Contacts of the helix formed by residues 248 - 268 (chain B) in PDB entry 1LUA
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 GLY 248 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220B ASP* 3.5 2.7 - - - -
232B ILE* 4.2 9.4 - - - -
233B ASP 3.8 11.7 - - - -
234B ALA* 3.0 20.4 - - - -
236B ASP* 2.6 18.1 + - - +
247B PHE* 1.3 74.7 - - - +
249B ALA* 1.3 65.8 + - - -
251B GLY 2.9 11.3 + - - -
252B ILE* 2.9 12.6 + - - +
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Residues in contact with ALA 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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220B ASP* 3.0 13.8 + - - +
221B TYR* 3.4 35.2 - - - +
222B ASN 3.5 6.1 + - - +
223B ALA* 3.5 27.4 - - + +
234B ALA* 3.3 5.1 + - + +
248B GLY* 1.3 71.4 - - - -
250B LEU* 1.3 58.9 + - - +
252B ILE* 3.4 5.7 + - - +
253B GLY* 2.8 24.4 + - - -
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Residues in contact with LEU 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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223B ALA* 4.2 17.9 - - + +
234B ALA* 2.9 28.1 + - + +
235B THR* 3.9 26.0 - - + -
249B ALA* 1.3 74.3 - - - +
251B GLY* 1.3 65.8 + - - +
252B ILE 3.2 0.4 - - - -
253B GLY* 3.7 3.4 - - - +
254B GLY* 3.1 19.8 + - - -
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Residues in contact with GLY 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 4.3 1.3 - - - +
234B ALA 3.2 6.7 + - - -
235B THR* 4.0 10.2 - - - +
236B ASP 3.7 15.5 - - - -
237B LYS* 3.8 34.2 - - - +
247B PHE* 5.6 0.7 - - - -
248B GLY 2.9 7.7 + - - -
250B LEU* 1.3 77.0 - - - +
252B ILE* 1.3 63.5 + - - +
254B GLY* 3.6 6.4 + - - -
255B LEU 4.0 1.9 + - - -
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Residues in contact with ILE 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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102B THR* 3.9 15.7 - - + +
105B ALA* 3.8 3.0 - - + +
106B GLY* 3.6 34.8 - - - +
109B LEU* 3.9 11.2 - - + -
219B ALA* 4.3 20.6 - - + -
220B ASP 3.7 22.7 - - - +
221B TYR* 3.9 25.1 - - + -
247B PHE* 4.1 15.2 - - + +
248B GLY 2.9 11.2 + - - +
249B ALA* 3.6 7.4 - - - +
251B GLY* 1.3 77.2 - - - +
253B GLY* 1.3 63.7 + - - +
255B LEU* 3.1 17.5 + - - +
256B LYS* 3.1 9.1 + - + -
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Residues in contact with GLY 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ALA 2.8 16.9 + - - -
250B LEU* 3.3 6.2 + - - -
252B ILE* 1.3 74.2 - - - +
254B GLY* 1.3 63.3 + - - +
256B LYS* 3.3 15.5 + - - +
257B LEU* 3.0 23.9 + - - +
1456B NAP 6.3 1.6 - - - -
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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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237B LYS* 6.0 1.1 - - - -
250B LEU 3.1 14.1 + - - -
251B GLY 3.6 3.8 + - - -
252B ILE 3.2 1.2 + - - -
253B GLY* 1.3 77.4 - - - +
255B LEU* 1.3 61.3 + - - +
257B LEU* 3.7 6.8 + - - +
258B LYS* 3.6 27.1 + - - +
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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
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105B ALA* 3.7 21.1 - - + +
108B ALA* 4.7 1.1 - - + -
109B LEU* 3.5 40.2 - - + -
237B LYS* 5.2 6.7 - - - +
251B GLY 4.0 3.5 + - - +
252B ILE 3.1 9.7 + - - +
254B GLY* 1.3 74.4 - - - +
256B LYS* 1.3 63.0 + - - +
257B LEU 3.1 0.3 + - - -
