Contacts of the helix formed by residues 249 - 261 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245M VAL* 4.7 1.1 - - - -
246M ASN* 3.1 38.8 + - - +
248M ALA* 1.3 75.5 - - - +
250M LEU* 1.3 58.9 + - - +
251M ALA 3.5 0.4 - - - -
252M GLN* 3.2 25.2 + - - +
253M TYR* 3.1 28.4 - - - -
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Residues in contact with LEU 250 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245M VAL* 3.6 20.0 - - + -
246M ASN 3.4 13.2 + - - +
247M LYS* 3.6 23.3 - - - +
248M ALA* 2.9 7.3 - - - +
249M SER* 1.3 75.4 - - - +
251M ALA* 1.3 85.7 + - + +
252M GLN 3.0 2.7 - - - -
253M TYR* 2.9 18.0 + - - +
254M GLU* 3.2 9.5 + - + +
276M LEU* 3.5 13.3 - - + +
278M LYS* 4.8 19.5 - - + -
279M PHE 4.9 4.9 - - - +
282M GLY 3.7 20.6 - - - +
336M ILE* 5.4 14.8 - - + -
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Residues in contact with ALA 251 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248M ALA 3.4 7.1 + - - +
250M LEU* 1.3 85.0 - - + +
252M GLN* 1.3 60.0 + - - +
254M GLU* 3.6 15.5 - - - +
255M VAL* 3.6 12.3 - - - +
322M LYS* 3.8 5.5 + - - -
336M ILE* 3.6 27.8 - - + -
337M GLU 4.6 0.4 - - - +
339M ASN* 3.4 41.0 - - + +
343M VAL* 5.2 0.2 - - + -
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Residues in contact with GLN 252 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248M ALA 4.9 0.2 + - - -
249M SER* 3.2 28.8 + - - +
250M LEU 3.0 1.0 - - - -
251M ALA* 1.3 74.4 - - - +
253M TYR* 1.3 73.7 + - + +
254M GLU 3.0 4.7 - - - -
255M VAL* 2.9 33.0 + - + +
256M LEU* 2.9 11.7 + - - +
313M ASP* 6.0 0.2 + - - -
343M VAL* 4.1 27.0 - - + +
344M LYS* 6.4 0.2 - - - -
345M ASP 3.0 31.9 + - - +
346M PHE* 3.9 19.9 - - - +
347M LYS* 4.2 14.4 + - - -
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Residues in contact with TYR 253 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243M ILE* 3.7 35.8 - - + +
244M PRO 5.3 0.9 - - - -
245M VAL* 3.6 15.5 - - + -
246M ASN* 5.7 0.7 - - - -
249M SER* 3.1 35.9 - - - -
250M LEU 2.9 9.0 + - - +
252M GLN* 1.3 94.2 - - + +
254M GLU* 1.3 55.4 + - - +
255M VAL 3.3 0.2 - - - -
256M LEU* 3.6 22.4 - - + -
257M ALA* 3.2 19.9 + - - +
276M LEU* 4.1 19.4 - - + +
285M PHE* 3.4 28.8 - + + -
346M PHE* 3.6 31.0 - + - -
347M LYS* 4.7 7.7 + - - -
349M GLY 5.7 2.8 + - - -
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Residues in contact with GLU 254 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250M LEU* 3.2 6.6 + - + +
251M ALA* 3.6 15.5 - - - +
252M GLN 3.0 0.2 - - - -
253M TYR* 1.3 76.8 - - - +
255M VAL* 1.3 61.0 + - - +
256M LEU 3.3 0.4 - - - -
257M ALA* 3.9 4.2 - - - +
258M ASN* 2.7 49.6 + - - +
276M LEU* 3.9 16.4 + - + +
278M LYS* 2.9 42.2 + - - +
321M THR* 3.3 6.8 + - - +
322M LYS* 4.7 6.4 + - - +
325M ASN* 2.9 29.0 + - - +
328M GLN* 4.6 2.1 + - - +
336M ILE* 4.6 7.9 - - + -
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Residues in contact with VAL 255 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251M ALA 3.6 15.7 - - - +
252M GLN* 2.9 21.9 + - + +
254M GLU* 1.3 74.6 - - - +
256M LEU* 1.3 61.6 + - - +
