Contacts of the helix formed by residues 248 - 268 (chain C) in PDB entry 1LU9
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220C ASP* 3.4 3.4 - - - -
227C LEU* 5.9 0.2 - - - -
232C ILE* 4.0 11.9 - - - -
233C ASP 3.7 11.7 - - - -
234C ALA* 3.0 19.1 - - - -
236C ASP* 2.7 14.9 + - - +
247C PHE* 1.3 75.8 - - - +
249C ALA* 1.3 62.3 + - - -
250C LEU 3.2 0.3 + - - -
251C GLY* 3.2 2.4 + - - -
252C ILE* 3.1 20.4 + - - +
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Residues in contact with ALA 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C ASP* 2.9 21.2 + - - +
221C TYR* 3.6 11.0 - - - +
222C ASN 3.5 32.8 + - - +
223C ALA* 3.5 14.1 - - + +
227C LEU* 6.1 0.2 - - - +
234C ALA* 3.2 5.6 + - + +
248C GLY* 1.3 70.5 - - - -
250C LEU* 1.3 59.5 + - - +
252C ILE* 3.7 5.0 + - - +
253C GLY* 2.8 23.6 + - - -
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Residues in contact with LEU 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C ALA* 4.2 21.1 - - + +
234C ALA* 2.8 37.1 + - + +
235C THR* 4.0 21.3 - - + -
249C ALA* 1.3 72.6 - - - +
251C GLY* 1.3 67.5 + - - +
253C GLY* 3.1 2.8 + - - +
254C GLY* 2.9 21.5 + - - -
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Residues in contact with GLY 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C LEU* 4.2 0.9 - - - +
234C ALA 3.3 5.5 + - - -
235C THR* 4.1 10.1 - - - +
236C ASP 3.8 13.2 - - - -
237C LYS* 4.0 30.6 - - - +
247C PHE* 5.8 0.2 - - - -
248C GLY 3.2 6.0 + - - -
250C LEU* 1.3 80.9 - - - +
252C ILE* 1.3 61.9 + - - +
254C GLY* 3.5 6.6 + - - -
255C LEU 3.7 6.2 + - - -
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Residues in contact with ILE 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C THR* 3.8 15.9 - - + +
105C ALA* 3.8 2.8 - - + +
106C GLY* 3.5 33.2 - - - +
109C LEU* 3.8 19.7 - - + -
219C ALA* 4.1 11.2 - - + -
220C ASP 4.0 13.2 - - - +
221C TYR* 4.0 24.9 - - + -
247C PHE* 4.1 23.1 - - + +
248C GLY 3.1 17.0 + - - +
249C ALA* 3.9 4.5 - - - +
251C GLY* 1.3 73.8 - - - +
253C GLY* 1.3 65.6 + - - +
255C LEU* 3.1 7.1 + - - +
256C LYS* 3.0 18.9 + - + +
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Residues in contact with GLY 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C THR* 6.4 0.9 - - - -
249C ALA 2.8 19.6 + - - -
250C LEU* 3.1 5.3 + - - -
252C ILE* 1.3 78.1 - - - +
254C GLY* 1.3 59.9 + - - +
256C LYS* 3.6 12.5 - - - +
257C LEU* 3.0 25.3 + - - +
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Residues in contact with GLY 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C LEU 2.9 13.8 + - - -
251C GLY 3.5 3.1 + - - -
252C ILE 3.2 0.6 - - - -
253C GLY* 1.3 76.2 - - - +
255C LEU* 1.3 61.7 + - - +
257C LEU* 3.4 8.0 + - - +
258C LYS* 3.3 31.6 + - - +
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Residues in contact with LEU 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ALA* 3.9 22.4 - - + +
108C ALA* 4.8 0.9 - - + -
109C LEU* 3.7 33.0 - - + -
237C LYS* 5.2 9.5 - - - +
251C GLY 3.7 4.9 + - - +
252C ILE 3.1 8.9 + - - +
