Contacts of the helix formed by residues 227 - 240 (chain A) in PDB entry 1CJY
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 LEU 227 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A GLY 3.9 3.8 + - - -
195A SER 3.8 0.2 - - - +
196A GLY* 3.3 22.4 + - - +
226A GLY* 1.3 74.4 - - - +
228A SER* 1.3 88.6 + - - +
229A GLY 3.0 3.5 + - - -
230A SER* 3.2 10.1 + - - -
231A THR* 3.7 6.0 + - - -
330A THR* 3.5 16.8 - - + +
346A TRP* 4.1 2.9 - - + -
549A ASP* 4.0 0.7 - - - +
550A SER* 3.9 15.5 - - - -
551A GLY 3.8 19.3 - - - +
554A PHE 3.7 9.2 - - - +
555A ASN* 3.6 27.4 - - - +
556A LEU 3.7 2.2 - - - -
557A PRO* 3.4 33.2 - - + -
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Residues in contact with SER 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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196A GLY* 3.5 14.6 - - - -
197A GLY 4.1 3.2 + - - -
227A LEU* 1.3 75.3 - - - +
229A GLY* 1.3 64.0 + - - -
231A THR* 2.9 32.8 - - - +
232A TRP* 3.7 10.7 + - - -
330A THR 5.1 0.6 + - - -
393A TRP* 3.1 24.8 + - - +
394A GLY* 3.9 4.2 - - - -
397A PHE* 4.2 12.6 - - - -
417A MET* 6.0 0.2 - - - +
549A ASP* 2.7 32.6 + - - -
550A SER 5.7 0.2 - - - +
555A ASN* 5.2 1.8 - - - -
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Residues in contact with GLY 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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196A GLY* 3.7 4.0 - - - -
197A GLY 3.9 1.2 - - - +
198A GLY 3.7 23.3 - - - +
201A ALA* 4.0 10.1 - - - -
202A MET* 3.7 10.3 - - - +
227A LEU 3.0 2.6 + - - -
228A SER* 1.3 79.4 + - - +
230A SER* 1.3 62.8 + - - -
232A TRP* 3.1 28.8 + - - +
233A TYR 3.7 2.8 + - - -
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Residues in contact with SER 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A GLY* 2.9 32.8 - - - -
195A SER 2.5 26.9 + - - -
201A ALA* 4.1 6.7 + - - +
205A PHE* 4.0 21.7 - - - +
226A GLY* 4.2 7.6 - - - -
227A LEU 3.2 6.1 + - - -
229A GLY* 1.3 74.5 - - - +
231A THR* 1.3 58.7 + - - +
233A TYR* 3.0 8.3 + - - +
234A MET* 3.0 29.8 + - - +
576A PHE* 4.2 2.1 - - - -
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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
----------------------------------------------------------
226A GLY 3.6 18.4 + - - -
227A LEU* 3.7 5.4 + - - +
228A SER 2.9 18.3 + - - +
230A SER* 1.3 76.9 - - - +
232A TRP* 1.3 72.9 + - + +
234A MET* 3.4 6.3 + - - +
235A SER* 2.9 30.9 + - - +
329A PHE* 3.4 23.4 - - - +
330A THR 4.9 0.2 + - - -
393A TRP* 3.0 44.4 - - + +
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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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198A GLY* 3.9 16.4 - - - -
199A PHE* 3.7 38.6 - + - -
202A MET* 4.0 5.6 - - - -
228A SER 3.9 8.0 + - - -
229A GLY* 3.1 18.4 + - - +
231A THR* 1.3 89.7 - - + +
233A TYR* 1.3 60.7 + - - +
235A SER* 3.7 2.4 + - - -
236A THR* 2.8 28.6 + - - -
295A PHE* 3.8 24.0 - + - -
299A ILE* 4.2 11.1 - - + +
303A LEU* 3.7 15.3 - - + -
390A MET* 3.2 44.8 + - + +
394A GLY* 4.0 16.2 - - - +
397A PHE* 3.7 25.6 - + - -
683A PHE* 3.9 12.6 - + - -
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Residues in contact with TYR 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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202A MET* 3.9 22.2 - - + +
205A PHE* 4.1 19.3 - + + -
206A SER* 3.2 25.0 + - - -
209A MET* 3.7 16.2 - - + -
229A GLY 3.7 2.2 + - - -
230A SER 3.0 10.8 + - - +
232A TRP* 1.3 77.4 - - - +
234A MET* 1.3 61.6 + - + +
236A THR* 3.2 6.6 + - - -
237A LEU* 2.8 61.4 + - + +
248A PRO* 3.7 20.4 - - - +
251A ILE* 4.8 5.5 - - + +
252A ASN* 2.6 32.2 + - - -
