Contacts of the helix formed by residues 223 - 242 (chain A) in PDB entry 2DQM
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 223 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A LEU* 3.8 18.1 - - + +
213A LEU* 3.4 30.2 - - + +
215A VAL* 4.5 10.1 - - + -
219A ASN 4.3 5.6 - - - +
220A LEU* 3.2 12.5 + - + +
222A ARG* 1.3 78.4 - - - +
224A PRO* 1.3 71.4 - - + +
225A TRP 3.4 2.5 - - - -
226A ALA 3.2 11.4 + - - -
227A MET 3.2 8.8 + - - -
276A VAL* 5.1 1.1 - - - -
277A LEU* 5.2 1.6 - - - -
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Residues in contact with PRO 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 3.8 18.1 - - + -
220A LEU 3.4 13.5 - - - +
221A ASP* 4.3 8.1 - - - +
222A ARG 3.8 2.0 - - - -
223A ALA* 1.3 90.5 - - + +
225A TRP* 1.3 57.2 + - - +
227A MET* 3.2 3.6 + - + +
228A THR* 2.8 34.6 + - - +
278A ALA 5.5 0.9 - - - +
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Residues in contact with TRP 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ARG 5.1 1.6 + - - +
223A ALA 3.4 1.0 - - - -
224A PRO* 1.3 78.3 - - - +
226A ALA* 1.3 57.3 + - - +
228A THR* 3.2 22.4 + - + -
229A SER* 2.8 49.8 + - - -
232A ASN* 4.9 5.4 - - - -
276A VAL 5.5 0.7 - - - +
278A ALA* 4.8 10.5 + - + +
288A TYR* 2.9 68.8 + + + -
289A LEU* 5.4 2.5 - - + -
291A ILE* 3.7 27.8 - - + +
292A GLU* 4.2 20.6 - - + -
670A VAL* 4.4 23.6 - - + -
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Residues in contact with ALA 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LEU* 3.9 7.4 - - + -
223A ALA 3.2 9.4 + - - +
225A TRP* 1.3 79.4 - - - +
227A MET* 1.3 58.8 + - - +
229A SER* 3.2 4.1 + - - -
230A LEU* 2.9 28.9 + - - +
252A ILE* 6.2 0.7 - - + -
276A VAL* 3.6 38.6 + - + +
291A ILE* 4.1 14.1 - - + -
295A ILE* 4.2 20.3 - - + +
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Residues in contact with MET 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 3.3 53.6 - - + +
199A ASP* 3.7 33.7 - - + +
211A LEU* 3.6 43.1 - - + +
212A GLU 4.4 0.4 - - - +
213A LEU* 4.1 15.8 - - + +
223A ALA 3.2 2.7 + - - +
224A PRO* 3.2 9.1 + - + +
226A ALA* 1.3 77.9 - - - +
228A THR* 1.3 62.4 + - - +
230A LEU* 3.2 13.6 + - + +
231A LYS* 3.1 25.4 + - - +
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Residues in contact with THR 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A PRO* 2.8 23.0 + - - +
225A TRP* 3.2 24.0 + - + -
227A MET* 1.3 75.2 - - - +
229A SER* 1.3 57.7 + - - +
231A LYS* 3.3 18.2 + - - +
232A ASN* 2.9 43.5 + - - +
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Residues in contact with SER 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A TRP* 2.8 48.4 + - - -
226A ALA* 3.5 7.9 - - - -
228A THR* 1.3 74.7 - - - +
230A LEU* 1.3 59.4 + - - +
232A ASN* 3.3 10.4 + - - +
233A SER* 2.8 32.7 + - - -
291A ILE* 4.9 0.2 - - - -
292A GLU* 3.7 24.6 - - - +
295A ILE* 3.8 11.2 - - - -
330A PHE* 4.3 1.0 - - - -
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Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 4.1 28.7 - - + -
212A GLU 5.7 1.1 - - - +
226A ALA 2.9 12.5 + - - +
227A MET* 3.2 15.2 + - + +
229A SER* 1.3 77.0 - - - +
231A LYS* 1.3 63.4 + - - +
233A SER* 3.1 4.2 + - - -
234A MET* 2.9 36.8 + - + +
250A TYR* 3.7 45.3 - - + +
252A ILE* 4.0 13.5 - - + -
295A ILE* 3.5 19.2 - - + +
299A TYR* 4.2 17.9 - - + -
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Residues in contact with LYS 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASP* 2.9 27.7 + - - +
200A THR 3.9 18.6 - - - +
201A PHE* 3.7 22.7 - - + -
211A LEU* 3.6 20.2 - - + -
227A MET* 3.1 17.7 + - - +
228A THR* 3.7 18.7 + - - +
230A LEU* 1.3 77.0 - - - +
232A ASN* 1.3 65.9 + - - +
234A MET* 3.3 3.4 + - - -
235A LYS* 3.0 24.8 + - - +
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Residues in contact with ASN 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A TRP* 4.9 6.2 - - - -
228A THR* 2.9 34.4 + - - +
229A SER* 3.5 12.1 - - - +
231A LYS* 1.3 77.4 - - - +
233A SER* 1.3 57.0 + - - +
235A LYS* 3.4 5.9 + - - +
236A TRP* 3.0 30.7 + - - +
292A GLU* 4.8 5.3 - - - +
330A PHE* 3.7 6.5 - - + -
334A LEU* 4.2 24.3 - - + +
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Residues in contact with SER 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A SER 2.8 21.0 + - - -
230A LEU* 3.4 9.6 - - - -
232A ASN* 1.3 74.5 - - - +
