Contacts of the helix formed by residues 285 - 298 (chain A) in PDB entry 1CYY
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 ILE 285 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A PHE* 1.3 77.1 - - - +
286A THR* 1.3 65.4 + - - +
287A SER* 3.2 23.3 + - - +
288A THR* 2.9 23.3 + - + +
289A LEU* 2.9 22.0 + - - +
322A THR* 3.3 10.3 - - - +
323A ASP* 3.8 19.1 - - + +
324A SER 3.1 42.4 - - - +
325A THR* 3.8 17.5 - - + +
368A ILE* 3.6 10.1 - - - -
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Residues in contact with THR 286 (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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285A ILE* 1.3 71.3 - - - +
287A SER* 1.3 63.9 + - - +
289A LEU* 3.9 2.3 - - - +
290A GLN* 3.0 51.5 + - - +
305A MET* 3.9 20.4 - - + -
320A MET 2.7 18.2 + - - +
321A ARG* 3.3 5.4 - - + -
322A THR 2.9 28.8 + - - -
368A ILE* 3.6 8.8 - - - +
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Residues in contact with SER 287 (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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285A ILE* 3.2 22.7 - - - +
286A THR* 1.3 79.0 - - - +
288A THR* 1.3 72.2 + - - +
290A GLN* 3.2 11.2 + - - +
291A GLN* 3.1 38.3 + - - +
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Residues in contact with THR 288 (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 ALA 6.1 0.2 - - - -
283A PRO 4.5 1.6 + - - -
284A PHE* 3.5 18.3 - - - -
285A ILE* 2.9 35.7 + - + +
287A SER* 1.3 87.2 + - - +
289A LEU* 1.3 57.4 + - - +
291A GLN* 3.5 16.6 + - - +
292A ALA* 2.9 29.8 + - - +
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Residues in contact with LEU 289 (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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284A PHE* 3.7 25.5 - - + -
285A ILE 2.9 17.2 + - - +
286A THR* 3.9 4.3 - - - +
288A THR* 1.3 76.9 + - - +
290A GLN* 1.3 58.7 + - - +
293A ALA* 2.9 28.8 + - - +
304A THR* 4.0 19.1 - - + -
305A MET* 5.6 4.3 - - - -
308A ALA* 4.4 15.3 - - + -
320A MET* 5.6 0.2 - - + -
368A ILE* 4.0 20.2 - - + -
390A LEU* 3.9 16.6 - - + -
393A LEU* 4.5 5.2 - - + -
394A ILE* 3.7 37.5 - - + -
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Residues in contact with GLN 290 (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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286A THR* 3.0 33.2 + - - +
287A SER* 3.2 8.4 + - - +
289A LEU* 1.3 77.8 - - + +
291A GLN* 1.3 61.5 + - + +
293A ALA* 4.1 1.2 - - - +
294A SER* 3.2 24.1 + - - -
299A PHE 4.6 1.9 - - - +
300A GLY 5.9 0.5 - - - -
301A VAL* 3.6 38.0 - - + +
304A THR* 4.2 16.5 + - + -
305A MET* 3.3 40.1 - - - +
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Residues in contact with GLN 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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287A SER* 3.1 32.8 + - - +
288A THR* 3.8 15.3 - - - +
290A GLN* 1.3 76.6 - - + +
292A ALA* 1.3 58.1 + - - +
294A SER* 3.4 5.6 + - - -
295A THR* 3.1 33.7 + - - +
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Residues in contact with ALA 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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284A PHE* 3.5 30.7 - - + -
288A THR 2.9 18.5 + - - +
289A LEU 4.0 2.0 - - - +
291A GLN* 1.3 73.6 - - - +
293A ALA* 1.3 60.7 + - - +
295A THR* 4.5 4.5 - - - +
296A ARG* 2.8 41.3 + - + +
393A LEU* 3.9 9.9 - - + -
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Residues in contact with ALA 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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289A LEU 2.9 18.1 + - - +
290A GLN 4.1 1.1 - - - +
292A ALA* 1.3 75.9 - - - +
294A SER* 1.3 58.1 + - - +
297A LEU* 2.9 27.2 + - - +
298A GLY 2.9 7.4 + - - -
299A PHE* 3.1 12.7 + - + -
304A THR* 3.3 25.8 - - + +
390A LEU* 3.9 22.4 - - + -
393A LEU* 3.8 9.6 - - + +
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Residues in contact with SER 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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290A GLN 3.2 19.1 + - - -
291A GLN* 3.6 6.3 - - - -
293A ALA* 1.3 77.2 - - - +
295A THR* 1.3 60.3 + - - +
298A GLY* 2.8 26.7 + - - -
299A PHE 3.2 20.3 + - - +
300A GLY* 5.6 0.7 - - - -
273B ASP* 4.9 0.2 - - - +
452B ALA* 5.1 11.3 - - - +
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Residues in contact with THR 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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291A GLN* 3.1 16.2 + - - +
292A ALA* 3.9 4.7 - - - -
294A SER* 1.3 82.9 + - - +
296A ARG* 1.3 62.5 + - + +
298A GLY 4.5 0.9 + - - -
441A LEU* 4.2 26.0 - - + -
273B ASP* 5.3 2.4 - - - +
411B THR* 5.7 1.0 + - - -
428B ILE* 3.1 21.2 - - + +
449B ILE* 3.8 30.0 - - + +
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Residues in contact with ARG 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 ALA* 2.8 26.7 + - - +
295A THR* 1.3 77.9 - - + +
297A LEU* 1.3 70.4 + - + +
393A LEU* 3.7 24.2 - - + +
397A GLN* 5.8 0.2 + - - -
434A TRP* 5.4 1.8 - - - -
438A MET* 3.5 31.8 - - - +
439A PRO* 2.9 36.3 + - - +
440A ALA* 4.4 1.2 - - - +
441A LEU* 3.4 45.6 - - + +
273B ASP* 5.5 0.4 - - - +
409B ASP* 3.4 27.3 - - - +
428B ILE* 3.7 22.6 - - + +
429B LEU 4.8 1.6 + - - -
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Residues in contact with LEU 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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293A ALA* 2.9 13.3 + - - +
296A ARG* 1.3 93.9 - - + +
298A GLY* 1.3 63.0 + - - +
299A PHE* 3.5 44.6 + - + -
389A LYS* 3.9 44.0 - - + +
390A LEU* 4.0 7.6 - - + +
393A LEU* 4.3 17.7 - - + -
273B ASP* 3.9 14.7 - - - +
409B ASP* 4.0 22.4 - - - +
430B ARG* 5.4 2.5 - - - -
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Residues in contact with GLY 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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293A ALA 2.9 0.2 + - - -
294A SER* 2.8 20.3 + - - -
295A THR 4.5 0.2 - - - -
296A ARG 3.8 0.4 - - - -
297A LEU* 1.3 78.3 - - - +
299A PHE* 1.3 63.5 - - - +
300A GLY 3.7 1.0 + - - -
273B ASP* 3.3 27.4 + - - +
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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