Contacts of the helix formed by residues 257 - 275 (chain B) in PDB entry 1K0Y
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 257 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B PHE* 2.9 25.1 + - - +
247B ASP* 3.3 24.2 + - - +
248B LEU* 4.1 4.8 - - - +
253B ALA 3.0 16.0 + - - +
254B VAL* 3.3 11.2 + - - +
256B GLY* 1.4 73.8 - - - +
258B PRO* 1.3 71.9 - - - +
259B LYS* 2.7 35.7 + - - +
260B VAL* 3.1 21.3 + - + +
261B LYS* 3.1 23.6 + - - +
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Residues in contact with PRO 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B GLY 3.2 8.5 - - - +
257B ASN* 1.3 87.8 - - - +
259B LYS* 1.4 63.1 + - + +
261B LYS* 3.4 14.9 + - + +
262B ALA* 2.9 28.1 + - - +
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Residues in contact with LYS 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B SER* 3.8 16.1 + - - +
245B PHE* 3.3 53.1 - - + +
257B ASN* 2.7 17.0 + - - +
258B PRO* 1.4 75.9 - - + +
260B VAL* 1.4 58.8 + - - +
262B ALA* 3.9 6.4 - - + +
263B HIS* 3.0 24.1 + - - +
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Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B GLY* 4.5 4.8 - - - +
228B LEU* 3.7 9.0 - - + +
229B GLY* 3.9 29.4 - - - +
232B LEU* 3.9 18.4 - - + -
245B PHE* 3.9 14.1 - - + -
248B LEU* 3.9 22.4 - - + -
254B VAL* 3.7 15.9 - - + +
255B MET* 5.7 0.7 - - - +
257B ASN* 3.1 27.7 + - + +
259B LYS* 1.4 75.5 - - - +
261B LYS* 1.4 59.6 + - + +
263B HIS* 3.3 1.3 + - - -
264B GLY* 2.8 27.4 + - - -
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Residues in contact with LYS 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ASP 5.0 1.0 - - - +
225B GLY* 4.3 21.1 + - - +
255B MET 3.6 23.8 + - - +
256B GLY* 4.1 16.5 - - - -
257B ASN 3.1 16.0 + - - +
258B PRO* 3.5 13.9 - - + +
259B LYS 3.3 0.2 - - - -
260B VAL* 1.4 77.6 - - + +
262B ALA* 1.4 61.9 + - - +
264B GLY* 3.1 2.6 + - - -
265B LYS* 3.1 24.5 + - - +
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Residues in contact with ALA 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B PRO 2.9 18.1 + - - +
259B LYS* 3.9 7.4 - - + +
260B VAL 3.3 0.2 - - - -
261B LYS* 1.4 75.1 - - - +
263B HIS* 1.4 61.5 + - - +
265B LYS* 3.2 26.5 - - + +
266B LYS* 3.3 14.7 + - - +
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Residues in contact with HIS 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU* 3.4 26.2 - - + -
242B PHE* 3.6 16.1 - + - -
245B PHE* 3.7 18.7 - + + -
259B LYS 3.0 17.4 + - - +
262B ALA* 1.4 73.7 - - - +
264B GLY* 1.4 66.9 + - - +
266B LYS* 3.2 16.9 + - + +
267B VAL* 2.9 47.7 + - + +
348B HEM 3.3 68.4 + + + +
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Residues in contact with GLY 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B GLY* 3.4 28.7 - - - +
228B LEU* 3.6 12.5 - - - +
260B VAL 2.8 15.3 + - - -
261B LYS 3.1 4.2 + - - -
263B HIS* 1.4 76.6 - - - +
265B LYS* 1.4 56.1 + - - +
267B VAL* 3.6 4.1 + - - +
268B LEU* 2.9 31.9 + - - +
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Residues in contact with LYS 265 (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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220B VAL* 4.8 1.8 - - - +
221B ASP* 3.2 56.2 + - + +
224B GLY* 4.4 1.9 - - - -
261B LYS 3.1 13.0 + - - +
262B ALA* 3.2 25.4 - - + +
264B GLY* 1.4 76.8 - - - +
266B LYS* 1.4 58.5 + - - +
268B LEU* 4.4 2.0 - - - +
269B GLY* 2.9 27.2 + - - -
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Residues in contact with LYS 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ALA 3.3 14.3 + - - +
263B HIS* 3.2 23.7 + - + +
265B LYS* 1.4 76.7 - - - +
267B VAL* 1.4 64.3 + - - +
269B GLY* 3.4 1.5 + - - -
270B ALA* 3.2 22.9 + - - +
348B HEM 3.7 65.7 + - + +
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Residues in contact with VAL 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU* 5.1 6.1 - - + -
