Contacts of the helix formed by residues 273 - 285 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267L GLU* 3.3 29.5 - - - +
271L SER* 3.1 4.8 + - - -
272L PRO* 1.3 90.7 + - - +
274L TYR* 1.3 63.4 + - - -
275L PHE 3.1 2.7 - - - -
276L VAL* 3.7 25.8 - - + +
277L ALA* 2.9 23.8 + - - +
416L ASP 5.7 0.8 + - - -
420L TRP* 3.6 21.4 - - + +
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Residues in contact with TYR 274 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267L GLU* 4.8 4.7 - - - -
268L PRO 4.2 1.3 - - - -
269L VAL* 3.7 32.7 - - + +
270L ASN 4.4 2.5 - - - +
271L SER* 3.0 27.2 + - - +
272L PRO 3.5 1.0 + - - -
273L ASN* 1.3 77.4 - - - +
275L PHE* 1.3 98.0 + + + +
277L ALA* 4.1 2.8 - - - +
278L LYS* 3.5 47.0 + - + +
318L SER* 4.8 2.1 + - - -
320L SER* 3.6 31.0 - - - -
373L LEU* 6.3 0.7 - - + -
377L TYR* 5.4 6.3 + - - -
396L LYS* 6.2 2.7 - - - -
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Residues in contact with PHE 275 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272L PRO 5.1 1.5 + - - -
273L ASN 3.1 0.2 - - - -
274L TYR* 1.3 108.1 - + + +
276L VAL* 1.3 67.5 + - + +
277L ALA 3.0 1.8 - - - -
278L LYS* 2.8 11.2 + - + +
279L LEU* 2.8 25.1 + - - +
369L LEU* 4.5 3.3 - - + +
373L LEU* 4.2 16.8 - - + -
377L TYR* 5.9 4.0 - - - -
396L LYS* 6.2 0.2 - - - -
400L LEU* 4.0 29.6 - - + -
405L ALA* 4.1 21.5 - - + -
408L LYS* 4.0 30.3 - - + -
409L ILE* 4.2 22.7 - - + -
412L ILE* 3.9 13.7 - - + -
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Residues in contact with VAL 276 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272L PRO 4.6 3.8 - - - +
273L ASN* 3.2 32.7 + - + +
275L PHE* 1.3 77.1 - - + +
277L ALA* 1.3 61.9 + - - +
279L LEU* 3.5 5.1 + - - +
280L ALA* 3.3 19.8 + - - +
412L ILE* 3.7 31.6 - - + +
416L ASP* 4.0 21.8 - - + +
417L VAL* 4.0 13.0 - - + +
420L TRP* 3.8 26.4 - - + -
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Residues in contact with ALA 277 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266L GLY* 6.4 0.2 - - - -
267L GLU* 4.0 12.3 - - + +
273L ASN 2.9 16.1 + - - +
274L TYR 4.1 2.9 - - - +
276L VAL* 1.3 77.3 - - - +
278L LYS* 1.3 62.9 + - - +
280L ALA* 3.5 0.9 + - - -
281L ALA 3.4 5.4 + - - -
318L SER* 3.9 14.6 - - - +
327L TRP* 3.0 26.8 + - + -
420L TRP* 3.5 39.2 - - + +
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Residues in contact with LYS 278 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274L TYR* 3.5 49.7 + - + +
275L PHE* 2.8 15.5 + - + +
277L ALA* 1.3 79.4 - - - +
279L LEU* 1.3 60.8 + - - +
281L ALA* 3.6 4.6 + - + +
282L GLN* 3.4 20.1 + - - +
318L SER* 3.8 37.7 + - - +
320L SER* 5.7 0.7 - - - -
369L LEU* 4.3 18.1 - - + +
372L GLN* 5.2 10.9 + - - +
373L LEU* 5.1 14.9 - - + +
376L LEU* 6.0 4.4 - - - +
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Residues in contact with LEU 279 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275L PHE 2.8 14.2 + - - +
276L VAL 3.7 4.0 - - - +
278L LYS* 1.3 75.6 - - - +
280L ALA* 1.3 63.3 + - - +
281L ALA 3.2 0.2 - - - -
282L GLN* 3.1 12.7 + - - +
