Contacts of the helix formed by residues 272 - 287 (chain C) in PDB entry 1KYZ
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 SER 272 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271C TRP* 1.3 78.8 - - - +
273C ASP* 1.3 55.9 + - - +
274C GLU* 3.6 12.3 + - - +
275C HIS* 3.1 28.5 + - - +
276C CYS* 2.8 32.6 + - - +
326C GLY* 4.1 17.0 + - - -
328C LYS* 5.9 2.0 - - - +
330C ARG* 3.4 2.2 - - - +
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Residues in contact with ASP 273 (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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272C SER* 1.3 73.2 - - - +
274C GLU* 1.3 62.6 + - - +
276C CYS* 3.8 0.7 - - - +
277C LEU* 3.1 33.0 + - + +
328C LYS* 3.6 19.5 + - - +
330C ARG* 2.7 40.9 + - - +
334C GLU* 5.7 2.9 - - - +
338C LEU* 4.1 15.8 - - + +
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Residues in contact with GLU 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C SER* 3.1 9.2 + - - +
273C ASP* 1.3 81.7 - - - +
275C HIS* 1.3 84.8 + - + +
277C LEU* 3.7 9.3 + - - +
278C LYS* 3.5 15.1 + - - +
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Residues in contact with HIS 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C PHE* 3.8 20.8 - + + -
271C TRP* 3.5 29.0 - + + -
272C SER* 3.1 18.3 + - - +
274C GLU* 1.3 98.3 + - + +
276C CYS* 1.3 66.4 + - - +
277C LEU 3.1 1.6 - - - -
278C LYS* 2.9 19.8 + - + +
279C PHE* 3.1 17.8 + - - -
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Residues in contact with CYS 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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268C CYS* 3.7 37.0 - - - -
271C TRP* 3.7 5.2 - - - -
272C SER 2.8 23.4 + - - +
273C ASP* 3.8 4.9 - - - +
275C HIS* 1.3 72.4 - - - +
277C LEU* 1.3 58.9 + - - +
279C PHE* 3.5 16.5 + - + -
280C LEU* 2.9 41.8 + - + +
330C ARG* 3.6 19.1 - - - -
338C LEU* 4.0 16.2 - - + -
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Residues in contact with LEU 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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273C ASP* 3.1 22.7 + - + +
274C GLU* 3.8 8.1 - - - +
275C HIS 3.1 0.4 - - - -
276C CYS* 1.3 76.2 - - - +
278C LYS* 1.3 62.2 + - - +
280C LEU* 3.9 2.4 - - - +
281C LYS* 3.0 46.6 + - - +
337C ASP 5.0 0.2 - - - +
338C LEU* 3.6 40.2 - - + +
341C GLY* 3.7 27.1 - - - +
342C ALA* 3.9 1.3 - - - +
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Residues in contact with LYS 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C PHE* 4.1 34.3 - - + +
274C GLU 3.5 9.6 + - - +
275C HIS* 2.9 15.9 + - + +
277C LEU* 1.3 81.8 - - - +
279C PHE* 1.3 60.2 + - - +
281C LYS* 3.5 17.7 + - + +
282C ASN* 3.5 16.5 + - - +
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Residues in contact with PHE 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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207C VAL* 6.0 0.7 - - + -
252C MET* 3.5 52.2 - - + +
253C PHE* 4.0 12.8 - + + -
256C ILE* 4.5 0.7 - - + +
264C MET* 3.6 28.0 - - - -
267C ILE* 3.9 20.9 - - + -
268C CYS* 4.2 6.1 - - - -
271C TRP* 4.2 15.3 - + + -
275C HIS 3.1 19.2 + - - -
276C CYS* 3.5 34.3 - - - -
278C LYS* 1.3 77.5 - - - +
280C LEU* 1.3 78.4 + - + +
282C ASN* 3.3 4.7 + - - +
283C CYS* 3.0 31.5 + - - -
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Residues in contact with LEU 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C MET* 3.7 31.6 - - + -
268C CYS* 4.9 3.8 - - - -
276C CYS* 2.9 34.7 + - + +
277C LEU* 3.9 2.5 - - - +
278C LYS 3.3 0.2 - - - -
279C PHE* 1.3 85.1 - - + +
281C LYS* 1.3 64.8 + - - +