263B HIS* 2.9 49.9 + - + +
264B GLY* 3.9 5.6 - - - +
266B LYS* 1.4 75.3 - - - +
268B LEU* 1.4 69.2 + - + +
270B ALA 3.3 2.6 + - - -
271B PHE* 3.1 19.2 + - - +
306B LEU* 3.8 20.0 - - + -
348B HEM 3.7 58.5 - - + +
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Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B TRP* 3.3 39.3 - - + -
220B VAL* 3.8 18.6 - - + +
223B VAL* 4.2 18.6 - - + +
224B GLY* 3.5 21.5 - - - +
227B ALA* 5.1 5.8 - - + -
264B GLY 2.9 17.5 + - - +
265B LYS 4.4 0.4 - - - +
267B VAL* 1.4 84.2 - - + +
269B GLY* 1.4 59.2 + - - +
271B PHE* 3.3 14.6 + - + +
272B SER* 2.9 30.5 + - - -
306B LEU* 5.6 5.6 - - + -
310B LEU* 4.4 20.6 - - + -
348B HEM 5.7 1.3 - - + -
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Residues in contact with GLY 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B VAL* 4.0 10.9 - - - +
265B LYS 2.9 19.8 + - - -
266B LYS 3.9 1.6 - - - -
267B VAL 3.3 0.2 - - - -
268B LEU* 1.4 76.8 - - - +
270B ALA* 1.4 55.4 + - - +
272B SER* 3.3 5.3 + - - -
273B ASP* 3.0 36.5 + - - +
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Residues in contact with ALA 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LYS 3.2 7.5 + - - +
267B VAL 3.8 7.2 - - - +
269B GLY* 1.4 72.4 - - - +
271B PHE* 1.4 65.2 + - - +
273B ASP* 3.4 9.7 + - - +
274B GLY* 3.0 17.3 + - - -
285B PHE* 3.8 9.9 - - + -
288B LEU* 4.4 8.3 - - + -
348B HEM 3.8 41.7 - - + -
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Residues in contact with PHE 271 (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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215B TRP* 3.8 33.7 - + - -
267B VAL 3.1 13.6 + - - +
268B LEU* 3.5 17.3 - - + +
270B ALA* 1.4 74.6 - - - +
272B SER* 1.4 64.9 + - - +
274B GLY* 3.0 11.8 + - - -
275B LEU* 3.2 27.3 + - + +
285B PHE* 4.6 5.1 - - - -
310B LEU* 3.8 22.9 - - + -
330B TYR* 5.2 6.3 - + - -
333B VAL* 3.9 19.1 - - + -
334B VAL* 4.1 18.8 - - + -
337B VAL* 3.9 28.9 - - + +
348B HEM 3.9 28.2 - - + +
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Residues in contact with SER 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B TRP* 2.9 37.5 + - - +
220B VAL* 4.0 12.1 - - - +
268B LEU 2.9 17.8 + - - -
269B GLY* 3.4 8.5 - - - -
271B PHE* 1.4 76.9 - - - +
273B ASP* 1.4 64.2 + - - +
275B LEU* 3.0 21.8 + - - +
276B ALA* 4.1 2.1 + - - +
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Residues in contact with ASP 273 (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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269B GLY 3.0 23.6 + - - +
270B ALA* 3.8 8.5 - - - +
272B SER* 1.4 77.0 + - - +
274B GLY* 1.4 61.2 + - - +
276B ALA* 3.3 16.2 + - - +
277B HIS* 3.4 17.5 + - + -
284B THR* 5.6 1.6 - - + -
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Residues in contact with GLY 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ALA 3.0 10.3 + - - -
271B PHE 3.0 10.8 + - - -
273B ASP* 1.4 77.8 - - - +
275B LEU* 1.4 57.2 + - - +
277B HIS 3.0 27.1 + - - -
278B LEU 3.6 1.2 + - - -
281B LEU* 3.7 12.1 - - - +
284B THR* 4.6 10.1 - - - -
285B PHE* 4.0 20.6 - - - -
337B VAL* 6.2 0.7 - - - -
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Residues in contact with LEU 275 (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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211B VAL* 4.3 19.1 - - + -
212B THR* 6.0 1.1 - - - -
215B TRP* 3.5 53.8 - - + +
271B PHE* 3.2 34.5 + - + +
272B SER* 3.0 14.0 + - - +
274B GLY* 1.4 76.4 - - - +
276B ALA* 1.4 57.6 + - - +
277B HIS 3.2 1.2 + - - -
278B LEU* 3.6 29.4 + - + +
330B TYR* 5.4 0.4 - - + -
333B VAL* 4.0 21.1 - - + -
337B VAL* 5.6 2.0 - - + -
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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
------------------------------------------------------------
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