Contacts of the helix formed by residues 290 - 305 (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 THR 290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A PRO* 5.2 1.8 - - + -
289A VAL* 1.3 82.2 - - - +
291A PHE* 1.3 65.8 + - - +
292A THR* 3.3 21.6 + - - -
293A ASP* 2.8 27.2 + - - +
294A ILE 3.7 1.9 + - - -
388A PHE* 5.5 0.5 - - - -
479A PHE* 3.6 19.7 - - - -
483A GLU* 4.0 10.3 - - - +
484A GLY 3.7 23.8 - - - +
485A ARG 4.7 0.2 - - - -
487A GLY* 3.7 11.1 + - - +
488A LYS* 4.1 31.3 + - + +
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Residues in contact with PHE 291 (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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290A THR* 1.3 75.8 - - - +
292A THR* 1.3 58.0 + - - +
294A ILE* 3.0 13.7 + - + +
295A PHE* 2.8 36.4 + - + -
398A SER* 3.9 18.8 - - - -
401A PHE* 3.5 48.7 - + + -
466A HIS* 4.9 4.7 - + - -
469A ILE* 3.9 17.7 - - + -
470A MET* 3.4 36.1 - - + -
479A PHE* 3.6 18.6 - + + -
484A GLY 4.8 0.6 + - - -
485A ARG* 3.6 39.5 + - + +
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Residues in contact with THR 292 (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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290A THR* 3.0 10.8 + - - -
291A PHE* 1.3 79.6 - - - +
293A ASP* 1.3 52.6 + - - +
295A PHE* 3.6 1.3 - - + +
296A GLY* 2.6 33.3 + - - -
388A PHE* 4.5 4.4 - - + +
391A GLY* 3.2 36.0 - - - +
392A VAL* 3.4 19.1 - - + +
395A SER* 3.9 1.9 - - - -
398A SER* 3.0 16.8 + - - +
485A ARG 2.7 23.6 + - - -
486A ALA 3.4 10.4 + - - +
487A GLY* 4.2 4.7 - - - -
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Residues in contact with ASP 293 (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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279A LEU* 3.7 18.2 - - + +
282A LYS* 2.6 37.0 + - - +
288A PRO 4.1 0.7 - - - +
289A VAL* 3.3 24.1 - - + -
290A THR* 2.8 34.5 + - - +
292A THR* 1.3 78.8 - - - +
294A ILE* 1.3 61.3 + - - +
296A GLY* 3.2 1.7 + - - -
297A MET* 3.0 27.4 + - - +
387A HIS* 5.0 2.1 - - - -
388A PHE* 3.3 21.2 - - - +
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Residues in contact with ILE 294 (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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267A LEU* 5.3 4.0 - - + -
272A VAL* 5.7 5.2 - - + -
275A TYR* 4.1 20.8 - - + -
276A VAL* 5.0 6.1 - - + -
279A LEU* 3.8 21.3 - - + -
290A THR 4.5 4.0 - - - +
291A PHE* 3.0 25.4 + - + +
293A ASP* 1.3 74.2 - - - +
295A PHE* 1.3 67.7 + - - +
297A MET* 3.1 8.6 + - - +
298A LEU* 3.0 19.9 + - + +
469A ILE* 4.3 21.3 - - + -
473A VAL* 3.7 29.6 - - + -
478A LEU* 4.7 4.5 - - + -
479A PHE* 4.1 16.4 - - + -
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Residues in contact with PHE 295 (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* 3.8 14.6 - + - -
291A PHE* 2.8 18.5 + - + +
292A THR 3.6 6.1 - - - +
294A ILE* 1.3 77.3 - - - +
296A GLY* 1.3 64.1 + - - +
298A LEU* 3.0 14.1 + - + +
299A ILE* 2.9 57.8 + - + +
391A GLY* 4.2 15.7 - - - -
394A GLY 3.8 20.9 - - - -
397A PHE* 3.5 24.7 - + + -
398A SER* 4.0 19.5 - - - -
401A PHE* 3.8 32.5 - + - -
683A PHE* 4.4 8.5 - + - -
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Residues in contact with GLY 296 (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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292A THR 2.6 21.6 + - - -
293A ASP 3.6 2.2 - - - -
295A PHE* 1.3 74.4 - - - +
297A MET* 1.3 57.4 + - - +
299A ILE* 3.3 4.5 + - - +
300A GLY 2.8 24.1 + - - -
387A HIS* 3.1 34.3 - - - +
388A PHE* 4.8 1.3 - - - -
391A GLY* 3.8 10.8 - - - -
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Residues in contact with MET 297 (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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275A TYR* 3.0 69.5 + - + +
278A SER* 3.9 16.4 - - - +
279A LEU* 3.3 24.2 - - + -
293A ASP 3.0 19.0 + - - +
294A ILE* 3.1 7.4 + - - +
