Contacts of the helix formed by residues 246 - 265 (chain B) in PDB entry 3N3B
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 TRP 246 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B GLU* 3.6 33.2 - - + -
55B LEU* 3.8 18.4 - - + -
167B TRP* 3.4 38.8 - + + -
168B LEU* 4.0 10.5 - - + -
171B TYR* 3.4 41.6 + + - -
172B PHE* 4.8 1.8 - + - -
241B TYR* 4.3 4.7 - + + -
244B THR* 3.4 36.9 + - + +
245B PRO* 1.3 100.1 - - + +
247B ALA* 1.3 66.3 + - - +
248B ASP 3.2 2.5 - - - -
249B ASP* 3.0 19.4 + - + +
250B VAL* 3.1 12.2 + - - +
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Residues in contact with ALA 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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237B THR* 4.3 17.0 - - + +
238B ASP* 4.4 18.8 - - - +
241B TYR* 4.4 20.1 + - + +
244B THR 5.6 0.9 - - - +
245B PRO 3.6 2.0 - - - -
246B TRP* 1.3 75.4 - - - +
248B ASP* 1.3 60.3 + - - +
250B VAL* 3.3 5.0 + - - +
251B LYS* 3.0 37.6 + - - +
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Residues in contact with ASP 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PRO 5.1 0.6 + - - -
246B TRP 3.1 0.8 + - - -
247B ALA* 1.3 81.0 - - - +
249B ASP* 1.3 58.1 + - - +
251B LYS* 3.7 17.4 + - - +
252B ALA* 3.2 24.6 + - - +
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Residues in contact with ASP 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B TRP* 2.8 33.0 + - + +
246B TRP* 3.0 12.0 + - + +
248B ASP* 1.3 76.1 - - - +
250B VAL* 1.3 60.9 + - - +
252B ALA* 3.4 5.8 + - - +
253B PHE* 3.0 27.5 + - - +
277B GLU 4.8 1.0 - - - +
278B VAL* 4.4 4.8 - - - +
279B ASN* 3.4 31.4 + - - +
282B ILE* 3.5 14.7 - - - +
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Residues in contact with VAL 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B SER* 3.8 33.7 - - - +
167B TRP* 3.6 34.3 - - + -
237B THR* 3.7 21.5 - - + +
241B TYR* 3.7 26.5 - - + -
246B TRP 3.1 17.0 + - - +
247B ALA 3.3 6.3 + - - +
249B ASP* 1.3 77.6 - - - +
251B LYS* 1.3 56.2 + - - +
253B PHE* 3.2 4.3 + - - +
254B LEU* 2.9 27.1 + - + +
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Residues in contact with LYS 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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230B TYR* 5.1 0.8 - - - +
234B LEU* 3.7 45.9 - - + +
237B THR* 4.1 15.0 - - + +
238B ASP* 2.9 34.2 + - - -
247B ALA* 3.0 26.2 + - - +
248B ASP* 3.9 16.2 + - - +
250B VAL* 1.3 74.6 - - - +
252B ALA* 1.3 59.3 + - - +
254B LEU* 3.2 9.7 + - + +
255B CYS* 3.0 34.4 + - - -
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Residues in contact with ALA 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 ASP 3.2 15.6 + - - +
249B ASP* 3.7 11.0 - - - +
250B VAL 3.3 0.2 - - - -
251B LYS* 1.3 78.9 - - - +
253B PHE* 1.3 56.9 + - - +
255B CYS 3.5 0.5 + - - -
256B TYR* 3.2 26.3 + - - +
274B GLU 6.0 0.2 - - - +
275B MET 3.3 20.4 - - - +
276B ALA* 3.7 8.0 - - - -
277B GLU 3.8 22.9 - - - +
278B VAL* 3.7 3.6 - - - +
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Residues in contact with PHE 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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163B TYR* 3.4 43.1 - + - -
166B PHE* 4.4 2.0 - - + -
167B TRP* 3.6 32.1 - + + -