254C GLY* 1.3 72.8 - - - +
256C LYS* 1.3 57.5 + - - +
258C LYS* 3.1 15.7 + - + +
259C LEU* 2.7 42.2 + - + +
284C ALA* 4.6 6.1 - - + +
287C MET* 4.0 34.8 - - + +
288C ALA* 3.9 20.4 - - + +
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Residues in contact with LYS 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C PHE* 3.9 26.9 - - + -
95C ASP* 3.7 2.4 + - - -
98C GLY* 4.1 8.3 - - - +
101C THR* 2.6 42.7 + - - +
102C THR* 3.7 28.3 - - + +
105C ALA* 3.7 10.4 - - + +
252C ILE* 3.0 14.0 + - + +
253C GLY* 3.6 15.0 - - - +
255C LEU* 1.3 77.4 - - - +
257C LEU* 1.3 63.6 + - + +
259C LEU* 3.6 4.8 - - - +
260C HIS* 2.8 56.0 + - - +
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Residues in contact with LEU 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B TYR 4.0 13.5 - - - +
52B THR* 3.6 24.7 - - - +
53B ARG* 5.4 0.9 - - - -
54B GLY 5.8 1.1 - - - +
18C PHE* 4.1 19.3 - - + -
22C VAL* 3.6 31.0 - - + -
253C GLY 3.0 16.5 + - - +
254C GLY* 3.8 7.9 - - - +
255C LEU 3.2 0.2 - - - -
256C LYS* 1.3 81.5 - - + +
258C LYS* 1.3 61.0 + - + +
260C HIS* 3.8 2.3 - - + +
261C ARG* 3.1 47.3 + - - +
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Residues in contact with LYS 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C GLY* 3.3 18.3 + - - +
255C LEU* 3.1 15.7 + - + +
257C LEU* 1.3 76.9 - - + +
259C LEU* 1.3 58.6 + - - +
261C ARG* 3.6 21.2 + - - +
262C ALA* 3.0 29.1 + - - +
287C MET* 3.5 17.3 - - + +
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Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C THR* 3.6 29.4 - - + +
104C ALA* 4.0 1.8 - - + -
105C ALA* 4.3 5.2 - - + +
255C LEU* 2.7 25.4 + - + +
256C LYS* 3.6 2.7 - - - +
258C LYS* 1.3 72.2 - - - +
260C HIS* 1.3 66.9 + - - +
262C ALA* 3.2 1.2 + - - +
263C CYS* 2.9 32.9 + - - -
280C ILE* 3.8 25.1 - - + +
283C LEU* 3.9 16.8 - - + -
284C ALA* 3.6 43.3 - - + +
287C MET* 3.9 11.4 - - - +
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Residues in contact with HIS 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C PHE* 4.1 8.0 - + - -
19C ASP* 3.4 28.7 + - - -
22C VAL* 3.4 30.7 - - + +
64C PHE* 3.7 18.1 - + - -
93C MET* 3.9 14.1 - - + -
95C ASP* 3.8 13.7 + - - -
98C GLY 6.1 0.2 - - - -
101C THR* 4.2 11.0 - - + -
256C LYS* 2.8 45.9 + - - +
257C LEU* 3.8 3.6 - - - +
259C LEU* 1.3 71.9 - - - +
261C ARG* 1.3 65.3 + - - +
263C CYS* 3.1 12.4 + - - +
264C ILE* 3.1 21.3 + - + +
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Residues in contact with ARG 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B THR 3.1 26.5 + - - -
53B ARG* 4.5 2.0 - - - +
54B GLY 5.2 1.2 - - - +
57B GLU* 4.1 16.8 + - - -
22C VAL* 3.6 24.5 - - + +
25C ASP* 3.7 33.3 + - + +
26C GLY* 3.3 21.8 - - - +
257C LEU* 3.1 35.5 + - - +
258C LYS* 3.7 20.7 - - - +
260C HIS* 1.3 77.3 - - - +
262C ALA* 1.3 63.0 + - - +
264C ILE* 3.2 10.8 + - - -
265C ALA* 3.2 9.5 + - - +
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Residues in contact with ALA 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C LYS 3.0 16.2 + - - +
