Contacts of the helix formed by residues 226 - 236 (chain A) in PDB entry 1QZW
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 ALA 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A ILE* 4.7 11.0 - - + -
222A ILE* 3.1 38.1 - - + +
223A GLY* 2.5 20.2 + - - +
225A LYS* 1.3 72.5 - - - +
227A TYR* 1.3 72.2 + - - +
228A ASP* 2.4 10.5 - - - +
229A LEU* 2.6 23.3 + - + +
230A ALA* 4.5 1.8 - - + -
256A ALA* 5.4 5.2 - - - +
260A VAL* 6.0 2.9 - - + -
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Residues in contact with TYR 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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224A GLN 2.8 20.1 + - - +
225A LYS 2.7 4.9 + - - +
226A ALA* 1.3 84.9 - - - +
228A ASP* 1.3 81.6 + - + +
230A ALA* 2.9 9.2 + - - +
231A SER* 2.6 32.2 + - - -
259A ALA* 3.1 38.7 - - + +
260A VAL* 4.6 3.7 - - - +
262A ALA* 2.8 36.9 + - + +
263A THR* 3.2 10.2 - - + +
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Residues in contact with ASP 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLU* 4.1 10.5 - - - +
222A ILE* 5.0 1.4 - - - +
225A LYS* 2.5 24.4 - - - +
226A ALA* 2.4 23.4 - - - +
227A TYR* 1.3 83.6 - - + +
229A LEU* 1.3 75.2 + - - +
231A SER* 2.6 21.9 + - - -
232A ARG* 2.7 12.3 + - - -
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Residues in contact with LEU 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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104A VAL* 3.1 28.0 - - + -
192A TYR* 3.4 30.3 - - + -
195A GLU* 3.3 23.9 + - + +
198A LEU* 4.5 9.0 - - + -
199A LEU* 5.4 1.0 - - - +
216A LEU* 3.5 18.8 - - + -
218A ILE* 3.4 30.5 - - + -
226A ALA* 2.6 21.8 + - + +
228A ASP* 1.3 83.0 + - - +
230A ALA* 1.3 65.0 + - + +
232A ARG* 2.5 31.2 + - - +
233A PHE* 4.4 0.2 - - - +
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Residues in contact with ALA 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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216A LEU* 4.0 20.4 - - + -
218A ILE* 5.8 2.2 - - + -
226A ALA* 4.6 2.0 - - + +
227A TYR* 2.9 10.9 + - - +
229A LEU* 1.3 90.1 - - + +
231A SER* 1.3 70.9 + - - +
232A ARG 2.6 11.1 - - - +
233A PHE* 2.9 16.2 - - + +
234A HIS* 3.4 3.6 + - - -
242A VAL* 5.6 7.6 - - + -
260A VAL* 5.9 6.1 - - + -
263A THR* 6.0 1.1 - - + +
265A ALA* 5.9 7.4 - - + -
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Residues in contact with SER 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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227A TYR* 2.6 37.0 + - - -
228A ASP* 2.6 19.3 + - - -
230A ALA* 1.3 68.9 - - - +
232A ARG* 1.3 50.4 + - - -
233A PHE 2.5 19.8 + - - -
234A HIS* 2.5 27.6 + - - +
235A GLN* 3.6 8.3 + - - +
263A THR* 3.6 26.5 + - - +
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Residues in contact with ARG 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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193A GLY 3.9 1.2 + - - -
195A GLU* 3.0 39.6 + - - +
196A THR* 2.5 43.3 + - - +
199A LEU* 3.7 33.0 - - + +
228A ASP 2.7 11.3 + - - +
229A LEU 2.5 22.5 - - - +
231A SER* 1.3 68.7 - - - +
233A PHE* 1.3 68.6 + - - +
235A GLN* 4.6 14.8 + - - +
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Residues in contact with PHE 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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102A VAL* 5.2 4.0 - - + -
199A LEU* 5.7 6.7 - - + -
202A MET* 5.2 9.4 - - - -
214A VAL* 4.7 15.3 - - + -
216A LEU* 4.0 32.5 - - + -
229A LEU 4.4 0.4 - - - +
230A ALA* 2.9 21.3 - - + +
231A SER 2.5 2.8 + - - -
232A ARG* 1.3 85.6 - - - +
234A HIS* 1.3 55.4 + - - -
235A GLN* 2.4 10.1 - - - +
236A ALA* 2.4 42.8 + - + +
237A SER* 2.4 50.6 + - - -
240A GLY* 3.2 30.5 - - - -
241A SER 4.6 0.2 - - - -
242A VAL* 4.2 9.6 - - + -
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Residues in contact with HIS 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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230A ALA 3.4 2.7 + - - +
231A SER* 2.5 23.3 + - - +
233A PHE* 1.3 78.1 - - - +
235A GLN* 1.3 58.7 + - + +
237A SER 3.5 5.2 - - - -
238A PRO* 3.0 59.4 + - + +
240A GLY 4.3 8.1 - - - -
263A THR* 2.8 22.6 + - - -
264A GLY* 2.9 41.6 + - - -
265A ALA* 3.4 6.6 + - - -
266A THR* 3.7 8.5 + - - -
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Residues in contact with GLN 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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231A SER* 3.8 13.7 - - - +
232A ARG* 4.6 13.9 + - - +
233A PHE 2.4 3.1 - - - +
234A HIS* 1.3 80.8 - - + +
236A ALA* 1.3 70.1 + - - +
237A SER* 3.2 1.8 + - - -
238A PRO* 4.2 6.8 - - - +
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Residues in contact with ALA 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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199A LEU* 5.5 9.4 - - + -
202A MET* 5.0 16.8 - - + -
233A PHE* 2.4 39.5 + - + +
235A GLN* 1.3 76.5 - - - +
237A SER* 1.3 64.2 + - - +
238A PRO* 4.2 2.3 - - - +
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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