Contacts of the helix formed by residues 246 - 265 (chain B) in PDB entry 4XZC
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 LYS 246 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244B GLY* 2.9 4.7 + - - -
245B HIS* 1.3 91.9 + - + +
247B ARG* 1.3 61.9 + - - +
248B LEU 3.1 2.2 - - - -
249B GLU* 3.0 53.8 + - - +
250B ASP* 2.9 14.6 - - - +
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Residues in contact with ARG 247 (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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203B ARG 5.0 1.0 + - - -
206B ALA* 3.3 35.8 + - + +
207B ALA* 4.2 7.9 - - - +
239B VAL* 3.6 21.3 - - + -
240B ALA* 5.1 0.4 - - - -
243B ASP* 3.6 37.5 + - + +
244B GLY 3.2 16.0 + - - +
246B LYS* 1.3 77.9 - - - +
248B LEU* 1.3 65.2 + - - +
250B ASP* 2.9 38.2 + - - +
251B ILE* 3.0 27.5 + - - +
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Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B MET* 3.9 23.6 - - + +
239B VAL* 6.4 0.2 - - + -
240B ALA* 3.9 24.9 - - + -
244B GLY 4.7 0.2 + - - -
245B HIS* 4.1 27.4 - - + +
247B ARG* 1.3 78.8 - - - +
249B GLU* 1.3 61.8 + - + +
251B ILE* 3.6 10.1 + - + +
252B ARG* 3.2 19.9 + - - +
285B LEU* 3.6 20.3 - - + +
288B ALA* 3.9 22.4 - - + -
289B ILE* 4.1 23.3 - - + +
292B ALA* 4.0 17.7 - - + -
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Residues in contact with GLU 249 (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 HIS 5.1 0.2 + - - -
246B LYS* 3.0 38.5 + - - +
248B LEU* 1.3 78.2 - - + +
250B ASP* 1.3 63.0 + - - +
252B ARG* 2.3 50.2 + - - +
253B LYS* 3.1 23.9 + - - +
289B ILE* 4.7 2.6 - - - +
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Residues in contact with ASP 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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206B ALA 3.4 20.1 - - - +
246B LYS* 2.9 23.4 - - - +
247B ARG* 2.9 36.4 + - - +
249B GLU* 1.3 77.0 - - - +
251B ILE* 1.3 58.7 + - - +
253B LYS* 3.1 11.7 + - - +
254B THR* 2.9 30.8 + - - -
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Residues in contact with ILE 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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202B GLY* 4.4 8.5 - - - +
205B LEU* 3.6 28.3 - - + -
206B ALA* 3.7 24.7 - - + +
236B MET* 3.9 36.6 - - + -
239B VAL* 5.0 6.1 - - + -
247B ARG 3.0 16.3 + - - +
248B LEU* 3.6 16.4 - - + +
250B ASP* 1.3 74.9 - - - +
252B ARG* 1.3 57.5 + - - +
254B THR* 3.2 8.7 + - - -
255B LEU* 3.0 40.6 + - + +
285B LEU* 4.1 12.6 - - + -
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Residues in contact with ARG 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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248B LEU 3.2 5.6 + - - +
249B GLU* 2.3 53.7 + - - +
250B ASP 3.2 0.6 - - - -
251B ILE* 1.3 80.0 - - - +
253B LYS* 1.3 61.4 + - - +
254B THR 3.3 0.7 + - - -
255B LEU* 3.4 5.5 + - - +
256B LEU* 3.3 30.9 + - + +
285B LEU* 3.7 22.9 - - + +
286B ALA* 5.6 2.8 - - - +
289B ILE* 3.2 32.2 - - - +
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Residues in contact with LYS 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 GLU 3.1 12.1 + - - +
250B ASP* 3.1 13.7 + - - +
252B ARG* 1.3 77.0 - - - +
254B THR* 1.3 60.0 + - - +
256B LEU* 3.4 26.8 - - + +
257B ASP* 3.5 15.7 - - - +
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Residues in contact with THR 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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205B LEU* 2.9 34.2 + - + +
206B ALA 4.3 0.7 + - - -
208B GLY* 3.3 37.4 + - - +
210B PHE* 3.6 19.5 - - + -
250B ASP 2.9 12.3 + - - -
251B ILE* 3.4 9.2 - - - -
252B ARG 3.1 0.4 - - - -
253B LYS* 1.3 73.7 - - - +
255B LEU* 1.3 51.4 + - - +
256B LEU 3.0 4.5 - - - -
257B ASP* 2.8 11.8 + - - +
258B LEU* 2.6 32.7 + - - +
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Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 4.5 18.6 - - + -
236B MET* 5.5 0.2 - - + -
251B ILE* 3.0 22.8 + - + +
252B ARG* 3.4 5.4 + - - +
254B THR* 1.3 75.3 - - - +
256B LEU* 1.3 58.8 + - - +
258B LEU* 3.7 27.2 - - + +
