Contacts of the helix formed by residues 228 - 248 (chain A) in PDB entry 1F9O
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 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A SER* 3.6 19.9 + - - +
55A GLU* 6.4 0.4 - - + -
152A MET 4.2 3.2 + - - -
154A TRP* 3.6 19.4 - - + +
227A ASN* 1.3 77.3 + - - +
229A PRO* 1.3 69.4 - - - +
230A ASP* 3.3 13.9 - - - +
231A ALA* 3.0 17.7 + - + +
232A ASP* 3.5 6.8 + - - +
298A TRP 4.6 2.2 - - - -
323A TYR* 5.0 5.4 - - - +
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Residues in contact with PRO 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ASN* 2.9 24.6 - - - +
228A ALA* 1.3 81.1 - - - +
230A ASP* 1.3 63.4 + - - +
232A ASP* 3.2 3.0 + - - +
233A ALA* 3.0 25.2 + - - +
267A LEU* 3.8 16.7 - - + +
270A SER* 3.8 20.6 - - - +
296A LEU* 4.4 11.6 - - + +
297A SER 3.3 22.0 - - - +
298A TRP 3.4 15.7 - - - +
299A TYR* 3.7 11.7 - - - -
300A TYR* 4.8 0.2 - - + -
323A TYR* 4.1 4.9 - - + -
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Residues in contact with ASP 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLU* 4.9 6.6 - - - +
228A ALA* 3.6 13.9 - - - +
229A PRO* 1.3 76.8 - - - +
231A ALA* 1.3 63.4 + - - +
233A ALA* 3.7 3.6 + - - +
234A ARG* 3.1 41.6 + - - +
322A GLY 4.8 3.3 - - - +
323A TYR* 3.7 65.1 + - + +
325A ASN* 5.0 1.2 + - - +
417A TRP* 4.9 10.2 - - - -
421A ARG* 4.8 10.3 + - - +
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Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A SER* 3.3 34.3 - - - +
55A GLU* 3.5 23.6 - - + +
58A SER* 3.5 10.3 - - - +
152A MET* 4.3 2.0 - - - -
228A ALA* 3.0 7.0 + - + +
230A ASP* 1.3 83.5 + - - +
232A ASP* 1.3 63.1 + - - +
234A ARG* 3.2 11.0 + - - +
235A ALA* 2.9 24.6 + - - +
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Residues in contact with ASP 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A SER* 4.7 0.7 - - - -
151A GLY* 3.5 8.3 - - - -
152A MET* 3.3 31.5 + - - +
227A ASN* 2.9 32.2 + - - -
228A ALA 3.5 5.0 + - - +
229A PRO 3.2 7.5 + - - +
231A ALA* 1.3 74.3 - - - +
233A ALA* 1.3 66.2 + - - +
235A ALA* 3.2 4.5 + - - +
236A VAL* 3.1 24.4 + - - +
263A MET* 3.5 26.9 - - + +
267A LEU* 3.9 20.8 - - + +
300A TYR* 4.5 1.0 + - - -
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Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A PRO 3.0 16.8 + - - +
230A ASP* 3.9 4.3 - - - +
232A ASP* 1.3 77.4 - - - +
234A ARG* 1.3 56.8 + - - +
236A VAL* 3.1 6.8 + - - +
237A GLN* 2.9 27.4 + - - +
267A LEU* 3.7 13.4 - - + +
296A LEU* 4.0 14.1 - - + -
325A ASN* 3.6 31.1 + - + +
328A ALA* 3.7 10.7 - - + +
349A TRP* 5.4 0.7 - - + -
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Residues in contact with ARG 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLU* 3.9 13.1 + - - +
58A SER* 3.0 32.4 + - - +
59A TYR* 3.5 41.7 + - - -
62A TRP* 4.3 20.3 - - + -
230A ASP* 3.1 27.3 + - - +
231A ALA* 3.2 18.8 + - - +
233A ALA* 1.3 77.5 - - - +
235A ALA* 1.3 57.6 + - - +
237A GLN* 3.5 12.8 - - - +
238A ALA* 3.0 27.0 + - - +
325A ASN* 3.8 9.4 - - - +
417A TRP* 4.0 21.8 - - - -
421A ARG* 3.3 28.5 - - - +
