Contacts of the helix formed by residues 231 - 247 (chain A) in PDB entry 1QX3
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 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A LEU* 1.3 76.6 - - - +
232A PHE* 1.3 77.7 + - - +
233A MET* 2.8 41.7 + - - +
234A HIS* 3.0 33.0 + - + +
235A ILE* 3.0 10.5 + - - +
269A LEU* 5.4 1.7 - - - +
271A LYS 4.5 1.4 - - - +
272A GLU* 3.4 34.2 - - + -
273A LEU* 2.7 31.1 + - - +
274A TYR* 3.4 26.9 - - + +
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Residues in contact with PHE 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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78A PHE* 6.3 1.6 - + - -
157A LEU* 3.5 24.7 - - + -
159A ILE* 5.3 9.9 - - + -
194A LEU* 3.5 40.6 - - + -
196A ALA* 5.3 1.3 - - + -
219A LEU* 4.8 6.3 - - + -
223A LEU* 4.4 11.0 - - + -
230A LEU 3.9 0.8 + - - -
231A GLU* 1.3 72.7 - - - +
233A MET* 1.3 63.3 + - + +
235A ILE* 3.0 16.4 + - + +
236A LEU* 2.9 49.8 + - + +
269A LEU* 5.8 0.7 - - + -
273A LEU* 2.8 43.8 + - + +
275A PHE* 3.5 28.0 - + + -
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Residues in contact with MET 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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194A LEU* 4.1 14.6 - - + -
231A GLU* 2.8 28.1 + - - +
232A PHE* 1.3 73.1 - - + +
234A HIS* 1.3 59.4 + - + +
236A LEU* 3.3 6.7 + - - +
237A THR* 2.8 33.9 + - - +
265A ILE* 3.6 33.7 - - + +
267A SER* 4.1 26.2 - - - +
269A LEU* 5.1 4.3 - - + -
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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 LEU* 4.3 23.1 - - + +
231A GLU* 3.0 27.7 + - + +
233A MET* 1.3 79.6 - - + +
235A ILE* 1.3 66.3 + - - +
237A THR* 3.2 15.8 + - - -
238A ARG* 3.2 23.8 + - - +
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Residues in contact with ILE 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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219A LEU* 5.5 0.7 - - + -
222A MET* 3.8 29.6 - - + +
223A LEU* 4.3 22.0 - - + +
226A TYR* 3.7 24.9 - - + +
227A ALA* 3.9 14.4 - - - +
230A LEU* 3.6 28.9 - - + +
231A GLU 3.0 10.0 + - - +
232A PHE* 3.0 19.0 + - + +
234A HIS* 1.3 77.8 - - - +
236A LEU* 1.3 63.2 + - + +
238A ARG* 3.1 11.7 + - - +
239A VAL* 3.1 21.1 + - + +
275A PHE* 4.4 7.4 - - + -
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Residues in contact with LEU 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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194A LEU* 4.2 12.6 - - + -
196A ALA* 4.3 11.7 - - + -
215A PHE* 5.1 4.0 - - + -
219A LEU* 3.9 28.7 - - + -
232A PHE* 2.9 54.7 + - + +
233A MET* 3.7 6.5 - - - +
235A ILE* 1.3 76.8 - - - +
237A THR* 1.3 57.3 + - - +
239A VAL* 3.2 11.4 + - + +
240A ASN* 3.0 30.3 + - - +
265A ILE* 3.2 43.1 - - + +
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Residues in contact with THR 237 (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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233A MET* 2.8 22.8 + - - +
234A HIS* 3.5 12.9 - - - -
235A ILE 3.2 0.4 - - - -
236A LEU* 1.3 74.1 - - - +
238A ARG* 1.3 66.2 + - + +
240A ASN* 3.2 13.1 + - + +
241A ARG* 3.1 27.9 + - - +
265A ILE* 5.6 2.5 - - - +
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Residues in contact with ARG 238 (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 MET* 3.6 19.0 - - + +
226A TYR* 3.2 43.7 + - - -
230A LEU* 3.5 32.7 - - - +
234A HIS* 3.2 16.7 + - - +
235A ILE* 3.1 7.5 + - - +
237A THR* 1.3 75.0 - - + +
239A VAL* 1.3 66.5 + - - +
241A ARG* 3.8 32.7 - - - +
242A LYS* 2.9 25.8 + - - +