170B MET* 5.1 3.1 - - + -
249B ASP 3.0 18.0 + - - +
250B VAL 3.2 4.9 + - - +
252B ALA* 1.3 73.7 - - - +
254B LEU* 1.3 62.1 + - - +
256B TYR* 3.6 13.9 + + - +
257B ASN* 2.7 56.2 + - - -
278B VAL* 3.7 29.1 - - + +
282B ILE* 3.8 17.5 - - + -
283B LEU* 5.2 2.9 - - + -
286B LEU* 4.6 21.1 - - + -
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Residues in contact with LEU 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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160B PHE* 3.4 43.0 - - + +
161B LEU 4.1 1.3 - - - +
163B TYR* 4.3 1.3 - - - -
164B SER* 3.7 29.2 - - - +
230B TYR* 5.2 5.2 - - + -
233B GLU* 3.9 26.0 - - + +
234B LEU* 5.3 4.3 - - + +
237B THR* 3.5 25.8 - - - +
250B VAL 2.9 18.1 + - - +
251B LYS* 3.4 17.5 - - + +
253B PHE* 1.3 75.2 - - - +
255B CYS* 1.3 60.7 + - - +
257B ASN* 3.4 3.3 + - - +
258B ALA* 2.9 27.9 + - - +
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Residues in contact with CYS 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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230B TYR* 3.4 32.1 - - - -
251B LYS* 3.0 19.9 + - - +
252B ALA 3.5 0.4 + - - +
254B LEU* 1.3 74.2 - - - +
256B TYR* 1.3 65.4 + - - +
258B ALA* 3.4 8.0 + - - +
259B ASN* 3.2 28.9 + - - -
271B PHE* 3.5 30.7 - - + +
275B MET* 3.7 31.4 - - - +
276B ALA* 4.2 2.2 - - - -
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Residues in contact with TYR 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 ALA 3.2 17.7 + - - +
253B PHE* 3.6 17.9 - + - +
255B CYS* 1.3 79.0 - - - +
257B ASN* 1.3 84.4 + - - +
259B ASN* 3.6 7.7 + - - +
260B LYS* 3.5 32.5 + - + +
276B ALA* 3.9 17.6 - - + +
278B VAL* 3.6 17.3 - - + -
283B LEU* 4.0 20.2 - - + -
286B LEU* 4.6 5.2 - - + -
84C ARG* 3.6 18.9 - - - +
110C GLU* 2.6 37.0 + - - -
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Residues in contact with ASN 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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159B SER 2.9 27.5 - - - +
160B PHE* 4.3 4.7 - - - +
163B TYR* 3.4 55.2 - - + +
253B PHE* 2.7 40.3 + - - +
254B LEU 4.0 2.9 - - - +
256B TYR* 1.3 90.7 - - - +
258B ALA* 1.3 60.4 + - - +
260B LYS* 3.3 16.5 + - - +
261B ALA* 3.0 19.1 + - - +
85C ASN* 4.9 0.5 - - - +
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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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160B PHE* 3.6 27.6 - - + -
226B LEU* 4.4 8.2 - - + +
254B LEU 2.9 18.3 + - - +
255B CYS* 3.6 7.2 - - - +
256B TYR 3.3 0.2 - - - -
257B ASN* 1.3 76.5 - - - +
259B ASN* 1.3 57.3 + - - +
261B ALA* 3.3 3.9 + - - +
262B LEU* 3.0 32.9 + - - +
271B PHE* 3.7 24.9 - - + -
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Residues in contact with ASN 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 CYS 3.2 10.3 + - - -
256B TYR* 3.7 8.9 + - - +
258B ALA* 1.3 76.8 - - - +
260B LYS* 1.3 57.3 + - - +
262B LEU* 3.6 7.5 + - - +
263B MET* 3.2 37.8 + - + +
269B PRO* 3.6 19.5 - - + +
270B LEU 3.0 9.2 + - - -
271B PHE* 2.8 56.3 + - - +
276B ALA* 4.2 9.9 - - - +
114C THR* 5.1 10.0 - - + +
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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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159B SER* 4.9 1.6 - - - +