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Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A SER* 4.1 3.6 - - - -
61A MET* 3.5 32.5 - - + +
81A TRP* 4.3 4.0 - - + -
152A MET* 4.2 5.4 - - + -
231A ALA 2.9 12.6 + - - +
232A ASP 3.3 11.4 - - - +
233A ALA 3.1 0.2 - - - -
234A ARG* 1.3 75.0 - - - +
236A VAL* 1.3 58.3 + - - +
238A ALA* 3.4 2.9 + - - +
239A THR* 2.7 37.8 + - - -
263A MET* 4.1 16.8 - - - -
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ASP 3.3 15.3 - - - +
233A ALA* 3.1 9.8 + - - +
235A ALA* 1.3 76.7 - - + +
237A GLN* 1.3 66.1 + - - +
239A THR* 3.2 6.3 + - - -
240A TYR* 3.1 22.3 + - - +
260A ALA* 3.7 25.4 - - + +
263A MET* 5.1 2.7 - - + -
264A GLY* 4.4 8.3 - - - +
267A LEU* 5.1 1.3 - - + -
328A ALA* 4.4 11.2 - - + -
331A VAL* 4.4 12.6 - - + -
332A LEU* 3.9 39.5 - - + -
338A PHE* 4.5 6.9 - - + -
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Residues in contact with GLN 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A TRP* 3.9 15.6 - - + -
233A ALA 2.9 13.0 + - - +
234A ARG* 3.5 17.8 - - - +
236A VAL* 1.3 80.2 - - - +
238A ALA* 1.3 60.9 + - - +
240A TYR* 3.4 11.4 + - - +
241A TRP* 3.2 22.5 + - + +
325A ASN* 3.2 27.0 + - - +
327A PHE* 3.6 27.8 - - + -
328A ALA* 4.7 3.3 - - + +
331A VAL* 5.6 0.4 - - - -
420A GLN* 3.4 15.4 + - - +
421A ARG* 3.9 10.0 + - - +
424A GLU* 2.9 34.5 + - - +
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Residues in contact with ALA 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A SER 4.5 2.0 - - - +
61A MET* 4.3 9.2 - - + -
62A TRP* 3.8 50.0 - - + +
65A ALA* 3.9 6.8 - - - +
77A PHE* 4.5 1.6 - - - -
234A ARG 3.0 17.0 + - - +
235A ALA 3.9 3.4 - - - +
236A VAL 3.2 0.2 - - - -
237A GLN* 1.3 75.8 - - - +
239A THR* 1.3 64.6 + - - +
241A TRP* 3.5 4.1 + - - +
242A ALA* 3.2 21.5 + - - +
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Residues in contact with THR 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A MET* 4.7 0.5 - - - -
77A PHE* 3.6 19.8 - - + -
81A TRP* 3.0 24.4 + - - -
235A ALA 2.7 21.8 + - - -
236A VAL 3.2 4.0 + - - -
238A ALA* 1.3 78.2 - - - +
240A TYR* 1.3 58.7 + - - +
242A ALA* 3.4 2.3 + - - +
243A ASP* 3.0 26.3 + - - +
253A VAL* 5.1 0.4 - - + +
256A SER 3.9 14.4 - - - +
257A VAL* 3.9 15.9 - - + +
260A ALA* 3.6 23.3 - - + -
338A PHE* 4.0 4.9 - - + -
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Residues in contact with TYR 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A VAL 3.1 12.0 + - - +
237A GLN 3.5 8.7 - - - +
238A ALA 3.2 0.2 - - - -
239A THR* 1.3 75.3 - - - +
241A TRP* 1.3 71.7 + + - +
243A ASP* 3.2 4.7 + - - +
244A GLN* 3.0 57.3 + - + +
327A PHE* 3.6 31.4 - + - -
330A TRP* 3.8 20.1 - + - -
331A VAL* 3.8 24.2 - - + -
335A ASP* 3.6 20.9 + - - -
338A PHE* 3.4 27.3 - + + -
428A LYS* 2.7 30.0 + - - -
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Residues in contact with TRP 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A TRP* 4.8 9.6 - - + +
65A ALA* 5.4 0.7 - - + -
237A GLN* 3.2 24.6 + - + -
238A ALA* 3.5 8.4 + - - +
239A THR 3.4 0.4 - - - -
240A TYR* 1.3 80.1 - + - +
242A ALA* 1.3 60.2 + - - +
244A GLN* 3.1 8.1 + - + +
245A TRP* 2.8 82.4 + + + -
327A PHE* 3.5 27.8 - + - -
424A GLU* 2.7 36.9 + - + -
