Contacts of the helix formed by residues 241 - 262 (chain L) in PDB entry 3FKS
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 ALA 241 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77L LEU 3.8 4.3 - - - +
78L PHE* 3.6 31.8 + - - +
79L GLY 4.0 11.2 - - - +
240L GLU* 1.3 78.5 - - - +
242L ALA* 1.3 66.5 + - - +
243L PRO* 3.3 12.6 - - + -
244L LEU* 3.0 22.9 + - + +
245L GLN* 3.3 6.2 + - - +
287O THR* 5.1 2.7 - - - -
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Residues in contact with ALA 242 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240L GLU 3.6 1.6 + - - -
241L ALA* 1.3 69.9 - - - +
243L PRO* 1.3 72.7 - - + +
245L GLN* 3.0 10.6 + - - +
246L TYR* 2.9 19.6 + - - +
279L ALA* 3.7 15.6 - - + +
282L GLN* 3.4 36.3 - - + +
283L LEU* 3.5 18.2 - - + -
287O THR* 4.1 9.0 - - + +
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Residues in contact with PRO 243 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39L GLY* 5.4 2.0 - - - +
64L MET* 6.1 0.4 - - - -
76L VAL* 3.8 30.3 - - + -
77L LEU 3.2 25.6 - - - +
78L PHE* 4.0 17.3 - - + -
241L ALA* 3.4 5.4 - - + -
242L ALA* 1.3 96.6 - - + +
244L LEU* 1.3 54.4 + - - +
246L TYR* 3.1 9.4 + - + +
247L LEU* 2.8 39.1 + - + +
283L LEU* 3.6 14.3 - - + -
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Residues in contact with LEU 244 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78L PHE* 3.3 49.8 - - + +
111L ASP* 5.3 6.1 - - - +
112L ALA* 3.2 29.3 - - + +
113L LEU* 4.1 18.4 - - + +
236L ALA* 4.0 2.5 - - + -
240L GLU* 3.4 39.5 - - + +
241L ALA* 3.0 14.1 + - + +
243L PRO* 1.3 75.9 - - - +
245L GLN* 1.3 60.0 + - - +
247L LEU* 4.7 0.9 - - + -
248L ALA* 2.9 27.5 + - - +
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Residues in contact with GLN 245 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208L VAL* 3.7 17.2 - - + +
209L GLY* 4.4 12.0 + - - -
236L ALA* 3.7 24.9 - - + +
237L THR 3.4 18.0 + - - +
238L ALA* 3.7 16.0 + - - +
240L GLU 3.6 13.6 + - - +
241L ALA 3.3 8.5 + - - +
242L ALA* 3.0 9.9 + - - +
244L LEU* 1.3 76.3 - - + +
246L TYR* 1.3 57.5 + - - +
249L PRO* 3.2 22.3 - - - +
275L LYS 3.8 9.7 - - - +
276L GLN* 3.8 4.9 - - - +
279L ALA* 3.3 25.0 - - + +
286O ALA* 5.4 9.8 - - - +
287O THR* 4.6 9.8 - - - +
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Residues in contact with TYR 246 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52L GLU* 4.6 5.7 + - - -
64L MET* 5.0 13.5 - - + -
66L LEU* 5.2 8.4 - - + +
132L GLN* 3.3 15.8 + - - -
242L ALA 2.9 11.8 + - - +
243L PRO* 3.1 9.6 + - + +
245L GLN* 1.3 79.4 - - - +
247L LEU* 1.3 87.0 + - + +
249L PRO* 3.6 0.2 - - - +
250L PHE* 3.4 20.7 - + - -
276L GLN* 3.6 14.1 + - - -
279L ALA* 4.6 1.5 - - - +
280L TYR* 3.6 42.2 - + + +
283L LEU* 4.1 24.0 - - + -
303L LEU* 3.6 22.2 - - + -
306L ARG* 3.3 21.9 + - - -
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Residues in contact with LEU 247 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64L MET* 4.3 12.3 - - + -
78L PHE* 3.7 24.5 - - + -
97L VAL* 3.4 34.3 - - + -
112L ALA* 4.5 6.3 - - + -
113L LEU* 4.2 9.2 - - + -
131L ALA* 4.8 6.5 - - + -
243L PRO* 2.8 26.8 + - + +
244L LEU* 4.1 3.6 - - - +
246L TYR* 1.3 103.9 - - + +
248L ALA* 1.3 67.2 + - - +
250L PHE* 2.8 9.3 + - + -
251L THR* 2.8 39.3 + - + -
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Residues in contact with ALA 248 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112L ALA* 3.9 9.6 - - + +
