Contacts of the helix formed by residues 285 - 298 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B PRO 4.3 0.2 - - - +
284B PHE* 1.3 76.3 - - - +
286B THR* 1.3 66.7 + - - +
287B SER* 3.4 21.7 + - - +
288B THR* 3.1 20.0 + - + +
289B LEU* 3.0 21.0 + - - +
322B THR* 3.4 16.4 - - - +
323B ASP* 3.9 21.5 - - + +
324B SER 3.3 37.0 - - - +
325B THR* 3.6 19.3 - - + -
368B ILE* 3.7 5.8 - - - -
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Residues in contact with THR 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ILE* 1.3 71.4 - - - +
287B SER* 1.3 64.2 + - - +
289B LEU* 3.3 2.9 + - - +
290B GLN* 3.1 46.6 + - - +
305B MET* 3.9 11.9 - - + -
320B MET 2.8 17.5 + - - +
321B ARG* 3.0 19.0 + - - +
322B THR 2.7 42.7 + - - -
323B ASP* 5.4 2.2 - - - -
368B ILE* 3.8 9.1 - - - +
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Residues in contact with SER 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ILE* 3.4 19.4 - - - +
286B THR* 1.3 78.4 - - - +
288B THR* 1.3 68.8 + - - +
290B GLN* 3.2 14.9 + - - +
291B GLN* 3.1 21.0 + - - +
322B THR 4.8 0.2 + - - -
323B ASP* 5.5 2.8 + - - -
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Residues in contact with THR 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ALA 5.6 0.2 + - - -
283B PRO 4.6 1.6 + - - -
284B PHE* 3.6 16.1 - - - -
285B ILE* 3.1 33.4 + - + +
286B THR 3.4 0.2 - - - -
287B SER* 1.3 83.9 + - - +
289B LEU* 1.3 57.3 + - - +
291B GLN* 3.4 7.5 + - - +
292B ALA* 2.9 30.0 + - - +
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Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PHE* 3.8 26.9 - - + -
285B ILE 3.0 18.0 + - - +
286B THR* 3.6 5.2 - - - +
288B THR* 1.3 74.0 + - - +
290B GLN* 1.3 62.0 + - - +
292B ALA* 3.3 0.5 + - - -
293B ALA* 2.8 32.7 + - - +
304B THR* 4.0 17.0 - - + -
305B MET* 5.4 4.3 - - - -
308B ALA* 4.7 14.8 - - + -
320B MET* 5.3 1.1 - - + +
368B ILE* 3.6 23.1 - - + -
390B LEU* 4.1 15.9 - - + -
393B LEU* 4.6 3.8 - - + -
394B ILE* 3.7 35.4 - - + -
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Residues in contact with GLN 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B THR* 3.1 29.5 + - - +
287B SER* 3.2 12.2 + - - +
289B LEU* 1.3 79.6 - - + +
291B GLN* 1.3 61.8 + - - +
293B ALA* 3.7 2.1 - - - +
294B SER* 3.0 23.4 + - - -
299B PHE 4.5 2.6 - - - +
301B VAL* 3.5 41.3 - - + +
304B THR* 4.3 15.8 + - + -
305B MET* 3.2 38.3 - - - +
321B ARG* 5.1 4.4 - - - +
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Residues in contact with GLN 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B SER 3.1 14.5 + - - +
288B THR* 3.8 8.1 - - - +
289B LEU 3.2 0.2 - - - -
290B GLN* 1.3 77.6 - - - +
292B ALA* 1.3 63.8 + - - +
294B SER* 3.1 10.8 + - - -
295B THR* 3.0 44.5 + - - +
473B PRO 5.3 0.7 - - - +
474B PRO* 3.5 39.5 - - - +
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PHE* 3.5 30.3 - - + -
288B THR 2.9 17.9 + - - +
289B LEU 3.9 1.3 - - - +
291B GLN* 1.3 76.6 - - - +
293B ALA* 1.3 57.8 + - - +
295B THR* 4.6 4.5 - - - +
296B ARG* 2.8 44.0 + - - +
393B LEU* 4.0 9.4 - - + +
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU 2.8 22.7 + - - +
290B GLN 3.7 1.6 - - - +
292B ALA* 1.3 70.7 - - - +
294B SER* 1.3 61.3 + - - +
297B LEU* 3.0 12.2 + - - +
298B GLY 2.9 22.2 + - - -
299B PHE* 3.0 13.0 + - + -
304B THR* 3.3 31.6 - - + +
390B LEU* 4.0 16.4 - - + -
393B LEU* 3.9 9.4 - - + +
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Residues in contact with SER 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B GLN 3.0 13.9 + - - -
291B GLN* 3.3 19.4 + - - -
293B ALA* 1.3 76.7 - - - +
295B THR* 1.3 58.9 + - - +
298B GLY* 2.7 29.1 + - - -
299B PHE 3.4 18.7 + - - +
472B LYS* 3.4 30.1 + - - +
473B PRO 4.6 5.0 + - - -
474B PRO 5.0 5.0 - - - -
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Residues in contact with THR 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A THR* 3.4 16.8 + - - +
460A THR* 3.6 10.7 - - - +
462A VAL* 3.4 33.2 - - + +
291B GLN* 3.0 30.0 + - - +
292B ALA* 4.0 3.8 - - - -
294B SER* 1.3 80.8 + - - +
296B ARG* 1.3 63.5 + - - +
441B LEU* 3.9 26.7 - - + -
472B LYS* 4.8 3.1 - - - +
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Residues in contact with ARG 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A THR* 2.9 24.0 - - - +
228A THR 3.7 5.5 - - - +
229A PRO 4.5 0.2 - - - +
231A GLY* 3.0 38.3 + - - +
460A THR* 4.2 1.8 + - - -
284B PHE* 6.0 0.2 - - - -
292B ALA* 2.8 28.2 + - - +
295B THR* 1.3 77.4 - - - +
297B LEU* 1.3 70.6 + - + +
393B LEU* 3.8 25.7 - - + +
397B GLN* 5.6 1.2 + - - -
434B TRP* 5.6 2.0 - - - -
438B MET* 3.6 28.9 - - - +
439B PRO* 2.8 30.1 + - - +
440B ALA* 4.6 1.4 - - - +
441B LEU* 3.3 42.2 - - + +
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Residues in contact with LEU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PRO 3.6 19.3 - - - +
230A SER 5.5 0.9 - - - -
231A GLY 5.0 1.8 - - - +
460A THR* 3.4 12.4 + - - -
293B ALA* 3.0 12.4 + - - +
296B ARG* 1.3 87.7 - - + +
298B GLY* 1.3 63.7 + - - +
299B PHE* 3.7 42.0 + - + -
389B LYS* 3.9 38.6 - - + +
390B LEU* 4.1 8.1 - - + -
393B LEU* 3.8 30.3 - - + -
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Residues in contact with GLY 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A THR* 3.6 18.4 + - - -
294B SER* 2.7 20.4 + - - -
297B LEU* 1.3 79.6 - - - +
299B PHE* 1.3 63.4 + - - +
300B GLY 3.8 1.7 + - - -
303B LYS* 5.5 0.9 + - - +
472B LYS* 3.9 8.5 + - - -
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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
------------------------------------------------------------
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