258B LYS* 3.1 11.3 + - + +
259B LEU* 2.8 42.4 + - + +
284B ALA* 4.7 6.7 - - + +
287B MET* 4.3 26.5 - - + +
288B ALA* 4.1 20.2 - - + +
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Residues in contact with LYS 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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18B PHE* 4.0 23.3 - - + -
95B ASP* 3.8 3.6 + - - -
98B GLY* 4.5 6.6 - - - -
101B THR* 2.8 48.6 + - - +
102B THR* 3.8 13.9 - - + +
105B ALA* 3.7 10.4 - - + +
252B ILE* 3.1 11.3 + - + +
253B GLY* 3.3 15.7 + - - +
255B LEU* 1.3 79.3 - - - +
257B LEU* 1.3 62.9 + - + +
259B LEU* 3.6 3.5 - - - +
260B HIS* 3.0 58.4 + - - +
1456B NAP 3.8 20.9 - - - +
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Residues in contact with LEU 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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51A TYR 4.2 8.3 - - - +
52A THR* 3.6 21.3 - - - +
53A ARG* 5.4 0.9 - - - -
18B PHE* 4.1 16.8 - - + -
22B VAL* 3.7 29.8 - - + -
253B GLY 3.0 15.2 + - - +
254B GLY* 3.9 7.2 - - - +
255B LEU 3.1 0.4 - - - -
256B LYS* 1.3 80.3 - - + +
258B LYS* 1.3 66.5 + - + +
260B HIS* 3.3 4.1 + - + +
261B ARG* 3.0 58.6 + - - +
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Residues in contact with LYS 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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254B GLY 3.6 14.7 + - - +
255B LEU* 3.1 12.6 + - + +
257B LEU* 1.3 77.8 - - + +
259B LEU* 1.3 57.6 + - - +
261B ARG* 3.4 25.8 + - - +
262B ALA* 3.0 29.1 + - - +
287B MET* 3.6 16.9 - - + +
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Residues in contact with LEU 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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101B THR* 3.8 25.1 - - + +
104B ALA* 4.0 2.9 - - + -
105B ALA* 4.3 5.4 - - + +
255B LEU* 2.8 22.0 + - + +
256B LYS 3.6 3.4 - - - +
258B LYS* 1.3 74.8 - - - +
260B HIS* 1.3 60.5 + - - +
262B ALA* 3.1 2.9 + - - +
263B CYS* 2.8 39.7 + - - -
280B ILE* 3.7 31.4 - - + +
283B LEU* 4.0 16.4 - - + -
284B ALA* 3.7 42.8 - - + +
287B MET* 4.1 11.8 - - - +
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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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18B PHE* 4.1 4.7 - + - -
19B ASP* 3.5 29.3 + - - -
22B VAL* 3.4 31.2 - - + +
64B PHE* 3.7 18.7 - + - -
93B MET* 4.0 13.2 - - + -
95B ASP* 3.9 12.3 + - - -
101B THR* 4.0 11.0 - - + +
256B LYS* 3.0 43.9 + - - +
257B LEU* 3.3 5.1 + - - +
259B LEU* 1.3 76.4 - - - +
261B ARG* 1.3 63.8 + - - +
263B CYS* 3.3 3.6 + - - +
264B ILE* 3.3 27.2 + - + +
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Residues in contact with ARG 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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52A THR 3.0 26.7 + - - -
53A ARG* 4.5 0.6 - - - +
57A GLU* 4.1 18.1 + - - -
22B VAL* 3.7 25.6 - - + +
25B ASP* 3.9 30.1 + - + +
26B GLY* 3.3 23.5 - - - +
257B LEU* 3.0 39.0 + - - +
258B LYS* 3.6 30.5 - - - +
260B HIS* 1.3 78.6 - - - +
262B ALA* 1.3 62.3 + - - +
264B ILE* 3.3 1.5 + - - -
265B ALA* 3.3 15.9 + - - +
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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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258B LYS 3.0 17.4 + - - +
259B LEU 3.1 4.0 + - - +
261B ARG* 1.3 74.8 - - - +