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Residues in contact with VAL 239 (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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215A PHE* 3.9 34.5 - - + -
218A SER* 4.0 7.7 - - - +
219A LEU* 3.7 40.8 - - + +
222A MET* 3.7 15.0 - - + -
235A ILE* 3.1 15.1 + - + +
236A LEU* 3.3 16.2 - - + +
237A THR 3.2 0.2 - - - -
238A ARG* 1.3 77.5 - - - +
240A ASN* 1.3 64.4 + - - +
242A LYS* 3.2 6.7 + - - +
243A VAL* 2.9 26.2 + - + +
263A PRO* 4.6 2.9 - - + -
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Residues in contact with ASN 240 (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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236A LEU 3.0 16.4 + - - +
237A THR* 3.4 15.6 - - + +
239A VAL* 1.3 77.1 - - - +
241A ARG* 1.3 57.4 + - - +
243A VAL* 3.0 8.1 - - - +
244A ALA* 3.0 30.9 + - - +
262A ILE* 3.9 23.5 - - + +
263A PRO* 3.1 30.9 + - - +
265A ILE* 3.9 23.5 - - - +
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Residues in contact with ARG 241 (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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237A THR* 3.1 15.6 + - - +
238A ARG* 3.3 42.5 + - - +
239A VAL 3.3 0.2 - - - -
240A ASN* 1.3 76.0 - - - +
242A LYS* 1.3 57.1 + - - +
244A ALA* 4.2 4.3 - - - -
245A THR* 2.6 57.9 + - + +
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Residues in contact with LYS 242 (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 GLN 5.1 0.9 - - - -
218A SER* 3.7 35.9 - - - +
221A ALA* 4.1 16.4 - - - +
222A MET* 4.2 19.7 - - - -
238A ARG 2.9 17.3 + - - +
239A VAL* 3.2 4.0 + - - +
241A ARG* 1.3 76.5 - - - +
243A VAL* 1.3 57.3 + - - +
245A THR* 4.1 3.1 - - - -
246A GLU* 2.8 79.0 + - - +
247A PHE* 3.7 7.4 - - + -
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Residues in contact with VAL 243 (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 TRP* 4.4 21.1 - - + +
215A PHE* 5.2 1.6 - - - +
218A SER* 4.2 8.6 + - - +
239A VAL* 2.9 21.9 + - + +
240A ASN 3.0 9.0 - - - +
242A LYS* 1.3 74.9 - - - +
244A ALA* 1.3 60.3 + - - +
247A PHE* 3.5 32.2 + - + +
261A GLN* 3.3 37.8 + - + +
263A PRO* 3.0 39.3 - - + -
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Residues in contact with ALA 244 (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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240A ASN 3.0 20.9 + - - +
241A ARG* 3.7 6.3 - - - +
243A VAL* 1.3 79.7 - - - +
245A THR* 1.3 59.0 + - + +
260A LYS* 2.7 34.4 + - - +
261A GLN 3.5 14.6 - - - +
262A ILE* 4.4 12.8 - - + -
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Residues in contact with THR 245 (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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241A ARG* 2.6 47.4 + - + +
242A LYS* 3.7 3.3 + - - -
244A ALA* 1.3 82.8 - - + +
246A GLU* 1.3 67.9 + - - +
247A PHE 3.5 0.6 + - - -
260A LYS* 3.8 8.2 + - - +
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Residues in contact with GLU 246 (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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242A LYS* 2.8 65.9 + - - +
245A THR* 1.3 80.5 + - - +
247A PHE* 1.3 71.0 + - + +
248A GLU 4.4 0.3 + - - -
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Residues in contact with PHE 247 (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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208A ASN* 6.2 0.2 - - + -
214A TRP* 3.2 64.9 - + + -
217A GLN* 3.9 28.9 - - + -
218A SER* 3.5 25.6 - - - -
242A LYS* 3.7 13.9 - - + -
243A VAL* 3.5 25.7 + - - +
245A THR 3.5 1.2 - - - -
246A GLU* 1.3 94.9 - - + +
248A GLU* 1.3 58.1 + - - +
260A LYS* 2.7 32.3 + - - +
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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