283L ILE* 3.2 16.8 + - + +
362L VAL* 4.2 14.6 - - + -
365L ALA* 3.6 9.8 - - + +
366L LYS* 3.5 47.3 - - + +
369L LEU* 3.8 20.8 - - + +
409L ILE* 4.4 3.1 - - + +
412L ILE* 4.2 21.1 - - + -
417L VAL* 3.7 30.3 - - + -
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Residues in contact with ALA 280 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276L VAL 3.3 9.3 + - - +
277L ALA 3.7 6.7 - - - +
278L LYS 3.4 0.2 - - - -
279L LEU* 1.3 79.7 - - - +
281L ALA* 1.3 63.0 + - - +
283L ILE* 3.3 27.2 + - - +
284L PHE* 3.6 14.4 - - - -
327L TRP* 3.7 7.9 - - + +
353L LEU* 4.0 9.9 - - + -
417L VAL* 4.7 6.1 - - + -
420L TRP* 3.6 33.2 - - + -
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Residues in contact with ALA 281 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277L ALA 3.4 5.3 + - - +
278L LYS* 3.8 9.2 - - + +
279L LEU 3.2 0.6 - - - -
280L ALA* 1.3 78.0 - - - +
282L GLN* 1.3 57.8 + - - +
283L ILE 3.1 0.3 + - - -
284L PHE 3.3 2.8 + - - -
285L GLY* 2.8 25.6 + - - -
316L HIS* 3.5 16.2 - - + +
317L PHE* 3.7 37.9 - - - +
318L SER* 4.4 2.2 - - - -
327L TRP* 3.6 15.4 - - + +
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Residues in contact with GLN 282 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278L LYS 3.4 10.5 + - - +
279L LEU* 3.1 12.2 + - - +
281L ALA* 1.3 79.7 - - - +
283L ILE* 1.3 60.8 + - - +
285L GLY* 3.4 13.9 + - - +
286L SER 5.5 0.2 + - - -
364L ARG* 3.2 19.4 + - - -
365L ALA* 3.8 27.1 - - + +
368L LEU* 3.9 26.3 - - + +
369L LEU* 3.8 10.5 - - + +
372L GLN* 3.4 37.0 - - - +
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Residues in contact with ILE 283 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279L LEU* 3.2 15.0 + - + +
280L ALA* 3.4 16.4 - - - +
281L ALA 3.1 0.2 - - - -
282L GLN* 1.3 80.6 - - - +
284L PHE* 1.3 80.3 + - + +
298L GLY 5.0 0.7 - - - +
299L ILE* 3.5 20.1 - - - +
353L LEU* 3.6 26.7 - - + -
357L VAL* 4.0 13.5 - - + -
361L GLU* 4.0 34.3 - - + +
362L VAL* 4.9 4.9 - - + -
364L ARG* 3.8 7.9 + - - +
365L ALA* 3.8 16.4 - - + -
417L VAL* 4.6 6.1 - - + -
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Residues in contact with PHE 284 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280L ALA 3.6 12.3 - - - -
281L ALA 3.3 1.8 + - - +
283L ILE* 1.3 88.3 - - + +
285L GLY* 1.3 67.3 + - - +
299L ILE* 3.0 28.5 - - + +
301L LEU* 5.2 5.2 - - + -
314L PHE* 3.5 13.4 - - + -
316L HIS* 3.3 29.6 - + + +
327L TRP* 4.1 4.0 - + - -
349L GLN* 3.4 56.3 - - + -
350L TRP* 3.5 22.9 - + - -
352L ARG* 5.1 4.3 - - + -
353L LEU* 3.5 40.4 - - + -
361L GLU* 5.4 0.4 - - - -
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Residues in contact with GLY 285 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281L ALA 2.8 17.0 + - - -
282L GLN* 3.4 19.5 + - - -
283L ILE 3.2 2.6 - - - -
284L PHE* 1.3 77.5 - - - +
286L SER* 1.3 62.6 + - - -
299L ILE* 4.3 3.8 - - - -
314L PHE* 3.5 1.6 - - - -
316L HIS* 2.9 37.8 + - - -
364L ARG* 5.0 1.6 - - - -
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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