259C LEU 3.2 3.8 + - - +
261C ARG* 1.3 79.4 - - - +
263C CYS* 1.3 62.5 + - - +
265C ALA* 3.2 9.5 + - - +
266C LYS* 3.1 26.1 + - + +
283C LEU* 4.0 9.6 - - + -
287C MET* 3.7 24.9 - - + -
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Residues in contact with CYS 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C MET* 3.7 23.3 - - + -
101C THR* 4.8 0.2 - - - -
259C LEU* 2.9 36.3 + - - -
260C HIS* 3.1 7.8 + - - +
262C ALA* 1.3 74.1 - - - +
264C ILE* 1.3 67.2 + - - +
266C LYS* 3.0 15.9 + - - +
267C LEU* 3.1 17.0 + - - +
275C PHE* 4.2 9.7 - - + -
280C ILE* 4.0 27.8 - - - -
283C LEU* 3.8 20.0 - - - -
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Residues in contact with ILE 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 4.1 18.6 - - + -
19C ASP 5.9 0.4 - - - +
22C VAL 4.4 3.1 - - - +
23C GLY* 3.7 34.8 - - - +
26C GLY* 4.0 10.1 - - - +
28C ALA 4.4 1.1 - - - +
64C PHE* 4.0 28.9 - - + -
93C MET* 4.2 4.9 - - - -
260C HIS* 3.1 22.3 + - + +
261C ARG 3.5 7.2 - - - +
263C CYS* 1.3 76.5 - - - +
265C ALA* 1.3 64.9 + - - +
267C LEU* 3.0 33.6 + - + +
268C PHE* 3.5 22.4 - - + -
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Residues in contact with ALA 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C GLY 3.3 20.3 + - - +
261C ARG 3.2 7.0 + - - +
262C ALA* 3.5 12.3 - - - +
263C CYS 3.1 0.8 - - - -
264C ILE* 1.3 80.8 - - - +
266C LYS* 1.3 61.6 + - - +
268C PHE* 3.2 18.9 + - - +
269C GLU* 3.6 18.7 - - - +
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Residues in contact with LYS 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C SER* 4.9 0.9 + - - -
262C ALA* 3.1 19.1 + - - +
263C CYS 3.0 9.2 + - - +
265C ALA* 1.3 78.6 - - + +
267C LEU* 1.3 61.8 + - - +
269C GLU* 3.2 42.7 + - - +
270C SER* 4.2 4.9 + - - -
275C PHE* 3.5 29.0 - - + -
283C LEU* 4.0 32.3 - - + +
286C GLU* 5.4 4.4 + - - -
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Residues in contact with LEU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 4.0 25.6 - - + -
59C GLN 3.8 3.5 - - - +
61C THR 4.9 0.3 - - - +
62C ALA* 3.7 16.7 - - + +
63C ILE 4.2 5.8 - - - +
64C PHE* 5.2 0.4 - - + -
91C SER* 3.2 20.1 + - - -
92C CYS 3.7 29.6 - - - +
93C MET* 3.9 17.3 - - + -
263C CYS 3.1 10.2 + - - +
264C ILE* 3.0 28.8 + - + +
266C LYS* 1.3 77.0 - - - +
268C PHE* 1.3 60.8 + - + +
269C GLU 3.4 0.2 - - - -
270C SER 3.0 19.9 - - - +
275C PHE* 3.8 19.5 - - + -
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Residues in contact with PHE 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LYS* 3.8 35.0 - - + -
5C LEU 3.6 35.2 - - - -
6C LEU* 4.1 13.0 - - + -
27C GLY 4.8 2.0 - - - -
28C ALA* 4.0 20.2 - - + -
59C GLN* 3.0 39.4 + - - +
60C SER* 3.6 17.7 + - - -
61C THR 4.3 0.2 - - - -
62C ALA* 3.8 16.4 - - + -
264C ILE* 3.5 34.8 - - + -
265C ALA* 3.2 10.4 + - - +
266C LYS 3.1 1.2 - - - -
267C LEU* 1.3 80.9 - - + +
269C GLU* 1.3 59.5 + - - +
270C SER 3.3 2.7 - - - -
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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