Contacts of the helix formed by residues 248 - 262 (chain B) in PDB entry 3BIL
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 ASP 248 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ASN* 6.1 2.9 - - - +
191B GLY* 3.8 20.8 - - - -
192B PRO* 4.0 9.5 - - - +
197B THR* 5.0 9.6 - - - +
201B ARG* 3.3 11.1 + - - +
223B GLY 4.6 2.8 - - - +
246B ALA* 3.5 1.0 - - - +
247B GLY* 1.3 84.6 - - - +
249B SER* 1.3 59.1 + - - +
250B MET* 3.8 11.4 - - + +
251B MET* 3.8 16.7 - - + +
252B THR* 2.6 33.4 + - - -
275B PHE* 3.6 9.7 - - - +
276B ASP* 4.5 2.9 - - - +
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Residues in contact with SER 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASN* 3.4 20.9 + - - +
78B HIS* 5.4 3.5 - - - +
79B TYR* 3.8 5.1 + - - +
248B ASP* 1.3 72.1 + - - +
250B MET* 1.3 80.3 + - - +
252B THR* 2.9 20.3 + - - -
253B ILE* 2.9 17.5 + - - +
275B PHE 3.7 10.5 - - - -
276B ASP* 3.2 28.8 + - - +
281B PHE* 4.6 6.3 - - - -
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Residues in contact with MET 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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76B ILE* 4.5 15.0 - - - +
77B ASN* 4.0 38.5 - - + +
78B HIS* 4.6 4.3 - - + +
223B GLY 5.5 1.8 - - - +
224B TYR 3.9 22.0 - - - +
226B GLN* 4.5 15.9 - - - +
248B ASP* 3.3 6.4 - - + +
249B SER* 1.3 103.1 - - - +
251B MET* 1.3 77.0 + - + +
253B ILE* 3.1 29.1 + - + +
254B GLY* 3.0 18.7 + - - -
278B HIS* 6.6 0.2 - - + -
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Residues in contact with MET 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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189B LEU* 3.5 34.7 - - + +
190B SER 3.6 23.3 - - - +
191B GLY* 4.5 0.7 - - - -
222B GLY* 4.1 1.3 - - - -
223B GLY 3.9 28.5 - - - +
225B GLU 3.8 14.8 - - - +
226B GLN 5.1 0.4 - - - +
229B GLY* 3.4 25.4 - - - +
246B ALA* 3.8 17.5 - - + -
247B GLY 4.2 1.8 - - - +
248B ASP* 3.6 24.3 + - + +
249B SER 3.3 0.4 - - - -
250B MET* 1.3 82.7 - - + +
252B THR* 1.3 56.1 + - - +
254B GLY* 3.2 2.6 + - - +
255B VAL* 2.8 32.4 + - - +
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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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246B ALA* 3.4 10.4 - - + +
248B ASP 2.6 20.6 + - - -
249B SER 2.9 9.6 + - - -
251B MET* 1.3 71.5 - - - +
253B ILE* 1.3 65.8 + - - +
255B VAL* 3.6 3.8 + - - +
256B ILE* 3.1 23.1 + - + +
272B VAL* 5.2 4.3 - - + -
274B GLY* 3.8 17.7 - - - -
275B PHE 2.9 19.6 + - - -
281B PHE* 3.5 30.3 - - + -
288B LEU* 3.8 14.6 - - + -
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Residues in contact with ILE 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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278A HIS* 5.0 4.7 - - + -
279A PRO* 4.7 16.2 - - + -
280A LEU* 3.9 30.3 - - + -
283A LEU* 4.4 13.0 - - + +
226B GLN* 3.4 37.2 - - + +
249B SER* 2.9 11.0 + - - +
250B MET* 3.1 38.3 + - + +
252B THR* 1.3 76.1 - - - +
254B GLY* 1.3 54.3 + - - +
256B ILE* 2.8 27.3 + - - +
257B GLU* 2.9 11.1 + - - +
278B HIS* 5.3 5.6 - - + -
281B PHE* 4.5 7.2 - - + -
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Residues in contact with GLY 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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226B GLN* 3.8 11.1 - - - +
229B GLY* 3.9 3.4 - - - -
230B PHE* 3.5 32.9 - - - -
250B MET 3.0 12.4 + - - -
251B MET 3.6 3.1 - - - -
253B ILE* 1.3 75.0 - - - +
255B VAL* 1.3 56.5 + - - +
257B GLU* 3.4 5.0 + - - +
258B ALA* 2.8 31.5 + - - +
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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