296A GLY* 1.3 77.3 - - - +
298A LEU* 1.3 56.9 + - - +
300A GLY* 3.1 0.9 + - - -
301A GLU* 2.7 31.7 + - - +
308A MET* 3.8 11.2 - - + +
387A HIS* 3.8 30.1 - - - +
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Residues in contact with LEU 298 (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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263A PRO* 3.8 18.8 - - + +
264A LEU* 4.9 6.1 - - + -
266A LEU* 3.7 30.7 - - + -
267A LEU* 3.6 36.6 - - + -
275A TYR* 3.8 18.5 - - + +
294A ILE* 3.0 10.8 + - + +
295A PHE* 3.0 15.9 + - + +
297A MET* 1.3 75.1 - - - +
299A ILE* 1.3 63.6 + - + +
301A GLU* 3.3 1.0 + - - -
302A THR* 2.8 36.7 + - + +
401A PHE* 4.2 16.8 - - + -
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Residues in contact with ILE 299 (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 PHE* 4.6 8.1 - - + -
232A TRP* 4.2 23.3 - - + +
295A PHE* 2.9 56.1 + - + +
296A GLY* 3.7 9.0 - - - +
298A LEU* 1.3 78.4 - - + +
300A GLY* 1.3 63.0 + - - +
302A THR* 3.2 8.0 + - + +
303A LEU* 3.0 44.3 + - + +
390A MET* 3.8 19.5 - - + -
391A GLY* 5.7 0.9 - - - -
683A PHE* 4.2 18.4 - - + -
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Residues in contact with GLY 300 (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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296A GLY 2.8 15.2 + - - -
297A MET 3.5 3.1 - - - -
299A ILE* 1.3 79.3 - - - +
301A GLU* 1.3 58.4 + - - +
304A ILE* 2.7 39.6 + - - -
305A HIS 3.3 4.7 + - - -
308A MET* 3.4 15.0 - - - -
387A HIS* 3.9 12.6 - - - -
390A MET* 5.1 1.3 - - - -
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Residues in contact with GLU 301 (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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266A LEU* 3.1 32.6 - - + +
271A LYS* 3.3 26.2 - - - +
275A TYR* 2.5 41.9 + - + +
297A MET 2.7 12.6 + - - +
298A LEU 3.9 2.9 - - - +
300A GLY* 1.3 72.1 - - - +
302A THR* 1.3 61.4 + - - +
305A HIS* 3.2 30.5 + - + +
308A MET* 3.6 14.4 - - + -
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Residues in contact with THR 302 (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 PHE* 4.1 10.9 - - + -
258A ASN* 3.3 36.3 + - - +
259A VAL* 5.4 0.7 - - - +
263A PRO* 3.8 28.3 - - + -
266A LEU* 3.6 22.7 - - + -
298A LEU* 2.8 24.4 + - + +
299A ILE* 3.4 9.3 + - + +
301A GLU* 1.3 79.3 - - - +
303A LEU* 1.3 75.4 + - - +
305A HIS* 4.0 2.4 + - - -
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Residues in contact with LEU 303 (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 PHE* 4.3 7.4 - - + -
202A MET* 3.8 18.2 - - + -
232A TRP* 3.7 18.2 - - + -
236A THR* 3.6 24.4 - - + +
255A LEU* 3.7 28.3 - - + +
258A ASN* 3.8 14.6 - - + +
259A VAL* 4.3 5.2 - - + -
299A ILE* 3.0 32.8 + - + +
302A THR* 1.3 96.2 + - - +
304A ILE* 1.3 65.7 + - + +
305A HIS* 3.8 3.0 + - - -
307A ARG* 5.0 2.6 + - - -
390A MET* 3.7 16.2 - - + -
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Residues in contact with ILE 304 (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 5.7 0.2 - - - +
236A THR* 4.1 17.0 - - - +
239A SER* 3.9 10.1 - - - +
300A GLY* 2.7 30.1 + - - +
303A LEU* 1.3 81.8 - - + +
305A HIS* 1.3 57.3 + - - +
306A ASN* 3.1 7.4 - - - +
307A ARG* 2.8 65.4 + - + +
308A MET* 3.2 12.2 + - - +
310A THR* 4.8 9.9 - - - +
386A LEU* 5.1 6.3 - - + -
387A HIS* 4.9 11.0 - - + +
390A MET* 4.2 22.4 - - + -
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Residues in contact with HIS 305 (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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258A ASN* 3.4 35.4 + - - -
300A GLY 3.3 2.9 + - - -
301A GLU* 3.2 34.5 + - + +
302A THR 4.0 5.2 + - - -
303A LEU 5.0 1.1 - - - -
304A ILE* 1.3 75.0 + - - +
306A ASN* 1.3 71.5 + - + +
307A ARG 3.2 1.2 + - - -
308A MET* 3.8 20.5 + - + +
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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