Contacts of the helix formed by residues 273 - 285 (chain A) 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 ASN 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A GLU* 3.8 21.1 - - - +
271A SER* 3.0 5.8 + - - -
272A PRO* 1.3 91.5 + - - +
274A TYR* 1.3 63.1 + - - +
275A PHE 3.1 3.1 - - - -
276A VAL* 3.5 24.7 - - + +
277A ALA* 3.2 22.7 + - - +
420A TRP* 3.9 25.5 - - + +
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Residues in contact with TYR 274 (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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267A GLU* 4.7 5.3 - - + +
268A PRO 3.9 15.0 - - - -
269A VAL* 3.7 22.2 - - + +
270A ASN* 4.2 3.6 - - - +
271A SER* 3.0 26.6 + - - +
272A PRO 3.5 1.0 - - - -
273A ASN* 1.3 78.5 - - - +
275A PHE* 1.3 97.8 + + + +
277A ALA* 4.3 2.3 - - - +
278A LYS* 3.6 46.3 + - + +
318A SER* 4.9 0.3 + - - -
320A SER* 3.3 33.9 + - - -
373A LEU* 6.3 1.6 - - + -
377A TYR* 5.0 9.9 + - - -
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Residues in contact with PHE 275 (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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272A PRO 5.1 0.8 + - - -
273A ASN* 4.2 0.4 - - - +
274A TYR* 1.3 109.6 - + + +
276A VAL* 1.3 65.9 - - + +
277A ALA 3.2 1.3 - - - -
278A LYS* 3.7 7.3 - - + +
279A LEU* 3.0 24.3 + - - +
369A LEU* 4.4 5.9 - - + +
373A LEU* 4.2 25.4 - - + -
377A TYR* 5.8 4.0 - + - -
400A LEU* 4.1 24.2 - - + -
405A ALA* 4.3 14.4 - - + -
408A LYS* 4.1 26.7 - - + -
409A ILE* 3.9 26.9 - - + -
412A ILE* 3.7 14.2 - - + +
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Residues in contact with VAL 276 (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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272A PRO 4.3 4.5 - - - +
273A ASN* 3.4 37.0 + - + +
275A PHE* 1.3 76.4 - - + +
277A ALA* 1.3 62.9 + - - +
279A LEU* 3.2 4.9 + - - +
280A ALA* 3.1 20.9 + - - +
412A ILE* 3.7 29.1 - - + +
416A ASP* 4.0 28.3 - - + +
417A VAL* 4.0 16.8 - - + +
420A TRP* 4.0 13.5 - - + -
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Residues in contact with ALA 277 (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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267A GLU* 3.7 22.2 - - + +
273A ASN 3.2 14.4 + - - +
274A TYR 4.3 2.7 - - - +
276A VAL* 1.3 79.8 - - - +
278A LYS* 1.3 61.9 + - - +
280A ALA* 3.1 9.4 + - - +
281A ALA 3.2 1.0 + - - -
318A SER* 3.5 16.6 - - - +
327A TRP* 3.0 23.7 + - + -
420A TRP* 3.8 27.0 - - + +
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Residues in contact with LYS 278 (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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274A TYR* 3.6 51.2 + - + +
275A PHE* 3.4 11.6 + - + +
276A VAL 3.3 0.4 - - - -
277A ALA* 1.3 78.6 - - - +
279A LEU* 1.3 60.8 + - - +
281A ALA* 3.6 5.5 + - - +
282A GLN* 3.4 20.6 + - - +
318A SER* 3.1 39.7 + - - +
320A SER* 4.7 2.7 - - - +
369A LEU* 4.5 22.0 - - + +
372A GLN* 5.3 9.0 - - - +
373A LEU* 4.8 14.4 - - + +
376A LEU* 6.1 2.6 - - - +
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Residues in contact with LEU 279 (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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275A PHE 3.0 13.1 + - - +
276A VAL 3.3 9.0 - - - +
278A LYS* 1.3 74.4 - - - +
