Contacts of the helix formed by residues 227 - 236 (chain A) in PDB entry 2QFZ
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 VAL 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A LEU* 3.9 15.0 - - + -
201A PHE* 3.6 31.2 - - + -
202A LYS* 3.8 29.6 - - + -
205A LEU* 4.0 21.8 - - + -
223A ILE* 3.9 6.7 - - + -
224A PRO* 3.3 14.1 - - + +
226A PRO* 1.3 81.1 - - + +
228A ARG* 1.3 55.7 + - - +
229A PRO* 3.5 3.1 - - - -
230A MET* 3.6 4.6 + - - +
231A THR* 2.7 35.8 + - - +
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Residues in contact with ARG 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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223A ILE* 3.3 28.9 + - + +
224A PRO 3.2 8.5 + - - +
225A LYS* 3.1 37.7 + - + +
227A VAL* 1.3 77.2 - - - +
229A PRO* 1.3 71.8 - - + +
231A THR 3.3 0.7 + - - -
232A TRP* 2.9 43.5 + - + +
332A VAL* 3.8 18.3 - - + +
436A ILE* 3.4 32.4 - - - +
437A ARG* 4.5 12.9 - - - +
440A ASP* 3.0 35.0 + - - +
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Residues in contact with PRO 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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225A LYS 3.5 13.0 - - - +
226A PRO 4.2 6.1 - - - +
227A VAL 3.6 2.9 - - - -
228A ARG* 1.3 91.9 - - + +
230A MET* 1.3 61.0 + - - +
233A LYS* 3.2 31.6 + - - +
332A VAL* 3.6 32.5 - - + +
333A PHE* 3.8 17.7 - - + -
335A CYS 5.6 0.2 - - - -
336A GLU* 3.7 39.7 - - + +
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Residues in contact with MET 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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205A LEU* 3.9 24.9 - - + -
227A VAL* 3.6 4.4 + - - +
228A ARG 3.4 0.4 - - - -
229A PRO* 1.3 77.0 - - - +
231A THR* 1.3 61.0 + - - +
233A LYS* 3.4 10.9 + - + +
234A LEU* 2.9 45.4 + - + +
239A LEU* 3.6 34.8 - - + -
246A ARG* 4.4 19.5 - - + +
250A LEU* 5.7 3.4 - - + -
336A GLU* 4.9 8.3 + - - +
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Residues in contact with THR 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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201A PHE* 4.0 7.4 - - + -
205A LEU* 4.0 16.4 - - - +
215A LEU* 4.0 18.4 - - + -
219A SER* 3.4 26.9 - - - +
223A ILE* 3.5 25.2 - - + +
227A VAL 2.7 25.1 + - - -
228A ARG 3.3 2.4 + - - -
230A MET* 1.3 76.0 - - - +
232A TRP* 1.3 57.4 + - - +
234A LEU* 3.1 2.9 + - - +
235A LEU* 2.9 36.5 + - + +
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Residues in contact with TRP 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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223A ILE* 3.7 16.0 - - + +
228A ARG* 2.9 36.0 + - + +
229A PRO 3.9 4.0 - - - +
231A THR* 1.3 72.2 - - - +
233A LYS* 1.3 62.4 + - - +
235A LEU* 4.7 2.5 - - + -
236A SER* 3.0 29.6 + - - -
328A PRO* 3.8 24.5 - - + -
329A PHE* 3.7 33.2 - + + -
332A VAL* 3.8 32.5 - - + -
333A PHE* 4.4 10.3 - + + -
366A CYS* 4.9 2.0 - - - -
436A ILE* 3.5 25.6 - - + -
439A TRP* 3.9 22.2 - + + -
440A ASP* 2.9 22.5 + - - +
443A GLN* 3.4 25.3 + - + +
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Residues in contact with LYS 233 (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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229A PRO* 3.2 21.1 + - - +
230A MET* 3.6 16.7 - - + +
231A THR 3.3 0.2 - - - -
232A TRP* 1.3 78.4 - - - +
234A LEU* 1.3 57.0 + - - +
236A SER* 3.1 7.5 + - - -
238A TYR* 3.0 56.7 + - + -
239A LEU* 3.2 29.2 + - + -
250A LEU* 5.0 7.9 - - + +
333A PHE* 3.8 33.1 - - + +
336A GLU* 4.6 11.5 + - - -
362A ASP* 2.7 29.5 + - - +
366A CYS* 4.3 1.6 - - - -
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Residues in contact with LEU 234 (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* 3.8 26.9 - - + -
210A THR* 4.7 5.4 - - + -
212A LEU* 4.0 27.8 - - + +
215A LEU* 4.1 8.1 - - + -
230A MET* 2.9 30.3 + - + +
231A THR 3.1 3.3 + - - +
233A LYS* 1.3 77.3 - - - +
235A LEU* 1.3 59.6 + - - +
237A GLY* 3.1 18.2 + - - -
239A LEU* 3.3 21.0 - - + +
240A PRO 3.1 30.3 - - - +
241A ALA* 4.1 4.5 - - - +
246A ARG* 3.8 29.2 - - - +
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Residues in contact with LEU 235 (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 LEU* 4.3 5.8 - - + +
215A LEU* 4.0 15.9 - - + -
216A ARG* 3.3 54.0 + - + +
219A SER* 3.5 32.1 - - - +
223A ILE* 4.5 5.6 - - + -
231A THR* 2.9 26.8 + - + +
232A TRP* 4.2 2.9 - - - +
234A LEU* 1.3 73.9 - - - +
236A SER* 1.3 60.9 + - - +
237A GLY 3.5 0.7 + - - -
440A ASP 4.8 0.2 - - - +
443A GLN* 3.8 37.7 - - + +
444A SER* 4.1 3.8 - - - +
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Residues in contact with SER 236 (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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232A TRP 3.0 19.3 + - - -
233A LYS 3.1 10.0 + - - -
235A LEU* 1.3 76.9 - - - +
237A GLY* 1.3 55.5 + - - +
238A TYR* 3.3 13.5 + - - +
366A CYS* 3.8 12.6 - - - -
369A LYS* 3.1 40.3 - - - +
443A GLN* 4.1 17.4 - - - +
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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