Contacts of the helix formed by residues 212 - 218 (chain A) in PDB entry 1W6J
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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210A THR* 3.0 26.2 + - + +
211A LEU* 1.3 77.7 - - - +
213A PRO* 1.3 71.8 - - - +
214A GLU* 3.1 28.8 + - + -
215A MET* 3.2 43.3 + - + +
216A TRP* 4.9 0.7 - - - -
218A PHE* 3.6 34.8 - + - -
241A SER* 4.9 0.3 + - - -
297A TYR* 6.1 0.2 - - + -
300A LEU* 3.7 46.0 - - + -
303A TYR* 4.2 19.5 - + - -
304A GLU* 5.0 0.9 - - - -
312A ARG* 5.5 0.7 - - - -
1735A C14 4.3 5.8 - - + -
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Residues in contact with PRO 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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211A LEU 3.1 6.0 - - - +
212A PHE* 1.3 89.3 - - - +
214A GLU* 1.3 72.0 + - - +
215A MET 3.2 0.9 + - - -
216A TRP* 3.3 22.2 + - + +
241A SER* 4.3 13.5 - - - +
244A TYR* 4.3 8.7 - - + -
245A ALA* 4.0 17.3 - - + -
312A ARG* 3.8 27.8 - - + +
315A ALA* 3.6 18.9 - - + +
316A VAL* 5.2 0.4 - - + +
319A LEU* 3.8 23.8 - - + +
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Residues in contact with GLU 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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212A PHE* 3.1 29.2 + - + -
213A PRO* 1.3 71.5 - - - +
215A MET* 1.3 59.2 + - - +
216A TRP 3.0 2.7 - - - -
217A LEU* 2.8 31.2 + - + +
218A PHE* 3.6 9.1 + - + -
303A TYR* 4.1 24.4 + - + +
307A HIS* 4.8 0.7 + - - -
308A SER 4.8 0.5 - - - +
311A LEU* 4.6 17.3 - - + +
312A ARG* 2.9 58.9 + - - +
315A ALA* 4.0 12.1 - - + -
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Residues in contact with MET 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 LEU 4.6 5.6 - - - +
212A PHE* 3.2 44.4 + - + +
213A PRO 3.1 0.2 - - - -
214A GLU* 1.3 78.8 - - - +
216A TRP* 1.3 69.0 - - + +
218A PHE* 3.3 45.9 - - + +
224A ALA 4.0 16.6 - - - +
226A PRO* 3.6 20.9 - - + +
229A LEU* 5.1 2.2 - - - -
241A SER* 5.7 0.9 - - - +
1735A C14 4.0 55.6 - - + -
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Residues in contact with TRP 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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212A PHE 4.9 0.4 - - - -
213A PRO* 3.6 16.6 - - + +
214A GLU 3.0 1.0 - - - -
215A MET* 1.3 88.4 - - + +
217A LEU* 1.3 60.1 + - + +
218A PHE 3.3 0.4 + - - -
225A HIS* 3.7 9.3 + - - -
226A PRO* 3.6 36.1 - - + +
234A ARG* 3.8 27.4 - - + -
235A GLN* 6.3 0.4 - - - -
237A TYR* 5.0 3.1 + - + +
238A LEU* 3.6 45.9 - - + +
241A SER* 4.8 7.3 + - - -
315A ALA* 5.5 0.9 - - + +
318A LYS* 2.8 40.1 + - + -
319A LEU* 3.4 29.3 - - + +
322A HIS* 4.1 18.2 - + - -
434A TYR* 3.7 32.6 + + - -
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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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214A GLU* 2.8 15.0 + - + +
216A TRP* 1.3 75.3 - - - +
218A PHE* 1.3 67.4 + - - +
219A PRO* 3.7 1.6 - - - +
311A LEU* 3.5 48.2 - - + +
314A ARG* 3.9 46.4 + - + +
315A ALA* 3.7 21.3 - - + +
318A LYS* 4.1 20.2 - - + +
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Residues in contact with PHE 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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212A PHE* 3.6 29.2 - + - -
214A GLU* 3.9 12.6 - - + -
215A MET* 3.3 34.5 + - + +
216A TRP 3.8 1.4 - - - +
217A LEU* 1.3 82.4 - - + +
219A PRO* 1.3 75.9 - - + +
220A ASP* 3.6 2.3 + - - +
222A ALA* 4.0 14.8 - - + -
223A PRO 4.5 8.1 - - - -
224A ALA 5.8 0.2 - - - -
225A HIS* 3.3 26.2 + - + -
318A LYS* 4.8 2.1 + - - -
1735A C14 3.9 37.5 - - + -
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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