Contacts of the helix formed by residues 275 - 284 (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 LEU 275 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90N PHE* 5.4 0.2 - - + -
125N ILE* 4.1 25.6 - - + +
129N PHE* 5.3 4.5 - - + -
147N ILE* 5.1 1.3 - - + -
271N PRO* 4.4 8.1 - - + -
272N GLU* 2.9 32.0 + - + +
274N TYR* 1.3 106.8 - - + +
276N LEU* 1.3 66.8 + - - +
277N PRO* 3.4 3.1 - - - -
278N PHE* 2.9 21.3 + - + +
279N TYR* 2.9 12.2 + - - +
525N SMA 3.7 58.4 - - + +
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Residues in contact with LEU 276 (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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270N VAL* 4.1 4.9 - - + -
271N PRO* 4.0 26.4 - - + +
272N GLU 3.4 8.2 + - - +
273N TRP* 3.5 27.1 - - + +
275N LEU* 1.3 75.7 - - - +
277N PRO* 1.4 60.5 - - + +
279N TYR* 3.0 7.1 + - + +
280N ALA* 2.7 36.2 + - - +
337N GLY* 3.4 23.3 - - - +
340N GLY* 3.5 31.2 - - - +
341N ALA* 3.6 16.2 - - + +
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Residues in contact with PRO 277 (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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94N PHE* 5.9 1.1 - - + -
273N TRP 4.1 7.2 - - - +
274N TYR 4.2 7.4 - - - +
275N LEU 3.5 4.0 - - - -
276N LEU* 1.4 93.3 - - + +
278N PHE* 1.3 63.7 + - + +
280N ALA* 3.4 3.5 + - - +
281N ILE* 3.1 28.4 + - + +
333N PHE* 3.5 51.4 - - + +
334N VAL* 5.9 0.4 - - - -
336N LEU* 4.1 6.1 - - + +
337N GLY* 3.6 27.6 - - - +
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Residues in contact with PHE 278 (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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94N PHE* 4.8 2.5 - + - -
121N PHE* 3.8 34.3 - + - -
125N ILE* 4.6 6.7 - - + -
274N TYR 4.4 15.5 - - - -
275N LEU* 2.9 13.0 + - + +
277N PRO* 1.3 75.2 - - + +
279N TYR* 1.3 67.9 + - - +
281N ILE* 3.2 9.7 + - + +
282N LEU 3.2 15.2 + - - -
295N MET* 3.7 21.2 - - + +
298N ALA* 4.6 13.9 - - + -
299N ILE* 3.9 23.1 - - + -
333N PHE* 4.2 28.3 - + - -
359N TYR* 4.4 18.2 - + - -
525N SMA 3.7 26.7 - - + -
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Residues in contact with TYR 279 (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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179E PRO 4.6 2.4 + - - -
180E CYS* 2.8 18.0 + - - -
181E HIS* 3.5 13.7 - + - -
269N ILE 4.5 8.7 + - - -
270N VAL* 5.4 1.1 - - + -
271N PRO* 3.4 31.8 - - + +
275N LEU 2.9 12.1 + - - +
276N LEU* 3.3 11.7 - - + +
278N PHE* 1.3 75.9 - - - +
280N ALA* 1.3 65.3 + - - +
282N LEU* 3.1 7.6 + - - +
283N ARG* 3.1 55.2 + - - +
295N MET* 4.8 0.2 - - - -
340N GLY* 3.3 23.1 - - - -
525N SMA 3.2 58.9 - + + +
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Residues in contact with ALA 280 (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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276N LEU 2.7 16.2 + - - +
277N PRO 3.4 6.1 - - - +
279N TYR* 1.3 75.0 - - - +
281N ILE* 1.3 59.8 + - - +
283N ARG* 3.3 9.5 + - - +
284N SER* 2.9 30.7 + - - +
336N LEU* 3.2 35.9 - - + +
339N ILE* 4.6 8.4 - - + +
340N GLY* 3.9 15.7 - - - +
352N GLY* 6.1 0.2 - - - -
356N THR* 5.0 0.4 - - - -
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Residues in contact with ILE 281 (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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277N PRO* 3.1 16.7 + - + +
278N PHE* 3.2 12.3 + - + +
280N ALA* 1.3 73.7 - - - +
282N LEU* 1.3 61.9 + - - +
284N SER* 3.3 14.6 + - - -
285N ILE* 3.7 11.1 - - - +
294N THR* 3.7 29.2 - - + +
295N MET* 4.3 12.3 - - - -
298N ALA* 3.8 21.8 - - + -
336N LEU* 3.8 25.1 - - + -
356N THR* 3.8 28.5 - - + +
359N TYR* 4.2 20.2 - - + -
360N PHE* 4.3 1.1 - - + -
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Residues in contact with LEU 282 (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* 4.4 15.7 - - + +
162E LEU* 4.6 2.0 - - + -
181E HIS* 3.9 30.5 - - + +
150N LEU* 4.1 7.0 - - + -
278N PHE 3.2 10.3 + - - +
279N TYR 3.1 9.7 + - - +
281N ILE* 1.3 78.8 - - - +
283N ARG* 1.3 63.7 + - - +
285N ILE 3.3 19.4 + - - +
291N GLY* 3.5 40.1 - - - +
292N VAL* 3.9 14.6 - - + +
295N MET* 3.8 31.1 - - + +
525N SMA 4.1 9.6 - - + +
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Residues in contact with ARG 283 (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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179E PRO 5.6 1.2 + - - -
180E CYS 4.4 3.0 + - - -
181E HIS* 3.9 33.0 - - + +
195E PRO* 6.0 2.6 - - - +
279N TYR* 3.1 60.5 + - - +
280N ALA* 3.3 10.9 + - - +
282N LEU* 1.3 79.0 - - - +
284N SER* 1.3 61.8 + - - +
285N ILE 3.1 7.3 + - - +
286N PRO* 4.6 1.2 - - - +
339N ILE* 3.3 22.6 + - - +
340N GLY* 3.6 2.9 + - - -
342N CYS 3.2 27.5 + - - -
343N HIS* 3.5 16.4 + - - +
344N VAL* 3.8 23.3 - - + +
349N VAL* 5.6 3.8 - - - +
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Residues in contact with SER 284 (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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280N ALA 2.9 17.4 + - - -
281N ILE 3.6 7.2 - - - -
282N LEU 3.2 1.0 - - - -
283N ARG* 1.3 77.1 - - - +
285N ILE* 1.3 64.8 + - - +
286N PRO* 3.6 2.4 - - - +
339N ILE* 5.5 1.4 - - - +
349N VAL* 4.4 4.6 + - - -
352N GLY* 3.3 24.4 + - - -
353N GLN* 3.2 42.9 + - - +
356N THR* 3.7 16.1 + - - -
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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