283C CYS* 3.2 9.2 + - + +
284C TYR 3.1 17.2 + - - -
293C VAL* 4.9 2.0 - - + -
338C LEU* 4.0 34.8 - - + +
342C ALA* 3.5 15.0 - - + -
344C PHE* 3.4 14.1 - - + -
361C PHE* 4.1 25.8 - - + -
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Residues in contact with LYS 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 LEU* 3.0 41.9 + - - +
278C LYS* 3.7 13.2 - - + +
279C PHE 3.3 0.2 - - - -
280C LEU* 1.3 76.7 - - - +
282C ASN* 1.3 63.7 + - - +
284C TYR* 3.2 10.6 - - - +
285C GLU* 3.2 25.7 + - - +
341C GLY 3.8 17.3 - - - -
342C ALA* 3.9 17.7 - - - +
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Residues in contact with ASN 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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252C MET 2.7 23.2 + - - +
253C PHE* 3.4 22.6 + - - +
254C VAL 3.8 15.1 + - - +
255C SER* 4.5 1.6 - - - -
256C ILE* 3.5 22.0 + - + +
278C LYS* 3.6 15.4 + - - +
279C PHE 3.3 8.2 + - - +
280C LEU 3.1 0.4 - - - -
281C LYS* 1.3 78.6 - - - +
283C CYS* 1.3 66.0 + - - +
284C TYR 3.1 0.2 - - - -
285C GLU* 3.1 12.9 + - - +
286C ALA* 3.0 23.0 + - - +
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Residues in contact with CYS 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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207C VAL* 4.7 4.7 - - - -
256C ILE* 4.2 13.2 - - - -
262C VAL* 4.0 24.6 - - + +
264C MET* 4.5 17.9 - - - -
279C PHE* 3.0 26.6 + - - -
280C LEU* 3.2 16.5 + - - +
282C ASN* 1.3 76.2 - - - +
284C TYR* 1.3 64.7 + - - +
286C ALA* 3.1 13.1 + - - +
287C LEU* 3.3 18.8 + - - +
293C VAL* 3.8 20.6 - - + -
344C PHE* 4.2 1.6 - - - -
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Residues in contact with TYR 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 LEU 3.1 8.9 + - - +
281C LYS 3.2 11.7 - - - +
283C CYS* 1.3 78.9 - - - +
285C GLU* 1.3 76.2 + - - +
287C LEU* 3.2 9.5 + - - +
342C ALA 3.7 19.5 - - - +
343C GLY* 3.2 24.0 + - - -
344C PHE* 3.5 34.7 - + + -
345C GLN* 3.8 14.4 + - - -
363C LYS* 2.8 62.4 + - + +
365C VAL* 3.9 16.3 - - + +
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Residues in contact with GLU 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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258C LYS* 3.0 25.5 + - - -
281C LYS 3.3 14.8 - - - +
282C ASN* 3.1 14.5 + - - +
284C TYR* 1.3 93.7 - - - +
286C ALA* 1.3 58.7 + - - +
287C LEU 3.2 3.6 + - - +
363C LYS* 4.7 2.4 + - - +
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Residues in contact with ALA 286 (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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256C ILE* 3.6 26.0 - - + +
257C PRO 3.5 22.0 - - - +
258C LYS* 3.5 18.3 - - - +
259C ALA 3.3 23.2 + - - +
262C VAL* 4.8 5.4 - - + -
282C ASN 3.0 12.0 + - - +
283C CYS* 3.1 8.9 + - - +
285C GLU* 1.3 78.4 - - - +
287C LEU* 1.3 59.8 + - - +
288C PRO* 4.4 0.2 - - - +
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Residues in contact with LEU 287 (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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258C LYS* 4.9 3.8 + - - -
259C ALA 3.7 3.4 - - - +
260C ASP 3.6 6.5 - - - +
261C ALA* 3.3 36.8 - - - +
262C VAL* 3.7 11.0 - - + -
283C CYS 3.3 16.2 - - - +
284C TYR* 3.2 8.1 + - - +
285C GLU 4.0 4.0 - - - +
286C ALA* 1.3 80.2 - - - +
288C PRO* 1.3 69.1 - - + +
291C GLY* 3.8 3.4 - - - -
292C LYS* 3.3 36.3 - - - +
293C VAL* 3.8 4.9 - - + -
344C PHE* 3.7 22.0 - - + -
363C LYS* 2.8 26.4 + - + -
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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