234A MET* 1.3 65.5 + - - +
236A TRP* 3.4 0.5 + - - +
237A ASP* 3.0 21.3 + - - +
295A ILE* 4.0 1.1 - - - +
296A GLY* 3.1 35.8 + - - -
299A TYR* 4.0 17.5 - - - -
300A PHE* 3.6 11.5 - - - -
330A PHE* 3.4 17.2 - - - -
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Residues in contact with MET 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PHE* 3.6 50.9 - - + -
203A THR* 5.4 0.2 - - + -
209A VAL* 4.2 15.9 - - + -
211A LEU* 3.9 13.9 - - + -
230A LEU* 2.9 28.5 + - + +
231A LYS 3.3 6.3 + - - +
233A SER* 1.3 78.5 - - - +
235A LYS* 1.3 61.6 + - - +
237A ASP* 3.5 2.3 + - - +
238A GLU* 3.3 26.0 + - - +
243A LEU 4.5 0.7 - - - +
245A TYR* 3.7 33.4 - - + +
250A TYR* 5.2 2.2 - - + -
299A TYR* 3.6 31.4 + - + +
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Residues in contact with LYS 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PHE* 3.7 16.0 - - + -
204A ARG* 5.5 5.3 - - - +
231A LYS 3.0 16.7 + - - +
232A ASN* 3.8 7.4 - - - +
234A MET* 1.3 77.3 - - - +
236A TRP* 1.3 62.4 + - - +
238A GLU* 3.2 20.4 + - - +
239A GLU* 2.8 61.4 + - - +
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Residues in contact with TRP 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 ASN 3.0 17.6 + - - +
233A SER 3.8 1.1 - - - +
235A LYS* 1.3 74.9 - - - +
237A ASP* 1.3 80.2 + - - +
239A GLU* 4.4 12.6 - - + +
240A ARG* 2.8 54.0 + - + +
241A PHE* 3.5 22.0 - + - -
300A PHE* 3.3 40.4 - + - -
326A ARG* 3.3 22.7 - - - -
329A GLU* 3.7 11.7 - - + -
330A PHE* 3.5 33.2 - + + +
333A ASP* 2.9 27.4 + - + +
334A LEU* 3.9 22.0 - - + -
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Residues in contact with ASP 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 SER 3.0 17.3 + - - +
234A MET 3.5 1.5 + - - +
236A TRP* 1.3 82.3 - - - +
238A GLU* 1.3 56.0 + - - +
241A PHE* 3.0 17.5 + - - +
242A GLY 2.9 21.7 + - - -
243A LEU* 3.1 28.7 + - - +
299A TYR* 3.9 16.3 - - + -
300A PHE* 3.5 14.9 - - + -
303A TRP* 4.7 4.7 - - - -
326A ARG* 2.8 46.0 + - - -
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Residues in contact with GLU 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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201A PHE* 3.8 16.4 - - - -
202A THR 5.0 0.2 - - - +
203A THR* 3.1 19.5 - - - +
204A ARG* 2.9 62.8 + - - +
234A MET 3.3 16.1 + - - +
235A LYS* 3.2 20.1 + - - +
236A TRP 3.1 0.4 - - - -
237A ASP* 1.3 78.4 - - - +
239A GLU* 1.3 60.3 + - + +
242A GLY* 2.9 25.6 + - - -
243A LEU 3.3 18.6 - - - +
244A GLU* 3.4 12.8 - - + +
245A TYR 5.4 0.2 + - - -
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Residues in contact with GLU 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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204A ARG* 5.3 2.1 + - - +
235A LYS* 2.8 53.3 + - + +
236A TRP* 3.8 12.1 - - + +
238A GLU* 1.3 79.1 - - + +
240A ARG* 1.3 60.4 + - + +
242A GLY 4.6 0.5 + - - -
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Residues in contact with ARG 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 TRP* 2.8 47.0 + - + +
239A GLU* 1.3 76.7 - - + +
241A PHE* 1.3 71.1 + - + +
325A PHE* 5.1 2.6 - - - -
329A GLU* 3.0 45.3 + - - +
333A ASP* 2.9 29.5 + - - -
337A ARG* 4.2 0.6 - - - +
392A HIS* 4.0 9.3 + - - -
397A GLU* 2.9 41.0 + - - +
400A PHE* 6.2 0.2 - - - -
401A GLN* 3.6 18.5 + - - +
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Residues in contact with PHE 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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236A TRP* 3.5 27.1 - + - -
237A ASP* 3.0 20.8 + - - +
240A ARG* 1.3 97.5 - - + +
242A GLY* 1.3 64.5 + - - +
243A LEU* 3.4 17.8 + - + +
322A LEU* 5.6 0.4 - - + -
325A PHE* 4.6 9.0 - + - -
326A ARG* 3.4 34.3 - - + -
329A GLU* 5.3 1.3 - - + -
400A PHE* 4.2 10.8 - + - -
401A GLN* 3.5 30.9 - - - +
404A MET* 3.8 38.3 - - + +
405A GLN* 5.8 4.3 + - - +
408A PHE* 5.5 1.1 - + - -
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Residues in contact with GLY 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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204A ARG* 3.6 27.9 + - - -
237A ASP 2.9 0.2 + - - -
238A GLU* 2.9 22.8 + - - -
239A GLU 4.6 0.4 + - - -
240A ARG 3.6 1.2 - - - -
241A PHE* 1.3 78.1 - - - +
243A LEU* 1.3 63.1 + - - +
244A GLU* 4.1 1.9 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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