427A TYR* 4.5 12.8 - + - -
428A LYS* 3.7 40.2 - - + -
507A TYR* 4.2 16.6 - + - -
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Residues in contact with ALA 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ALA* 3.7 19.6 - - + +
74A PHE* 3.6 12.5 - - + -
77A PHE* 3.6 31.6 - - + -
238A ALA 3.2 13.9 + - - +
239A THR 3.5 9.0 - - - +
241A TRP* 1.3 76.8 - - - +
243A ASP* 1.3 58.2 + - - +
245A TRP* 4.5 2.0 - - - -
246A ALA* 3.0 32.1 + - - +
253A VAL* 4.1 4.7 - - + -
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Residues in contact with ASP 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A THR 3.0 14.7 + - - +
240A TYR* 3.3 9.7 - - - +
242A ALA* 1.3 76.8 - - - +
244A GLN* 1.3 72.2 + - - +
246A ALA* 3.8 0.9 - - - +
247A LYS* 2.9 63.8 + - - +
253A VAL* 3.9 12.7 + - - +
254A SER* 5.7 1.0 + - - -
257A VAL* 3.8 24.6 - - + +
335A ASP* 5.3 1.0 - - - +
337A ASN* 4.6 4.6 + - - +
338A PHE* 4.1 15.0 - - + -
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Residues in contact with GLN 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A TYR* 3.0 60.9 + - + +
241A TRP* 3.1 17.3 + - + +
243A ASP* 1.3 88.3 + - - +
245A TRP* 1.3 68.1 + - + +
247A LYS* 3.9 10.3 - - - +
248A GLU* 3.1 30.7 + - + +
335A ASP* 4.8 4.2 + - - -
428A LYS* 3.5 10.6 + - - -
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Residues in contact with TRP 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A TRP* 5.3 6.7 - + - -
65A ALA* 3.3 39.9 - - + -
66A MET* 3.8 31.0 - - + -
69A ARG* 3.6 32.0 - - + +
74A PHE* 3.9 9.0 - - + -
241A TRP* 2.8 68.4 + + + +
242A ALA* 4.2 1.3 - - - +
244A GLN* 1.3 75.2 - - + +
246A ALA* 1.3 66.5 + - - +
248A GLU* 3.4 28.8 + - - +
249A GLN* 3.4 20.8 + - - +
507A TYR* 5.1 7.4 - - - -
622A VAL* 6.5 0.2 - - + -
625A ILE* 4.2 21.0 - - + +
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Residues in contact with ALA 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PHE* 3.6 26.6 - - + -
242A ALA 3.0 20.3 + - - +
243A ASP* 3.8 3.8 - - - +
245A TRP* 1.3 74.2 - - - +
247A LYS* 1.3 60.3 + - + +
249A GLN* 2.9 18.5 + - - +
251A LYS* 2.9 39.8 + - + +
252A SER* 4.1 8.5 - - - -
253A VAL* 4.4 7.4 - - + +
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Residues in contact with LYS 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A ASP* 2.9 50.4 + - - +
244A GLN* 3.9 10.8 - - - +
246A ALA* 1.3 73.9 - - + +
248A GLU* 1.3 59.7 + - - +
249A GLN 2.9 10.9 + - - -
250A GLY* 3.0 13.0 + - - +
251A LYS 3.7 8.5 - - - +
252A SER* 6.0 3.4 - - - -
337A ASN* 3.1 35.4 + - - +
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Residues in contact with GLU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ALA* 3.0 34.3 + - - +
2A SER* 3.3 29.7 + - - +
3A SER* 5.1 7.3 + - - -
69A ARG* 4.4 2.9 + - - -
244A GLN* 3.1 15.9 + - - +
245A TRP* 3.6 29.4 - - - +
246A ALA 3.2 0.6 - - - -
247A LYS* 1.3 76.9 - - + +
249A GLN* 1.3 57.3 + - - +
250A GLY 3.6 0.4 - - - -
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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
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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