257M ALA 3.2 0.2 - - - -
258M ASN* 3.9 0.2 - - - +
259M TYR* 2.8 34.2 + - - +
313M ASP* 3.7 23.8 - - - +
317M ALA* 4.2 6.4 - - + +
318M ILE* 3.9 20.9 - - + -
321M THR* 3.3 38.6 - - + +
322M LYS* 4.2 7.4 - - - +
339M ASN 5.6 0.2 - - - +
340M PHE* 5.1 1.3 - - + -
343M VAL* 5.6 3.8 - - + +
344M LYS* 6.1 2.0 - - - -
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Residues in contact with LEU 256 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243M ILE* 5.5 0.9 - - + -
252M GLN 2.9 11.9 + - - +
253M TYR* 3.5 31.0 - - + +
255M VAL* 1.3 80.0 - - + +
257M ALA* 1.3 59.1 + - - +
259M TYR* 3.7 10.0 - - + +
260M LEU* 3.0 50.0 + - + +
285M PHE* 3.6 22.0 - - + -
308M LEU* 5.0 7.4 - - + -
313M ASP* 5.2 4.3 - - - +
346M PHE* 3.4 55.9 - - + -
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Residues in contact with ALA 257 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253M TYR 3.2 9.1 + - - +
254M GLU* 3.9 9.9 - - - +
255M VAL 3.2 0.2 - - - -
256M LEU* 1.3 79.7 - - - +
258M ASN* 1.3 60.0 + - - +
260M LEU* 3.2 5.5 + - - +
261M THR* 2.6 32.5 + - - -
274M ALA* 3.8 18.7 - - - +
275M LYS* 3.9 11.2 - - - -
276M LEU 4.4 2.0 - - - +
285M PHE* 3.3 26.0 - - + -
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Residues in contact with ASN 258 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254M GLU* 2.7 39.9 + - - +
255M VAL 3.3 0.9 + - - +
257M ALA* 1.3 78.5 - - - +
259M TYR* 1.3 65.2 + - - +
261M THR* 3.1 21.8 + - - +
262M SER* 3.1 15.3 + - - -
320M TYR* 3.9 11.8 - - + -
321M THR* 3.5 29.0 + - - +
324M LYS* 3.3 38.2 - - - +
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Residues in contact with TYR 259 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255M VAL 2.8 23.3 + - - +
256M LEU* 3.7 10.5 - - + +
258M ASN* 1.3 72.4 - - - +
260M LEU* 1.3 75.6 + - + +
262M SER* 2.9 19.1 + - - -
264M LEU* 3.3 42.3 + - + -
265M SER* 3.1 31.2 - - - -
266M GLU 4.5 1.0 + - - -
308M LEU* 5.8 1.3 - - + -
312M LYS* 3.9 41.9 + - + +
313M ASP* 5.3 27.2 + - - +
316M PRO* 5.6 5.2 - - + -
317M ALA* 4.1 20.4 - - + +
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Residues in contact with LEU 260 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256M LEU* 3.0 37.7 - - + +
257M ALA* 3.2 5.7 + - - +
259M TYR* 1.3 88.4 - - + +
261M THR* 1.3 57.2 + - - +
262M SER 3.3 2.0 - - - -
265M SER* 3.9 8.7 - - - +
267M LEU* 3.5 29.6 - - + -
268M SER* 3.1 26.5 - - - +
271M ILE* 3.5 22.1 - - + +
274M ALA* 4.4 2.2 - - + -
285M PHE* 4.1 10.1 - - + -
287M LEU* 3.9 23.6 - - + -
308M LEU* 4.4 20.0 - - + -
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Residues in contact with THR 261 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257M ALA 2.6 22.8 + - - -
258M ASN* 3.1 12.8 + - - +
260M LEU* 1.3 79.0 - - - +
262M SER* 1.3 60.8 + - - +
268M SER* 4.8 1.6 - - - -
271M ILE* 5.5 0.2 - - - -
273M SER* 6.2 1.6 - - - -
274M ALA* 3.4 26.6 + - - +
320M TYR* 3.8 8.8 + - - -
324M LYS* 5.7 1.4 - - - -
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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