Contacts of the helix formed by residues 250 - 272 (chain B) in PDB entry 1O4X
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 250 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248B LEU 3.7 1.4 + - - -
249B LEU* 1.3 74.7 - - - +
251B GLU* 1.3 58.6 + - - +
252B THR* 3.6 7.7 + - - -
253B GLU* 3.1 36.0 + - - +
254B LYS* 2.8 31.4 + - - +
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Residues in contact with GLU 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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250B SER* 1.3 75.4 - - - +
252B THR* 1.3 54.4 + - - +
254B LYS* 4.2 8.5 - - + +
255B ARG* 1.5 83.2 + - - +
258B ILE* 5.2 5.6 - - + -
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Residues in contact with THR 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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250B SER* 3.3 7.6 + - - -
251B GLU* 1.3 77.4 - - - +
253B GLU* 1.3 61.1 + - + +
255B ARG* 3.4 8.9 - - + +
256B PRO* 2.8 25.1 - - - +
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Residues in contact with GLU 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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249B LEU* 3.9 26.1 - - + +
250B SER* 3.1 27.5 + - - +
252B THR* 1.3 79.8 - - + +
254B LYS* 1.3 59.4 + - - +
256B PRO* 3.0 23.0 - - - +
257B PHE* 3.5 13.5 - - - -
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Residues in contact with LYS 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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246B TRP* 3.3 68.0 + - + +
247B LYS* 4.6 6.1 + - - +
249B LEU* 3.5 27.7 + - + +
250B SER 2.8 22.4 + - - +
251B GLU* 3.8 7.9 - - - +
253B GLU* 1.3 75.8 - - - +
255B ARG* 1.3 67.3 + - - +
257B PHE* 2.8 22.5 + - - +
258B ILE* 3.0 24.5 + - + +
308C G 4.3 7.9 + - - -
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Residues in contact with ARG 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 GLU* 1.5 79.5 + - - +
252B THR* 3.4 8.7 - - + +
254B LYS* 1.3 71.6 - - - +
256B PRO* 1.3 72.6 - - + +
258B ILE* 2.8 33.9 + - + +
259B ASP* 2.9 33.1 + - - +
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Residues in contact with PRO 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 THR 2.8 28.0 - - - +
253B GLU* 3.0 18.2 - - - +
255B ARG* 1.3 82.8 - - + +
257B PHE* 1.3 67.9 + - + +
259B ASP* 4.2 7.7 - - + +
260B GLU* 3.4 23.0 + - - +
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Residues in contact with PHE 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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214B ALA* 3.6 22.1 - - - +
217B VAL* 5.4 7.5 - - + +
218B TRP* 3.6 48.7 - + + -
246B TRP* 4.3 12.3 - + + -
249B LEU* 5.7 3.8 - - + -
253B GLU 3.5 22.2 - - - -
254B LYS* 2.8 14.8 + - - +
256B PRO* 1.3 80.5 - - + +
258B ILE* 1.3 64.9 + - - +
260B GLU* 3.5 11.3 + - - +
261B ALA* 3.1 17.7 + - - +
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Residues in contact with ILE 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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214B ALA* 3.8 20.6 - - + -
246B TRP* 5.7 2.0 - - + -
251B GLU* 5.2 3.4 - - + +
254B LYS* 3.0 28.0 + - + +
255B ARG* 2.8 31.2 + - + +
257B PHE* 1.3 76.8 - - - +
259B ASP* 1.3 64.7 + - - +
261B ALA* 3.1 3.2 + - + +
262B LYS* 2.8 52.1 + - + +
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Residues in contact with ASP 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 ARG* 2.9 34.1 + - - +
256B PRO* 4.2 7.3 - - + +
258B ILE* 1.3 81.2 - - - +
260B GLU* 1.3 58.5 + - - +
262B LYS* 3.1 10.5 + - - +
263B ARG* 2.7 52.9 + - - +
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Residues in contact with GLU 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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217B VAL* 4.6 15.6 - - + +
256B PRO 3.4 17.4 + - - +
257B PHE* 3.8 12.5 - - - +
258B ILE 3.2 0.6 - - - -
259B ASP* 1.3 78.7 - - - +
261B ALA* 1.3 57.5 + - - +
263B ARG* 3.0 14.9 + - + +
264B LEU* 2.7 53.0 + - + +
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Residues in contact with ALA 261 (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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212B MET 3.8 10.3 - - - +
213B ASN* 3.8 2.0 - - - -
214B ALA* 3.3 32.5 - - + +
217B VAL* 4.7 1.9 - - + +
257B PHE 3.1 11.7 + - - +
258B ILE* 3.5 7.6 - - + +
260B GLU* 1.3 77.2 - - - +
262B LYS* 1.3 58.9 + - + +
264B LEU* 3.3 12.7 + - - +
265B ARG* 2.8 40.2 + - - +