255A LEU* 3.8 23.1 - - + -
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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
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205A PHE* 4.0 16.6 - - + -
209A MET* 6.1 1.1 - - + -
224A VAL* 3.1 40.4 - - + +
225A ALA 3.8 3.6 - - - +
226A GLY* 3.6 27.4 - - - -
230A SER 3.0 18.4 + - - +
231A THR* 3.4 10.3 + - - +
233A TYR* 1.3 78.1 - - + +
235A SER* 1.3 55.8 + - - +
237A LEU* 3.3 3.5 + - - -
238A TYR* 2.8 50.0 + - + +
327A PRO* 4.0 9.0 - - + -
328A LEU 3.2 21.8 - - - +
329A PHE* 3.7 17.7 - - + -
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Residues in contact with SER 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 THR 2.9 21.6 + - - -
232A TRP 3.8 4.9 - - - -
233A TYR 3.2 0.2 - - - -
234A MET* 1.3 75.6 - - - +
236A THR* 1.3 52.0 + - - +
238A TYR* 5.1 1.6 - - - -
239A SER* 2.8 40.9 + - - -
304A ILE* 5.1 1.8 - - - -
315A LEU* 4.9 0.8 - - - +
329A PHE* 3.8 7.8 - - - -
386A LEU* 3.8 21.8 - - - +
390A MET* 3.7 21.6 - - - +
393A TRP* 3.7 22.0 - - - -
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Residues in contact with THR 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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202A MET* 5.5 0.2 - - - -
232A TRP 2.8 20.4 + - - -
233A TYR* 3.2 10.1 + - + -
235A SER* 1.3 77.7 - - - +
237A LEU* 1.3 63.5 + - - +
239A SER* 4.0 3.8 - - - -
240A HIS* 3.4 6.1 + - - +
251A ILE* 4.6 14.0 - - + +
255A LEU* 4.9 18.2 - - + +
303A LEU* 3.6 36.2 - - + +
304A ILE* 4.1 6.9 - - + +
307A ARG* 3.0 33.6 + - - +
390A MET* 4.4 1.2 - - - +
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Residues in contact with LEU 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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209A MET* 3.9 23.6 - - + -
218A LEU* 5.8 0.2 - - + -
233A TYR* 2.8 57.8 + - + +
234A MET* 3.8 3.1 - - + +
236A THR* 1.3 75.0 - - - +
238A TYR* 1.3 70.3 + - + +
240A HIS* 3.1 18.9 + - - +
243A PHE* 3.4 43.7 - - + +
248A PRO* 4.5 14.1 - - + -
251A ILE* 3.3 35.9 - - + -
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Residues in contact with TYR 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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209A MET* 5.0 4.5 - - + +
218A LEU* 6.1 0.2 - - - +
224A VAL* 3.9 23.3 - - + +
234A MET* 2.8 34.0 + - + +
237A LEU* 1.3 85.8 - - + +
239A SER* 1.3 56.4 + - - +
240A HIS 3.3 0.2 - - - -
243A PHE* 3.8 22.0 - + - -
315A LEU* 3.7 25.7 - - + +
318A LYS* 3.3 43.6 - - + +
319A VAL* 6.2 0.7 - - + -
324A CYS* 3.9 15.5 - - + -
325A PRO* 2.9 38.5 + - - +
327A PRO* 3.0 40.3 - - + +
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Residues in contact with SER 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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235A SER 2.8 25.2 + - - -
236A THR 3.6 2.4 + - - -
238A TYR* 1.3 76.3 - - - +
240A HIS* 1.3 65.7 + - - +
241A PRO* 3.3 1.9 - - - +
304A ILE* 3.9 8.0 - - - +
307A ARG* 2.7 38.4 + - - +
310A THR* 3.7 29.7 + - - +
315A LEU* 3.8 9.6 - - - +
318A LYS* 4.7 2.8 - - - +
386A LEU* 4.5 3.6 - - - -
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Residues in contact with HIS 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 THR 3.4 5.9 + - - +
237A LEU 3.1 15.8 + - - +
239A SER* 1.3 76.7 - - - +
241A PRO* 1.3 70.7 - - + +
242A ASP* 2.9 51.6 + - + +
243A PHE* 3.2 7.3 + - + +
246A LYS* 5.5 0.9 - - + -
250A GLU* 6.3 0.2 - - - +
251A ILE* 3.6 34.7 - - + +
254A GLU* 3.0 33.5 + - - -
307A ARG* 3.5 23.3 + - - +
318A LYS* 2.6 30.4 + - - -
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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