Contacts of the helix formed by residues 249 - 260 (chain B) 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 SER 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245B VAL* 4.7 2.7 - - - -
246B ASN* 3.2 38.1 + - - +
248B ALA* 1.3 73.7 - - - +
250B LEU* 1.3 58.1 + - - +
251B ALA 2.9 11.4 + - - -
252B GLN* 3.2 26.8 + - - +
253B TYR* 3.6 21.2 - - - -
347B LYS* 5.6 1.2 + - - -
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B VAL* 3.5 27.1 - - + +
246B ASN 3.6 5.7 + - - +
247B LYS* 3.2 31.9 - - - +
248B ALA* 3.8 4.7 - - - +
249B SER* 1.3 76.9 - - - +
251B ALA* 1.3 64.7 + - + +
252B GLN 3.4 0.4 - - - -
253B TYR* 3.9 3.6 - - - -
254B GLU* 3.3 19.9 + - - +
276B LEU* 3.3 18.6 - - + +
278B LYS* 4.8 18.2 - - + -
279B PHE 4.8 7.9 - - - +
282B GLY* 4.3 17.0 - - - +
335B PRO* 6.0 4.7 - - + -
336B ILE* 3.6 26.8 - - + +
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B ALA 3.4 16.4 + - - +
249B SER 2.9 0.6 + - - +
250B LEU* 1.3 81.1 - - - +
252B GLN* 1.3 61.7 + - - +
254B GLU* 3.7 13.2 - - - +
255B VAL* 3.8 12.5 - - - +
322B LYS* 4.2 6.4 + - - +
336B ILE* 4.1 21.1 - - + -
339B ASN* 3.4 41.3 - - + +
343B VAL* 5.1 0.4 - - + -
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Residues in contact with GLN 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B SER* 3.2 16.6 + - - +
251B ALA* 1.3 74.9 - - - +
253B TYR* 1.3 79.4 + - + +
254B GLU 3.0 2.5 - - - -
255B VAL* 3.0 30.9 - - + +
256B LEU* 3.0 8.6 + - - +
313B ASP* 5.6 0.8 + - - +
339B ASN 5.6 0.2 - - - -
343B VAL* 3.9 31.3 - - + +
345B ASP 3.0 27.1 + - - +
346B PHE* 3.4 20.3 - - + +
347B LYS* 3.1 27.3 + - - +
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Residues in contact with TYR 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B ILE* 3.6 39.7 - - + +
244B PRO 5.2 1.6 - - - -
245B VAL* 3.5 27.8 - - + -
249B SER* 3.6 27.1 + - - -
250B LEU 3.7 4.9 + - - +
251B ALA 3.5 0.4 - - - -
252B GLN* 1.3 95.1 - - + +
254B GLU* 1.3 60.4 + - - +
256B LEU* 3.6 13.9 + - + +
257B ALA* 3.4 20.4 + - - +
276B LEU* 4.0 15.1 - - + +
285B PHE* 3.8 29.6 - + + -
346B PHE* 3.7 29.6 - + - -
347B LYS* 4.9 6.2 + - - -
349B GLY 5.5 4.2 + - - -
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Residues in contact with GLU 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B LEU 3.3 12.7 + - - +
251B ALA 3.7 7.6 - - - +
252B GLN 3.0 0.8 - - - -
253B TYR* 1.3 76.4 - - - +
255B VAL* 1.3 65.5 + - + +
257B ALA* 3.3 11.3 - - - +
258B ASN* 2.8 39.0 - - - +
276B LEU* 3.5 24.8 + - + +
278B LYS* 2.9 39.3 + - - +
321B THR* 4.6 2.0 - - - +
322B LYS* 5.0 2.2 - - - +
325B ASN* 2.9 34.3 + - - +
328B GLN* 5.4 0.7 + - - -
336B ILE* 4.0 11.9 - - + -
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Residues in contact with VAL 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B ALA 3.8 13.0 - - - +
