Contacts of the helix formed by residues 287 - 301 (chain N) in PDB entry 1KYO
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 ASP 287 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161E HIS* 5.4 0.3 + - - -
195E PRO* 4.7 2.8 - - - +
285N ILE* 3.1 10.5 + - + +
286N PRO* 1.3 81.6 - - + +
288N LYS* 1.3 66.0 + - - +
289N LEU* 3.1 13.3 + - - +
290N LEU* 2.7 55.3 + - + +
291N GLY* 2.9 18.4 + - - -
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Residues in contact with LYS 288 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160E THR 3.9 14.7 + - - +
161E HIS* 2.9 49.3 + - + +
162E LEU* 4.2 8.1 - - + -
195E PRO 4.0 18.0 + - - +
197E PRO* 4.4 17.4 - - + +
152N SER* 2.8 34.7 + - - -
153N ALA* 4.4 17.0 - - + +
287N ASP* 1.3 77.4 + - - +
289N LEU* 1.3 65.6 + - - +
291N GLY* 3.3 6.2 + - - -
292N VAL* 3.4 16.6 + - + +
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Residues in contact with LEU 289 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153N ALA* 3.5 40.6 - - + +
154N ILE* 5.3 0.2 - - - -
155N PRO* 5.2 7.6 - - + -
287N ASP* 3.1 7.4 + - - +
288N LYS* 1.3 75.1 - - + +
290N LEU* 1.3 69.8 + - + +
291N GLY 3.1 1.6 - - - -
292N VAL* 3.1 7.6 + - + +
293N ILE* 2.9 51.9 + - + +
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Residues in contact with LEU 290 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285N ILE* 3.6 20.0 - - + -
287N ASP* 2.7 34.5 + - + +
289N LEU* 1.3 79.5 - - + +
291N GLY* 1.3 56.9 + - - +
293N ILE* 4.3 17.0 - - + -
294N THR* 2.8 40.2 + - - +
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Residues in contact with GLY 291 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E HIS* 6.3 0.2 - - - -
282N LEU* 3.5 32.3 - - - +
285N ILE* 3.8 17.0 - - - +
287N ASP 2.9 20.1 + - - -
288N LYS 3.6 2.2 - - - -
289N LEU 3.1 0.6 - - - -
290N LEU* 1.3 76.8 - - - +
292N VAL* 1.3 56.4 + - - +
294N THR* 4.0 1.0 - - - -
295N MET* 3.2 21.3 + - - +
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Residues in contact with VAL 292 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E HIS* 5.8 0.9 - - - +
162E LEU* 5.2 6.1 - - + -
150N LEU* 3.5 45.5 - - + +
153N ALA* 3.9 22.7 - - + -
282N LEU* 3.9 9.9 - - + -
288N LYS* 3.4 14.1 + - + +
289N LEU* 3.1 14.3 + - + +
291N GLY* 1.3 74.1 - - - +
293N ILE* 1.3 72.2 + - + +
295N MET* 3.8 2.6 - - + +
296N PHE* 3.0 39.9 + - + -
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Residues in contact with ILE 293 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289N LEU* 2.9 50.1 + - + +
290N LEU* 3.3 15.0 + - + +
292N VAL* 1.3 79.5 - - + +
294N THR* 1.3 61.0 + - - +
296N PHE* 3.4 5.3 + - - +
297N ALA* 2.9 33.5 + - + +
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Residues in contact with THR 294 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281N ILE* 3.7 14.4 - - + -
285N ILE* 3.8 26.3 - - + +
290N LEU* 2.8 30.3 + - - +
291N GLY 4.0 2.9 - - - -
293N ILE* 1.3 74.3 - - - +
295N MET* 1.3 55.5 + - - +
297N ALA* 3.1 8.0 + - - +
298N ALA* 2.9 25.6 + - - +
356N THR* 4.5 3.4 - - + -