263B CYS* 1.3 65.6 + - - +
265B ALA* 3.3 9.4 + - - +
266B LYS* 3.2 25.4 + - - +
283B LEU* 3.9 9.6 - - + -
287B MET* 3.7 26.2 - - + -
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Residues in contact with CYS 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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93B MET* 3.7 24.7 - - + -
101B THR* 5.0 0.2 - - - -
259B LEU* 2.8 34.0 + - - +
260B HIS 3.3 3.8 + - - +
262B ALA* 1.3 69.7 - - - +
264B ILE* 1.3 67.7 + - - +
266B LYS* 3.1 16.4 + - - +
267B LEU* 3.2 17.0 + - - +
275B PHE* 4.0 11.5 - - + -
280B ILE* 3.9 30.3 - - - -
283B LEU* 3.9 19.3 - - - +
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Residues in contact with ILE 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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6B LEU* 4.3 16.8 - - + -
19B ASP 6.0 0.4 - - - +
22B VAL 4.6 1.6 - - - +
23B GLY* 3.7 33.2 - - - +
26B GLY* 4.1 9.2 - - - +
28B ALA* 4.5 2.5 - - + +
64B PHE* 4.0 24.5 - - + -
93B MET* 4.0 5.4 - - - -
260B HIS* 3.3 25.6 + - + +
261B ARG 3.6 8.1 - - - +
263B CYS* 1.3 75.9 - - - +
265B ALA* 1.3 65.9 + - - +
267B LEU* 3.0 38.7 + - + +
268B PHE* 3.6 22.6 - - + -
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Residues in contact with ALA 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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26B GLY 3.3 21.2 + - - +
261B ARG 3.3 6.2 + - - +
262B ALA* 3.3 11.6 + - - +
263B CYS 3.2 0.8 - - - -
264B ILE* 1.3 79.3 - - - +
266B LYS* 1.3 61.4 + - - +
268B PHE* 3.2 19.8 + - - +
269B GLU* 3.8 18.1 - - - +
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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
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91B SER* 4.9 0.3 + - - -
262B ALA* 3.2 15.8 + - - +
263B CYS 3.1 8.4 + - - +
265B ALA* 1.3 74.2 - - + +
267B LEU* 1.3 67.5 + - - +
269B GLU* 3.0 44.0 + - - +
270B SER* 4.1 6.2 + - - -
273B GLY* 6.2 0.3 - - - -
275B PHE* 3.5 30.1 - - + -
283B LEU* 3.8 34.4 - - + +
286B GLU* 4.8 9.4 + - - -
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Residues in contact with LEU 267 (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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6B LEU* 4.1 18.4 - - + -
59B GLN 3.8 3.1 - - - +
61B THR 4.9 0.3 - - - +
62B ALA* 3.8 16.9 - - + +
63B ILE 4.2 7.0 - - - +
64B PHE* 5.2 0.4 - - + -
91B SER* 3.3 23.1 + - - -
92B CYS 3.9 18.2 - - - +
93B MET* 4.1 16.6 - - + -
263B CYS 3.4 11.2 - - - +
264B ILE* 3.0 36.5 + - + +
266B LYS* 1.3 79.8 - - - +
268B PHE* 1.3 59.2 + - + +
270B SER 3.0 19.1 - - - +
275B PHE* 3.8 26.9 - - + -
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Residues in contact with PHE 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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4B LYS* 3.7 39.3 - - + -
5B LEU 3.6 26.5 - - - -
6B LEU* 4.1 12.8 - - + -
27B GLY 5.0 0.9 - - - -
28B ALA* 3.9 24.5 - - + -
59B GLN* 3.0 39.6 + - - +
60B SER* 3.5 24.9 + - - -
61B THR 4.2 0.2 - - - -
62B ALA* 3.8 15.7 - - + -
264B ILE* 3.6 25.8 - - + -
265B ALA* 3.2 11.0 + - - +
266B LYS 3.1 1.0 - - - -
267B LEU* 1.3 81.2 - - + +
269B GLU* 1.3 60.6 + - - +
270B SER 3.4 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
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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