252B GLN* 3.0 20.9 - - + +
254B GLU* 1.3 72.0 - - + +
256B LEU* 1.3 60.8 + - - +
257B ALA 3.1 1.8 - - - -
258B ASN* 3.2 1.7 + - - +
259B TYR* 2.7 38.1 + - + +
313B ASP* 4.8 15.5 - - - +
315B SER* 5.5 7.2 - - - -
317B ALA* 4.6 6.4 - - + +
318B ILE* 4.9 9.4 - - + -
321B THR* 3.0 38.0 + - + +
322B LYS* 4.1 13.5 - - - +
339B ASN 5.1 3.6 - - - +
340B PHE* 5.9 0.7 - - + -
343B VAL 5.5 5.8 - - - +
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Residues in contact with LEU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B GLN 3.0 11.4 + - - +
253B TYR* 3.6 17.5 - - + +
255B VAL* 1.3 83.4 - - - +
257B ALA* 1.3 56.6 + - - +
259B TYR* 3.4 17.4 + - + +
260B LEU* 2.9 55.4 + - + +
285B PHE* 3.8 24.9 - - + -
308B LEU* 4.8 9.9 - - + -
312B LYS 6.1 0.4 - - - +
313B ASP* 5.7 3.6 - - - +
346B PHE* 3.3 56.3 - - + -
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Residues in contact with ALA 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B TYR 3.4 10.4 + - - +
254B GLU* 3.3 14.5 + - - +
255B VAL 3.1 0.2 - - - -
256B LEU* 1.3 76.7 - - - +
258B ASN* 1.3 67.4 + - - +
260B LEU* 3.2 9.5 + - - +
261B THR* 2.8 22.7 + - - -
274B ALA* 4.0 6.1 - - - +
275B LYS* 3.9 31.4 - - - -
276B LEU 4.3 2.2 - - - +
285B PHE* 4.1 13.7 - - + -
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Residues in contact with ASN 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B GLU* 2.8 36.8 + - - +
255B VAL 3.2 1.4 + - - -
257B ALA* 1.3 74.6 - - - +
259B TYR* 1.3 61.9 + - - +
261B THR* 3.3 14.0 + - - -
262B SER* 3.0 21.9 + - - -
320B TYR* 3.9 9.7 + - + -
321B THR* 3.5 30.8 + - - +
324B LYS* 2.9 43.2 - - + +
325B ASN* 4.7 2.4 - - - +
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Residues in contact with TYR 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B VAL* 2.7 18.7 + - + +
256B LEU* 3.4 22.2 - - + +
258B ASN* 1.3 77.8 - - - +
260B LEU* 1.3 68.9 + - + +
261B THR 3.1 2.5 + - - -
262B SER* 2.8 18.8 + - - -
264B LEU* 3.7 33.3 + - + -
265B SER* 3.3 35.4 + - - -
266B GLU 5.2 0.2 + - - -
308B LEU* 5.3 3.6 - - + -
312B LYS* 3.3 45.7 + - + +
313B ASP* 5.2 21.3 + - - +
316B PRO* 5.4 7.2 - - + -
317B ALA* 4.0 21.9 - - + +
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Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B LEU* 2.9 38.2 + - + +
257B ALA 3.2 5.6 + - - +
259B TYR* 1.3 84.1 - - + +
261B THR* 1.3 58.4 + - - +
262B SER 3.5 0.7 - - - -
265B SER* 4.0 7.2 - - - +
267B LEU* 3.8 29.2 - - + -
268B SER* 3.6 14.6 - - - +
271B ILE* 3.1 33.5 - - + +
274B ALA* 4.1 4.9 - - + -
285B PHE* 3.9 14.6 - - + -
287B LEU* 3.8 25.4 - - + -
304B ILE* 5.3 0.9 - - + -
308B LEU* 4.5 16.6 - - + -
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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