 62.0 + - - +
222A SER 3.0 11.9 + - - -
223A SER* 3.1 7.8 + - - +
224A VAL* 3.1 37.7 + - + +
227A LEU* 4.4 10.1 - - + -
251A MET* 3.6 29.3 - - + +
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Residues in contact with LEU 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 PHE* 3.1 48.5 + - + +
218A ALA* 4.3 5.5 + - - +
219A ASP 3.7 0.8 - - - -
220A ILE* 1.3 78.7 - - + +
222A SER* 1.3 57.3 + - - +
242A LEU* 3.5 24.2 - - + -
244A VAL* 3.7 24.0 - - + -
247A VAL* 3.1 22.8 - - + +
249A SER* 3.0 33.6 - - - +
250A PRO* 3.4 2.4 - - - +
251A MET* 5.7 0.9 - - + -
275A TYR* 4.0 19.5 - - + +
276A ILE* 4.1 17.3 - - + -
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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