----------------------------------------------------------
189B LEU* 3.4 29.4 - - + -
229B GLY 4.6 0.2 + - - -
233B ALA* 4.1 8.3 - - + -
244B LEU* 3.7 36.6 - - + -
246B ALA* 4.3 14.4 - - + +
251B MET 2.8 18.6 + - - +
252B THR* 3.7 8.1 - - - +
253B ILE 3.1 0.2 + - - -
254B GLY* 1.3 73.1 - - - +
256B ILE* 1.3 61.6 + - + +
258B ALA* 3.4 2.4 + - - +
259B CYS* 3.1 23.2 + - - -
272B VAL* 3.7 30.1 - - + -
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Residues in contact with ILE 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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280A LEU* 3.8 15.3 - - + -
283A LEU* 4.1 30.1 - - + +
252B THR* 3.1 12.8 + - + +
253B ILE 2.8 13.3 + - - +
255B VAL* 1.3 70.3 - - + +
257B GLU* 1.3 59.7 + - - +
259B CYS* 3.2 4.0 + - - +
260B HIS* 2.9 27.4 + - + +
266B ILE* 4.4 22.9 - - + -
272B VAL* 5.8 0.4 - - + -
281B PHE* 3.6 35.2 - - + -
284B GLN* 4.4 21.1 - - - +
288B LEU* 4.4 14.8 - - + -
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Residues in contact with GLU 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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283A LEU* 3.9 29.5 - - + +
226B GLN* 2.9 40.4 + - - +
227B SER* 5.5 1.7 - - - -
230B PHE* 3.6 32.5 - - + +
253B ILE 2.9 9.5 + - - +
254B GLY* 3.6 6.7 - - - +
256B ILE* 1.3 75.4 - - - +
258B ALA* 1.3 54.6 + - - +
260B HIS* 3.3 1.3 + - - +
261B LYS* 2.7 66.0 + - + +
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Residues in contact with ALA 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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230B PHE* 3.5 14.4 - - + -
233B ALA* 3.4 27.8 - - + -
234B THR* 3.8 17.7 + - - +
237B LEU* 4.3 8.3 - - + +
254B GLY 2.8 22.1 + - - +
255B VAL 3.5 4.0 - - - +
257B GLU* 1.3 74.0 - - - +
259B CYS* 1.3 56.9 + - - +
261B LYS* 4.2 1.2 - - - +
262B ALA* 3.1 30.1 + - - +
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Residues in contact with CYS 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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237B LEU* 5.2 0.2 - - - -
244B LEU* 3.8 23.1 - - - -
255B VAL 3.1 17.0 + - - -
256B ILE 3.2 5.3 + - - +
258B ALA* 1.3 72.7 - - - +
260B HIS* 1.3 60.6 + - - +
262B ALA* 3.6 1.7 + - - -
263B GLY 3.0 5.5 + - - -
264B LEU* 2.5 58.1 + - + +
266B ILE* 4.0 21.5 - - + -
270B VAL* 3.9 19.3 - - - -
272B VAL* 4.3 3.4 - - - -
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Residues in contact with HIS 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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282A ALA 4.1 3.6 + - - -
283A LEU* 4.1 31.7 + - + +
284A GLN 3.6 24.4 + - - -
285A PRO* 4.5 8.8 - - - +
287A PRO* 4.0 22.8 - - + +
256B ILE* 2.9 17.2 + - + +
257B GLU* 3.7 5.8 - - - +
259B CYS* 1.3 74.0 - - - +
261B LYS* 1.3 76.2 + - + +
263B GLY* 2.9 15.3 + - - -
264B LEU 5.1 1.1 - - - -
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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
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283A LEU* 5.6 3.4 - - + +
230B PHE* 3.6 32.5 - - + -
257B GLU* 2.7 53.1 + - + +
258B ALA 4.2 0.4 - - - +
260B HIS* 1.3 83.2 - - + +
262B ALA* 1.3 58.7 + - - +
263B GLY 3.4 0.2 + - - -
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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
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234B THR* 6.3 2.9 - - + -
237B LEU* 4.5 7.0 - - + -
258B ALA 3.1 20.0 + - - +
259B CYS 3.9 0.9 - - - +
260B HIS 3.1 0.8 - - - -
261B LYS* 1.3 78.0 - - - +
263B GLY* 1.3 59.4 + - - +
264B LEU* 3.8 29.5 - - + +
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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