256B TYR* 3.5 39.2 + - + +
257B ASN* 3.3 18.7 + - - +
258B ALA 3.2 0.6 - - - -
259B ASN* 1.3 76.5 - - + +
261B ALA* 1.3 59.2 + - - +
263B MET* 3.3 19.6 + - + -
264B ASN* 3.0 33.2 + - - +
322B PEO 3.4 21.8 - - - +
83C ASN* 2.8 26.6 + - - +
85C ASN* 3.2 24.0 + - - +
110C GLU* 3.1 26.8 + - - +
111C LEU* 3.5 9.7 - - + +
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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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155B VAL* 3.4 21.3 - - + +
156B PHE* 4.1 18.2 - - + -
159B SER* 3.9 20.8 + - - -
160B PHE* 3.8 21.1 - - + -
226B LEU* 5.5 0.2 - - + -
257B ASN 3.0 13.7 + - - +
258B ALA 3.3 8.0 + - - +
260B LYS* 1.3 75.6 - - - +
262B LEU* 1.3 62.6 + - - +
264B ASN* 3.5 1.5 + - - -
265B LEU* 3.5 13.5 + - - +
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Residues in contact with LEU 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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156B PHE* 4.3 15.0 - - + -
222B ALA 5.5 1.8 - - - +
223B PHE* 3.8 26.5 - - + -
226B LEU* 3.8 31.4 - - + -
258B ALA 3.0 19.6 + - - +
259B ASN* 3.7 10.1 - - - +
261B ALA* 1.3 76.4 - - - +
263B MET* 1.3 59.3 + - - +
265B LEU* 3.1 14.0 + - - +
266B GLY 3.2 0.2 + - - -
267B TYR* 2.9 36.6 + - + +
268B GLU 3.7 22.0 - - - +
269B PRO* 4.3 0.2 - - + -
270B LEU* 3.7 25.1 - - + +
271B PHE* 5.2 0.4 - - + -
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Residues in contact with MET 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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204B GLN* 4.5 1.0 + - - -
259B ASN* 3.2 23.4 + - + +
260B LYS* 3.7 22.9 - - + +
261B ALA 3.3 0.4 - - - -
262B LEU* 1.3 75.9 - - - +
264B ASN* 1.3 61.8 + - - +
266B GLY* 3.0 17.5 + - - -
267B TYR 3.4 12.3 - - - +
269B PRO* 3.9 21.1 - - + -
13C ASN* 3.8 11.2 - - - +
110C GLU* 4.1 13.9 - - + +
111C LEU* 3.7 17.0 - - + -
112C MET* 3.5 41.2 - - + +
113C GLY 3.7 16.2 - - - +
114C THR* 4.7 12.6 - - + -
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Residues in contact with ASN 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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155B VAL* 4.1 6.5 - - + -
159B SER* 3.6 21.5 + - - -
193B ALA 4.9 1.5 + - - +
196B GLY 3.6 22.5 - - - +
197B TYR* 3.8 23.1 + - - +
200B GLY* 3.3 16.1 - - - -
201B TYR 3.9 0.5 + - - -
204B GLN* 2.9 17.5 + - - -
260B LYS 3.0 16.9 + - - +
261B ALA 3.6 9.9 - - - +
263B MET* 1.3 76.7 - - - +
265B LEU* 1.3 57.2 + - - +
322B PEO 3.8 11.7 + - - -
13C ASN* 5.4 3.1 - - - +
83C ASN* 5.4 0.8 - - - +
111C LEU* 3.7 25.2 - - - +
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Residues in contact with LEU 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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151B LYS 4.3 0.7 - - - +
152B ILE* 4.3 24.9 - - + -
155B VAL* 3.9 27.8 - - + -
156B PHE* 3.7 36.3 - - + -
200B GLY* 4.2 4.0 - - - -
203B TYR* 3.7 38.9 - - + -
204B GLN* 3.2 21.8 - - - +
207B MET* 5.5 0.5 - - - +
222B ALA* 5.1 0.7 - - + -
261B ALA 3.5 9.6 + - - +
262B LEU* 3.1 9.4 + - - +
264B ASN* 1.3 72.8 - - - +
266B GLY* 1.3 59.9 + - - +
267B TYR* 3.5 25.1 - - + -
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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