Contacts of the helix formed by residues 275 - 285 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90C PHE* 5.6 0.2 - - + -
125C ILE* 3.6 36.1 - - + +
129C PHE* 5.5 5.2 - - + +
147C ILE* 5.1 2.0 - - + -
271C PRO* 4.6 4.5 - - + -
272C GLU* 3.2 33.7 + - - +
273C TRP 3.2 0.2 + - - -
274C TYR* 1.3 105.6 - - + +
276C LEU* 1.3 59.3 + - - +
277C PRO* 3.5 2.0 - - - -
278C PHE* 3.0 13.3 + - + +
279C TYR* 2.9 25.1 + - - +
505C SMA 3.7 50.3 - - + +
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Residues in contact with LEU 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C VAL* 4.2 8.3 - - + -
271C PRO* 3.8 21.8 - - + +
272C GLU 3.6 6.9 + - - +
273C TRP* 3.3 27.8 + - + +
275C LEU* 1.3 76.1 - - - +
277C PRO* 1.3 58.2 - - + +
279C TYR* 2.8 19.7 + - + +
280C ALA* 2.6 36.5 + - - +
337C GLY* 3.8 24.5 - - - +
340C GLY* 3.7 24.2 - - - +
341C ALA* 4.1 14.4 - - + -
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Residues in contact with PRO 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C PHE* 5.9 0.2 - - + -
273C TRP 4.0 7.0 - - - +
274C TYR* 4.2 7.9 - - - +
275C LEU 3.6 4.3 - - - -
276C LEU* 1.3 93.5 - - + +
278C PHE* 1.3 62.2 + - + +
280C ALA* 3.3 4.6 - - + +
281C ILE* 3.1 28.4 + - - +
333C PHE* 3.5 53.8 - - + +
334C VAL* 5.9 0.2 - - - -
336C LEU* 3.9 6.3 - - + +
337C GLY* 3.7 24.8 - - - +
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Residues in contact with PHE 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C PHE* 4.9 2.5 - + - -
121C PHE* 3.9 33.9 - + - -
125C ILE* 4.6 7.9 - - + -
274C TYR 4.2 16.4 - - - -
275C LEU* 3.0 12.2 + - - +
277C PRO* 1.3 75.1 - - + +
279C TYR* 1.3 66.2 + - - +
281C ILE* 2.9 19.5 + - + +
282C LEU 3.1 10.4 + - - -
295C MET* 3.7 17.2 - - - +
298C ALA* 4.4 14.6 - - + -
299C ILE* 3.8 24.5 - - + -
333C PHE* 4.3 27.6 - + - -
359C TYR* 4.3 18.6 - + - -
505C SMA 3.6 26.5 - - + -
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Residues in contact with TYR 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C ILE 4.8 5.5 + - - -
270C VAL* 5.5 0.4 - - + -
271C PRO* 3.6 20.6 - - + +
275C LEU 2.9 13.2 + - - +
276C LEU* 2.8 21.3 + - + +
278C PHE* 1.3 75.4 - - - +
280C ALA* 1.3 63.2 + - - +
282C LEU* 3.4 2.6 + - - +
283C ARG* 3.1 44.7 + - - +
295C MET* 4.6 0.4 - - - -
340C GLY* 3.3 28.9 - - - -
505C SMA 3.1 70.6 - + + +
179P PRO 4.5 2.6 + - - -
180P CYS 2.7 21.4 + - - -
181P HIS* 3.7 11.9 - + - -
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Residues in contact with ALA 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C LEU 2.6 17.5 + - - +
277C PRO 3.3 6.3 - - - +
279C TYR* 1.3 72.0 - - - +
281C ILE* 1.3 65.2 + - - +
283C ARG* 3.4 8.3 + - - +
284C SER* 3.2 26.1 + - - -
336C LEU* 3.0 38.1 - - + +
339C ILE* 4.5 7.0 - - + +
340C GLY* 3.7 16.4 - - - +
352C GLY* 5.6 0.2 - - - -
356C THR* 5.0 0.7 - - - -
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Residues in contact with ILE 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C PRO* 3.1 15.7 + - + +
278C PHE* 2.9 13.2 + - + +
280C ALA* 1.3 76.9 - - - +
282C LEU* 1.3 65.9 + - - +
284C SER* 2.9 18.7 + - - -
285C ILE* 3.7 7.1 + - - +
294C THR* 4.0 33.0 - - + +
295C MET* 4.4 7.2 - - - -
298C ALA* 3.7 23.1 - - + -
333C PHE* 6.5 0.4 - - + -
336C LEU* 4.0 21.1 - - + -
356C THR* 3.6 29.4 - - + +
359C TYR* 4.4 17.3 - - + -
360C PHE* 4.5 1.3 - - + -
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Residues in contact with LEU 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C LEU* 4.8 8.3 - - + -
278C PHE 3.1 5.7 + - - -
279C TYR 3.8 6.3 - - - +
281C ILE* 1.3 75.3 - - - +
283C ARG* 1.3 62.6 + - - +
284C SER 3.3 0.7 + - - -
285C ILE 3.3 18.4 + - - +
291C GLY* 3.7 40.9 - - - +
292C VAL* 3.8 17.3 - - + +
295C MET* 4.0 31.8 - - + +
505C SMA 4.3 11.0 - - + -
161P HIS* 4.3 14.8 - - + +
162P LEU* 4.6 2.9 - - + -
181P HIS* 3.5 35.4 - - + +
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Residues in contact with ARG 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279C TYR* 3.1 61.7 + - - +
280C ALA* 3.6 6.2 - - - +
281C ILE 3.2 0.4 - - - -
282C LEU* 1.3 80.8 - - + +
284C SER* 1.3 62.0 + - - +
285C ILE 3.5 5.6 + - - +
286C PRO* 5.4 0.9 - - - +
339C ILE* 3.2 21.2 + - - +
340C GLY* 3.4 7.5 + - - -
342C CYS 2.6 29.9 + - - -
343C HIS* 4.1 7.7 + - - +
344C VAL* 3.5 30.6 - - + +
349C VAL* 5.8 2.8 - - - +
179P PRO 5.1 4.0 + - - -
180P CYS 4.2 8.4 + - - -
181P HIS* 4.3 26.8 - - + +
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Residues in contact with SER 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C ALA 3.2 12.0 + - - -
281C ILE 2.9 12.5 + - - -
283C ARG* 1.3 78.8 - - - +
285C ILE* 1.3 63.2 + - - +
286C PRO* 3.2 5.8 - - - +
339C ILE* 5.5 1.0 - - - +
349C VAL* 4.4 4.8 + - - +
352C GLY* 3.2 26.9 + - - -
353C GLN* 3.1 47.4 + - - +
356C THR* 4.0 10.8 - - - -
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Residues in contact with ILE 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C ILE 4.0 10.5 - - - +
282C LEU 3.3 11.2 + - - +
283C ARG 3.3 4.2 - - - +
284C SER* 1.3 82.5 - - - +
286C PRO* 1.3 64.6 - - + +
287C ASP* 3.1 15.3 + - + +
290C LEU* 3.5 35.4 - - + -
291C GLY* 3.7 12.1 - - - +
294C THR* 3.7 35.2 - - + +
356C THR* 5.2 8.1 - - + -
195P PRO* 4.8 5.4 - - - +
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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