206L VAL* 4.2 7.0 - - + -
208L VAL* 3.8 11.7 - - + -
234L VAL* 4.4 4.5 - - + +
236L ALA* 3.4 24.9 - - + +
244L LEU 2.9 17.5 + - - +
245L GLN 3.9 1.1 - - - +
247L LEU* 1.3 75.0 - - - +
249L PRO* 1.3 71.7 - - + +
251L THR* 3.2 6.4 + - - -
252L ALA* 3.0 29.7 + - - +
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Residues in contact with PRO 249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206L VAL* 4.2 6.5 - - + -
208L VAL* 3.7 17.3 - - + -
245L GLN 3.2 15.5 - - - +
246L TYR 3.6 4.0 - - - +
247L LEU 3.5 3.4 - - - -
248L ALA* 1.3 92.3 - - + +
250L PHE* 1.3 59.1 + - - +
252L ALA* 3.9 0.3 - - - +
253L ALA 3.2 14.9 + - - -
270L TYR* 3.2 29.1 - - + -
273L LEU* 4.4 3.8 - - + -
276L GLN* 3.3 33.7 - - + +
307L LEU* 3.5 21.7 - - + +
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Residues in contact with PHE 250 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131L ALA* 3.7 16.3 - - + +
132L GLN* 3.2 33.0 - - - +
246L TYR* 3.4 27.8 - + - -
247L LEU* 2.8 10.9 + - + +
249L PRO* 1.3 77.7 - - - +
251L THR* 1.3 61.5 - - - +
253L ALA* 2.8 25.3 + - - +
254L SER 3.3 3.6 + - - -
276L GLN* 3.8 8.3 - - - -
303L LEU* 3.5 44.9 - - + -
306L ARG* 3.6 28.0 - - + -
307L LEU* 4.1 18.4 - - + -
310L ARG* 3.7 22.5 + - - -
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Residues in contact with THR 251 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97L VAL* 5.3 1.1 - - + -
99L VAL* 3.5 28.2 - - + +
112L ALA* 2.8 30.6 + - - +
131L ALA* 3.8 25.8 - - + +
234L VAL* 4.5 3.6 - - - +
247L LEU* 2.8 28.3 + - + +
248L ALA* 3.2 10.9 + - - -
250L PHE* 1.3 72.0 - - - +
252L ALA* 1.3 64.4 + - - +
254L SER* 3.0 15.9 + - - +
255L ILE* 3.1 18.2 + - - +
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Residues in contact with ALA 252 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204L VAL* 3.7 11.6 - - + +
206L VAL* 3.4 30.7 - - + -
234L VAL* 4.0 19.7 - - + -
248L ALA 3.0 19.8 + - - +
249L PRO 3.9 2.7 - - - +
251L THR* 1.3 77.8 + - - +
253L ALA* 1.3 60.9 + - - +
255L ILE* 3.4 14.3 + - - +
256L GLY* 3.4 15.2 + - - -
268L ILE* 4.4 4.4 - - - +
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Residues in contact with ALA 253 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249L PRO 3.2 9.2 + - - +
250L PHE 2.8 14.6 + - - +
252L ALA* 1.3 76.4 - - - +
254L SER* 1.3 57.3 + - - +
256L GLY* 3.3 2.3 + - - -
257L GLU* 2.9 32.6 + - + +
268L ILE* 5.3 1.8 - - - -
270L TYR* 3.4 25.4 - - - +
307L LEU* 4.1 6.3 - - + +
310L ARG* 3.6 24.0 - - + +
323L LEU* 4.1 8.0 - - + +
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Residues in contact with SER 254 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99L VAL* 4.3 6.3 - - - -
101L VAL* 3.4 22.0 - - - +
129L SER* 4.2 9.2 + - - -
130L ARG 2.8 27.7 + - - -
131L ALA* 4.1 0.9 + - - -
133L VAL* 3.6 3.3 - - - +
250L PHE 3.3 3.4 + - - -
251L THR 3.0 10.0 + - - -
253L ALA* 1.3 76.9 - - - +
255L ILE* 1.3 66.1 + - - +
257L GLU* 3.2 16.9 + - - +
258L TRP 3.3 9.7 + - - -
310L ARG* 2.9 20.7 + - - +
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Residues in contact with ILE 255 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99L VAL* 4.1 11.2 - - + -
100L PRO* 3.5 24.9 - - + +
101L VAL* 3.9 10.9 - - + +
102L GLY 5.3 1.2 + - - -
105L LEU* 3.5 25.4 - - + -
110L VAL* 6.1 1.6 - - + -
114L GLY* 6.2 2.9 - - - -
204L VAL* 4.5 6.3 - - + -
232L ILE* 3.8 31.9 - - + -
234L VAL* 4.4 11.0 - - + -
251L THR* 3.1 18.4 - - - +