259B LYS* 3.1 25.5 + - - +
278B VAL* 4.9 6.6 - - + +
281B LEU* 3.5 48.2 - - + +
282B THR* 4.4 9.0 - - + +
285B LEU* 3.9 20.6 - - + -
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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 ARG* 3.3 23.9 + - + +
253B LYS* 3.4 17.5 - - - +
254B THR 3.0 0.2 - - - -
255B LEU* 1.3 77.7 - - - +
257B ASP* 1.3 67.5 + - - +
259B LYS* 3.1 15.9 + - + +
260B LYS* 3.0 23.4 + - - +
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Residues in contact with ASP 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B GLY* 5.3 5.6 - - - +
210B PHE* 4.1 19.0 - - + -
253B LYS 3.5 15.1 - - - +
254B THR* 2.8 14.6 + - + +
256B LEU* 1.3 76.2 - - - +
258B LEU* 1.3 62.4 + - - +
260B LYS* 3.8 8.8 - - - +
261B TRP* 3.0 25.1 + - - +
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Residues in contact with LEU 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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210B PHE* 3.6 39.3 - - + -
213B VAL* 4.0 12.1 - - + -
214B PHE* 4.2 13.9 - - + -
254B THR 2.6 15.5 + - - +
255B LEU* 3.7 20.9 - - + +
257B ASP* 1.3 73.6 - - - +
259B LYS* 1.3 64.0 + - - +
261B TRP* 3.3 2.4 + - - +
262B ILE* 3.1 42.8 + - + +
277B LEU* 4.6 5.4 - - + -
278B VAL* 4.8 10.1 - - + -
281B LEU* 3.7 30.3 - - + -
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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
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255B LEU 3.1 14.8 + - - +
256B LEU* 3.1 16.9 + - + +
258B LEU* 1.3 77.0 - - - +
260B LYS* 1.3 66.0 + - - +
262B ILE* 3.2 5.7 + - - +
263B GLU* 3.1 49.5 + - + +
278B VAL* 4.3 34.8 - - + -
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Residues in contact with LYS 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 3.0 14.6 + - - +
257B ASP* 3.8 9.6 - - - +
259B LYS* 1.3 75.6 - - - +
261B TRP* 1.3 64.6 + - - +
263B GLU* 3.2 12.6 + - - +
264B ASP* 3.0 53.5 + - - +
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Residues in contact with TRP 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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210B PHE* 3.8 28.5 - + + -
214B PHE* 3.8 32.8 - + - -
257B ASP 3.0 18.5 + - - +
258B LEU* 3.6 4.3 - - + +
259B LYS 3.3 0.2 - - - -
260B LYS* 1.3 78.3 - - - +
262B ILE* 1.3 73.1 + - + +
264B ASP* 3.6 2.4 + - - -
265B ASN* 2.8 62.8 + - + +
268B GLU* 4.8 10.5 - - + -
269B LEU* 4.3 23.6 - - + -
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Residues in contact with ILE 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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214B PHE* 5.0 1.6 - - + -
258B LEU* 3.1 30.5 + - + +
259B LYS* 3.5 6.5 - - - +
260B LYS 3.2 0.4 - - - -
261B TRP* 1.3 88.6 - - + +
263B GLU* 1.3 57.5 + - + +
265B ASN 3.1 2.3 - - - -
266B LYS* 2.6 37.2 + - + -
269B LEU* 3.5 28.0 - - + -
274B GLY* 3.7 35.9 - - - +
275B ASP* 5.5 2.9 - - - +
277B LEU* 4.4 10.1 - - + -
278B VAL* 3.7 15.9 - - + -
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Residues in contact with GLU 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 LYS* 3.1 47.3 + - + +
260B LYS* 3.2 12.9 + - - +
262B ILE* 1.3 76.2 - - + +
264B ASP* 1.3 69.7 + - - +
265B ASN 3.1 1.7 + - - -
266B LYS* 3.6 14.0 + - - +
275B ASP* 6.1 0.9 - - - +
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Residues in contact with ASP 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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260B LYS* 3.0 52.1 + - - +
261B TRP* 3.8 1.5 - - - +
263B GLU* 1.3 78.9 - - - +
265B ASN* 1.3 74.5 + - - +
266B LYS 3.7 0.4 + - - -
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Residues in contact with ASN 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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261B TRP* 2.8 63.4 + - + +
262B ILE* 3.1 6.0 + - - -
263B GLU 3.1 0.4 - - - -
264B ASP* 1.3 91.1 - - - +
266B LYS* 1.3 63.9 + - - +
267B ASP 3.0 3.8 - - - -
268B GLU* 2.8 35.6 + - + +
269B LEU* 4.0 4.7 + - - +
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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