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Residues in contact with LYS 262 (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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25A ILE* 5.0 16.8 + - + +
28A GLY* 3.7 35.2 + - - -
29A PHE 3.9 18.0 + - - -
30A THR* 4.1 14.6 - - - +
258B ILE* 2.8 36.1 + - + +
259B ASP* 3.2 13.7 - - - +
261B ALA* 1.3 79.1 - - + +
263B ARG* 1.3 58.3 + - + +
265B ARG* 3.2 33.5 + - - +
266B ALA* 2.9 28.1 + - - +
309C T 5.3 3.3 + - - -
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Residues in contact with ARG 263 (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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259B ASP* 2.7 39.1 + - + +
260B GLU* 3.5 15.1 - - + +
262B LYS* 1.3 71.6 - - + +
264B LEU* 1.3 62.1 + - + +
266B ALA* 3.2 5.8 + - - +
267B LEU* 2.8 33.6 + - - +
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Residues in contact with LEU 264 (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 PRO* 4.8 4.5 - - + -
212B MET* 4.7 19.3 - - + +
217B VAL* 3.7 33.4 - - + -
260B GLU* 2.7 47.3 + - + +
261B ALA* 3.6 6.1 - - - +
263B ARG* 1.3 72.9 - - + +
265B ARG* 1.3 58.0 + - + +
267B LEU* 4.0 12.4 - - + +
268B HIS* 2.7 31.9 + - - +
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Residues in contact with ARG 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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24A ARG* 5.1 2.2 - - - +
25A ILE* 5.0 26.5 - - + +
30A THR* 6.0 1.4 - - - +
211B PRO* 3.5 34.0 - - + +
212B MET 5.0 2.9 - - - +
213B ASN* 6.0 2.2 - - - +
261B ALA* 2.8 30.2 + - - +
262B LYS* 3.4 35.1 - - - +
264B LEU* 1.3 77.7 - - - +
266B ALA* 1.3 58.1 + - - +
268B HIS* 3.4 2.1 + - - +
269B MET* 2.9 29.7 + - - +
309C T 3.8 31.3 + - - -
310C C 3.5 23.2 + - - -
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Residues in contact with ALA 266 (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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25A ILE* 4.6 16.7 - - + +
26A LYS* 6.3 4.0 - - + -
262B LYS 2.9 16.0 + - - +
263B ARG* 3.8 6.5 - - - +
265B ARG* 1.3 76.2 - - - +
267B LEU* 1.3 65.3 + - - +
269B MET* 3.1 12.1 + - - +
270B LYS* 3.0 21.0 + - - +
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Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263B ARG 2.8 22.7 + - - +
264B LEU* 4.0 12.1 - - + +
266B ALA* 1.3 73.1 - - - +
268B HIS* 1.3 62.2 + - - +
270B LYS* 3.0 28.3 + - + +
271B GLU* 3.2 27.5 + - + +
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Residues in contact with HIS 268 (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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208B VAL* 3.4 30.4 - - + +
209B LYS 3.3 20.2 + - - -
211B PRO* 3.6 33.2 - - + +
264B LEU 2.7 25.2 + - - +
265B ARG 3.6 4.5 - - - +
267B LEU* 1.3 73.7 - - - +
269B MET* 1.3 65.8 + - - +
271B GLU* 3.2 18.7 + - - +
272B HIS* 3.2 25.1 + + - +
275B TYR* 4.7 16.7 - + + +
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Residues in contact with MET 269 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LYS* 4.7 11.7 - - + +
22A GLN* 2.6 40.4 - - - +
25A ILE* 3.2 38.6 - - + -
265B ARG 2.9 14.3 + - - +
266B ALA* 3.1 12.1 + - - +
268B HIS* 1.3 80.6 - - - +
270B LYS* 1.3 58.3 + - - +
272B HIS 4.1 6.1 - - - +
273B PRO* 2.9 42.1 - - + +
275B TYR* 6.3 0.2 - - - -
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Residues in contact with LYS 270 (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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266B ALA 3.0 12.4 + - - +
267B LEU* 3.0 25.3 + - + +
269B MET* 1.3 78.1 - - - +
271B GLU* 1.3 64.2 + - + +
273B PRO* 3.4 15.1 - - + +
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Residues in contact with GLU 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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267B LEU* 3.2 28.3 + - + +
268B HIS* 3.2 19.9 + - - +
270B LYS* 1.3 79.2 - - + +
272B HIS* 1.3 83.4 + - + +
273B PRO* 3.4 5.9 - - - +
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Residues in contact with HIS 272 (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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208B VAL* 3.7 41.1 - - + +
268B HIS* 3.2 14.3 + + - +
269B MET* 3.1 11.6 - - - +
271B GLU* 1.3 102.4 + - + +
273B PRO* 1.3 62.2 - - - +
274B ASP 3.1 5.8 - - - -
275B TYR* 3.0 33.6 + - + +
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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