252L ALA* 3.5 15.7 - - - +
253L ALA 3.3 0.2 - - - -
254L SER* 1.3 78.8 - - - +
256L GLY* 1.3 59.4 + - - +
258L TRP* 3.7 9.2 - - - +
259L PHE* 3.4 16.5 - - - -
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Residues in contact with GLY 256 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204L VAL* 4.1 14.3 - - - +
252L ALA 3.4 6.3 + - - -
253L ALA 3.3 6.3 + - - -
254L SER 3.2 0.2 - - - -
255L ILE* 1.3 76.0 - - - +
257L GLU* 1.3 64.1 + - - +
258L TRP 3.2 2.7 - - - -
259L PHE* 3.3 17.8 + - - +
260L ARG* 3.3 16.6 + - - +
266L ALA* 3.8 7.0 - - - +
268L ILE* 5.9 0.4 - - - -
323L LEU* 4.1 19.2 - - - +
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Residues in contact with GLU 257 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129L SER* 5.9 0.5 - - - -
133L VAL* 3.5 20.0 - - - +
135L ALA* 5.6 0.2 - - - -
253L ALA 2.9 17.7 + - - +
254L SER* 3.2 9.3 + - - +
256L GLY* 1.3 76.0 - - - +
258L TRP* 1.3 59.3 + - - +
260L ARG* 3.2 33.9 + - - +
261L ASP* 2.8 43.3 + - - +
310L ARG* 2.7 58.5 + - + +
323L LEU* 4.1 11.4 - - + -
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Residues in contact with TRP 258 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101L VAL* 3.8 34.3 - - + -
102L GLY* 3.9 15.3 - - - +
103L PRO* 3.2 40.1 - - + +
126L ALA* 4.6 11.4 + - + +
254L SER 3.3 5.8 + - - -
255L ILE 3.7 12.6 - - - +
256L GLY 3.2 0.4 - - - -
257L GLU* 1.3 76.9 - - - +
259L PHE* 1.3 110.8 + + - +
261L ASP* 3.4 4.2 + - - +
262L ASN* 3.1 54.6 + - + +
264L LYS* 3.9 25.4 - - + -
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Residues in contact with PHE 259 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102L GLY 5.2 2.9 - - - -
103L PRO* 5.1 6.5 - - + -
106L LEU* 4.0 16.4 - - + -
202L TYR* 3.6 42.0 - + + -
204L VAL* 4.7 3.1 - - + -
232L ILE* 3.9 28.0 - - + -
255L ILE 3.4 22.9 - - - -
256L GLY* 3.6 13.7 - - - +
258L TRP* 1.3 104.9 - + + +
260L ARG* 1.3 63.0 + - - +
262L ASN 3.1 5.9 + - - -
264L LYS* 2.8 46.0 + - + +
265L HIS 4.4 0.2 - - - +
266L ALA* 3.8 20.0 - - + -
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Residues in contact with ARG 260 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133L VAL* 5.2 6.5 - - - +
134L LYS 5.7 1.6 + - - -
136L PRO* 3.5 27.6 - - - +
256L GLY 3.3 5.9 + - - +
257L GLU* 3.1 44.4 + - - +
259L PHE* 1.3 79.7 - - - +
261L ASP* 1.3 93.9 + - - +
263L GLY 3.8 1.2 + - - -
264L LYS 3.6 8.5 + - - -
310L ARG 2.9 28.6 + - - -
312L ALA* 4.5 5.6 - - - +
314L LEU* 3.2 36.7 - - + +
318L GLU 4.7 0.3 - - - +
321L GLY* 3.2 15.4 + - - -
322L SER* 3.9 25.5 + - - +
323L LEU* 4.0 10.1 - - + +
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Residues in contact with ASP 261 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257L GLU* 2.8 28.2 + - - +
258L TRP* 4.1 5.1 - - - +
260L ARG* 1.3 110.4 + - - +
262L ASN* 1.3 64.9 + - - +
263L GLY 3.4 3.0 + - - -
314L LEU* 3.9 10.3 - - - +
318L GLU* 4.1 11.6 - - - +
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Residues in contact with ASN 262 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258L TRP* 3.1 67.4 + - + +
259L PHE 3.1 1.9 + - - +
261L ASP* 1.3 84.1 - - - +
263L GLY* 1.3 61.7 + - - +
264L LYS* 2.8 24.0 + - + +
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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
------------------------------------------------------------
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