360N PHE* 3.3 26.9 - - + -
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Residues in contact with MET 295 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150N LEU* 4.0 18.4 - - + -
278N PHE* 3.7 29.9 - - + +
281N ILE* 4.3 10.5 - - + +
282N LEU* 3.8 24.5 - - + -
291N GLY 3.2 16.1 + - - +
292N VAL* 3.8 4.9 - - - +
293N ILE 3.3 0.4 - - - -
294N THR* 1.3 78.5 - - - +
296N PHE* 1.3 67.1 + - + +
298N ALA* 3.2 17.2 + - - +
299N ILE* 3.7 8.0 + - + +
525N SMA 3.2 68.6 - - + +
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Residues in contact with PHE 296 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122N THR* 6.5 1.6 - - + -
150N LEU* 5.0 10.8 - - + -
151N PHE* 4.3 31.0 - + - -
292N VAL* 3.0 36.7 + - + +
293N ILE* 3.9 4.9 - - - +
295N MET* 1.3 80.8 - - + +
297N ALA* 1.3 62.6 + - - +
299N ILE* 3.1 14.6 + - + +
300N LEU* 3.1 31.9 + - + +
525N SMA 3.5 40.6 - - + -
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Residues in contact with ALA 297 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293N ILE* 2.9 23.9 + - + +
294N THR* 3.2 10.5 - - - +
296N PHE* 1.3 77.0 - - - +
298N ALA* 1.3 54.9 - - - +
299N ILE 3.0 0.4 + - - -
300N LEU* 3.0 11.7 + - - +
301N VAL* 2.7 37.2 + - - +
360N PHE* 3.7 13.7 - - + -
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Residues in contact with ALA 298 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278N PHE* 4.6 7.9 - - + -
281N ILE* 3.8 20.0 - - + -
294N THR 2.9 8.0 + - - +
295N MET* 3.2 15.4 + - - +
297N ALA* 1.3 75.1 - - - +
299N ILE* 1.3 57.6 + - - +
301N VAL* 3.3 8.8 - - - +
302N LEU* 3.7 1.7 - - - +
359N TYR* 2.4 40.0 + - + +
360N PHE* 3.3 24.0 - - + -
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Residues in contact with ILE 299 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118N VAL* 4.5 10.6 - - + +
121N PHE* 4.3 27.4 - - + -
122N THR* 4.0 26.0 - - + +
125N ILE* 4.4 14.4 - - + -
278N PHE* 3.9 28.3 - - + -
295N MET 3.7 5.4 + - - +
296N PHE* 3.1 14.2 + - + +
297N ALA 3.0 0.4 - - - -
298N ALA* 1.3 77.1 - - - +
300N LEU* 1.3 71.2 + - + +
301N VAL 3.2 1.9 + - - -
302N LEU* 3.4 26.6 + - - +
525N SMA 4.7 22.4 - - + +
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Residues in contact with LEU 300 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118N VAL* 5.5 3.6 - - + -
122N THR* 5.9 1.3 - - - +
296N PHE* 3.1 25.9 + - + +
297N ALA* 3.0 10.0 + - + +
299N ILE* 1.3 80.4 - - + +
301N VAL* 1.3 63.5 + - - +
302N LEU 3.1 3.1 - - - -
303N LEU* 3.0 44.5 + - + +
304N VAL* 4.3 2.4 + - - +
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Residues in contact with VAL 301 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297N ALA 2.7 18.6 + - - +
298N ALA* 3.3 21.3 - - - +
300N LEU* 1.3 72.0 - - - +
302N LEU* 1.3 63.8 - - + +
304N VAL* 3.1 35.1 + - + +
305N LEU 4.0 1.9 + - - -
359N TYR* 3.8 6.5 - - + -
360N PHE* 4.2 16.8 - - + +
363N PHE* 3.4 49.2 - - + -
364N LEU* 4.4 13.7 - - + -
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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