Contacts of the helix formed by residues 385 - 394 (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 PRO 385 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A LYS* 6.2 1.1 - - + -
308A MET 4.0 9.0 - - - +
309A ASN* 5.0 11.9 - - - +
310A THR 3.7 6.1 - - - +
311A THR* 4.4 5.8 - - + -
383A GLU 3.9 4.5 - - - +
384A ASN* 1.3 97.2 - - + +
386A LEU* 1.3 66.7 + - - +
387A HIS* 3.5 36.3 - - + +
388A PHE* 3.0 22.9 + - + +
389A LEU* 3.6 3.6 + - - +
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Residues in contact with LEU 386 (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* 3.8 38.8 - - - +
239A SER* 4.5 1.1 - - - -
304A ILE* 5.1 5.8 - - + -
310A THR* 2.7 42.6 + - + +
311A THR* 3.8 7.4 - - - +
312A LEU* 4.1 22.0 - - + +
315A LEU* 4.5 12.1 - - + -
329A PHE* 5.5 0.4 - - + -
384A ASN 3.7 1.0 + - - -
385A PRO* 1.3 72.4 - - - +
387A HIS* 1.3 57.8 + - - +
389A LEU* 3.0 9.6 + - + +
390A MET* 2.8 33.8 + - + +
393A TRP* 3.8 29.4 - - + -
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Residues in contact with HIS 387 (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* 5.7 3.2 - - - +
293A ASP 5.0 1.3 - - - -
296A GLY* 3.1 26.1 - - - +
297A MET* 3.8 35.9 - - + +
300A GLY* 3.9 16.4 - - - +
304A ILE* 4.9 5.1 - - + +
308A MET* 3.3 43.8 + - + +
309A ASN* 5.7 2.2 - - - -
310A THR 4.7 0.2 + - - -
385A PRO* 3.5 26.6 - - + +
386A LEU* 1.3 78.0 - - - +
388A PHE* 1.3 66.4 + - + +
390A MET* 3.5 14.6 - - - +
391A GLY 3.0 19.8 + - - -
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Residues in contact with PHE 388 (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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282A LYS* 3.4 12.6 - - - -
288A PRO 5.8 0.2 - - - -
290A THR* 5.5 1.1 - - - -
292A THR* 4.7 4.9 - - + -
293A ASP* 3.3 46.4 - - - +
296A GLY* 4.8 2.7 - - - -
368A PHE* 4.9 3.1 - + - -
384A ASN* 3.3 36.3 - - + +
385A PRO* 3.0 23.0 + - + +
387A HIS* 1.3 84.5 - - + +
389A LEU* 1.3 71.5 + - + +
391A GLY* 2.9 3.8 + - - -
392A VAL* 2.9 47.7 + - + +
487A GLY* 5.6 1.8 - - - -
488A LYS 4.2 20.2 - - - -
489A VAL* 4.5 10.5 - - + -
547A VAL* 5.9 0.4 - - + -
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Residues in contact with LEU 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A LEU* 3.7 42.2 - - + +
349A PHE* 3.7 24.9 - - + -
354A ILE* 5.2 2.2 - - + -
368A PHE* 4.0 20.9 - - + -
383A GLU* 5.8 0.2 - - - +
384A ASN* 5.1 7.9 - - + +
385A PRO 3.6 6.7 + - - +
386A LEU* 3.0 14.2 + - + +
388A PHE* 1.3 87.7 - - + +
390A MET* 1.3 56.1 + - - +
392A VAL* 3.0 8.2 + - + +
393A TRP* 2.7 64.7 + - + +
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Residues in contact with MET 390 (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* 3.2 41.9 + - + +
235A SER* 3.7 29.4 - - - +
236A THR* 4.4 3.4 - - - +
299A ILE* 3.8 18.6 - - + +
300A GLY* 5.1 1.1 - - - -
303A LEU* 3.7 33.7 - - + -
304A ILE* 4.2 18.8 - - + -
386A LEU* 2.8 16.6 + - + +
387A HIS* 3.5 24.5 - - - +
389A LEU* 1.3 75.6 - - - +
391A GLY* 1.3 63.7 + - - +
393A TRP* 3.3 10.7 + - + +
394A GLY* 3.1 18.4 + - - -
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Residues in contact with GLY 391 (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* 3.2 16.6 - - - +
295A PHE* 4.2 10.5 - - - -
296A GLY* 3.8 21.0 - - - -
299A ILE* 5.7 0.2 - - - -
387A HIS 3.0 7.3 + - - -
388A PHE 2.9 8.6 + - - -
390A MET* 1.3 75.7 - - - +
392A VAL* 1.3 55.2 + - - +
394A GLY 3.2 3.1 + - - -
395A SER* 2.9 30.0 + - - -
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Residues in contact with VAL 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A THR* 3.8 10.5 - - + -
331A CYS* 4.1 15.9 - - + +
349A PHE* 5.4 3.6 - - + -
368A PHE* 5.7 2.2 - - + -
388A PHE* 2.9 50.3 + - + +
389A LEU* 3.5 12.6 - - + +
391A GLY* 1.3 76.2 - - - +
393A TRP* 1.3 62.7 + - + +
395A SER* 2.8 23.7 + - - -
486A ALA 5.1 0.2 - - - -
487A GLY* 5.1 2.7 - - - -
547A VAL* 3.6 40.4 - - + +
548A VAL 3.9 0.5 - - - -
549A ASP 3.5 6.4 + - - -
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Residues in contact with TRP 393 (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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228A SER* 3.1 22.4 + - - +
231A THR* 3.0 42.2 - - + +
235A SER* 3.7 15.5 - - - -
312A LEU* 4.6 2.0 - - + -
329A PHE* 3.4 44.1 - + + +
330A THR 3.1 27.6 + - - +
331A CYS* 3.9 8.3 - - + -
349A PHE* 3.6 42.3 - + + -
386A LEU* 3.8 17.0 - - + -
389A LEU* 2.7 51.5 + - + +
390A MET* 3.7 6.5 - - - +
392A VAL* 1.3 74.1 - - + +
394A GLY* 1.3 56.9 + - - +
395A SER 3.5 0.2 - - - -
549A ASP* 3.3 14.5 - - - +
550A SER 4.6 0.9 + - - -
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Residues in contact with GLY 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A SER* 3.9 8.3 - - - -
232A TRP* 4.0 14.1 - - - -
295A PHE* 3.8 6.7 - - - -
390A MET 3.1 12.5 + - - -
391A GLY 3.3 4.3 - - - -
393A TRP* 1.3 78.6 - - - +
395A SER* 1.3 56.2 + - - +
396A ALA 2.8 12.9 + - - -
397A PHE* 3.1 24.1 + - - +
549A ASP* 3.3 9.2 - - - -
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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