280A ALA* 1.3 65.9 + - - +
282A GLN* 3.1 8.5 + - - +
283A ILE* 3.0 23.4 + - + +
362A VAL* 4.0 27.1 - - + -
365A ALA* 3.5 13.0 - - + +
366A LYS* 3.4 42.0 - - + +
369A LEU* 4.0 15.9 - - + +
409A ILE* 4.4 4.7 - - + -
412A ILE* 4.1 17.5 - - + -
417A VAL* 4.0 20.0 - - + -
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Residues in contact with ALA 280 (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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276A VAL* 3.1 11.3 + - + +
277A ALA 3.1 10.2 + - - +
279A LEU* 1.3 74.0 - - - +
281A ALA* 1.3 66.4 + - - +
283A ILE* 2.9 32.7 + - + +
284A PHE* 3.6 9.5 - - - -
327A TRP* 3.6 20.2 - - + +
353A LEU* 3.9 10.1 - - + -
417A VAL* 5.0 5.8 - - + -
420A TRP* 3.8 19.3 - - + -
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Residues in contact with ALA 281 (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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277A ALA 3.2 3.9 + - - +
278A LYS 3.8 9.0 - - - +
280A ALA* 1.3 78.0 - - - +
282A GLN* 1.3 51.8 + - - +
284A PHE* 3.2 2.8 + - - -
285A GLY* 2.6 33.7 + - - -
316A HIS* 3.4 23.6 - - + +
317A PHE* 3.6 34.1 - - - +
318A SER* 4.3 1.8 - - - +
327A TRP* 3.5 16.2 - - - +
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Residues in contact with GLN 282 (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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278A LYS 3.4 12.3 + - - +
279A LEU* 3.1 16.1 + - - +
281A ALA* 1.3 78.6 - - - +
283A ILE* 1.3 64.1 + - - +
285A GLY* 3.2 16.4 + - - +
364A ARG* 3.4 14.9 + - - -
365A ALA* 3.7 26.5 - - + +
368A LEU* 3.5 37.8 - - + +
369A LEU* 4.0 8.8 - - + +
372A GLN* 4.3 23.4 - - - +
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Residues in contact with ILE 283 (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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279A LEU* 3.0 16.9 + - + +
280A ALA* 2.9 19.3 + - - +
282A GLN* 1.3 77.6 - - - +
284A PHE* 1.3 78.5 + - + +
298A GLY 5.0 0.5 - - - +
299A ILE* 3.9 17.5 - - - +
352A ARG* 5.9 0.7 - - - +
353A LEU* 3.6 26.7 - - + -
357A VAL* 4.1 11.0 - - + -
361A GLU* 4.1 33.9 - - + +
362A VAL* 4.8 7.4 - - + -
364A ARG* 4.0 7.3 + - - +
365A ALA* 3.8 17.3 - - + -
417A VAL* 4.3 9.0 - - + -
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Residues in contact with PHE 284 (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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280A ALA 3.6 11.7 - - - -
281A ALA 3.2 1.6 + - - -
282A GLN 3.1 0.4 - - - -
283A ILE* 1.3 87.2 - - + +
285A GLY* 1.3 66.7 + - - +
299A ILE* 3.5 23.9 - - + +
301A LEU* 5.0 11.0 - - + -
314A PHE* 3.5 13.7 - - - -
316A HIS* 3.4 28.9 - + + +
327A TRP* 4.1 5.2 - + - -
349A GLN* 3.6 52.5 - - + -
350A TRP* 3.6 24.9 - + - -
352A ARG* 5.0 3.4 - - + -
353A LEU* 3.4 45.3 - - + -
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Residues in contact with GLY 285 (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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281A ALA 2.6 20.5 + - - -
282A GLN* 3.2 21.6 + - - -
284A PHE* 1.3 72.8 - - - +
286A SER* 1.3 59.8 + - - -
299A ILE* 4.8 3.8 - - - -
316A HIS* 2.8 39.8 + - - -
364A ARG* 5.2 1.3 - - - -
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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