Contacts of the helix formed by residues 235 - 255 (chain E) in PDB entry 1XPU
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 PRO 235 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D HIS* 3.5 30.0 - - + +
234E GLU* 1.3 96.5 - - + +
236E ALA* 1.3 65.0 + - - +
237E SER* 3.2 20.2 - - - +
238E ARG* 3.1 25.1 + - + +
239E HIS* 3.4 6.9 - - - -
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Residues in contact with ALA 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234E GLU 3.8 0.2 + - - -
235E PRO* 1.3 70.8 - - - +
237E SER* 1.3 64.4 + - - +
239E HIS* 3.4 19.4 + - + +
240E VAL* 3.3 25.5 + - - +
273E ALA* 3.8 6.2 - - - +
276E THR* 3.2 28.0 - - - +
277E VAL* 3.6 10.7 - - + +
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Residues in contact with SER 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E PRO* 3.6 18.3 - - - +
236E ALA* 1.3 78.7 - - - +
238E ARG* 1.3 57.1 + - - +
240E VAL* 3.5 5.6 + - - +
241E GLN* 3.0 28.2 + - - +
277E VAL* 3.8 15.5 - - - +
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Residues in contact with ARG 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E SER 2.7 29.5 + - - -
71E SER* 3.0 29.2 + - - -
72E TYR* 3.3 9.3 + - - +
73E LEU* 3.3 27.1 - - - +
229E ALA 4.5 3.0 + - - -
230E SER* 4.1 5.6 - - - -
234E GLU* 3.1 41.0 + - + +
235E PRO* 3.1 25.2 + - + +
237E SER* 1.3 79.5 + - - +
239E HIS* 1.3 65.2 + - - +
241E GLN* 3.0 30.6 + - - +
242E VAL* 2.9 41.4 + - - +
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Residues in contact with HIS 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E ILE* 3.0 42.6 + - + +
210E ASP* 3.6 24.1 + - - -
230E SER* 3.0 17.9 + - - -
231E THR 3.2 27.1 - - - -
232E PHE* 4.6 1.8 + - - -
234E GLU* 3.3 20.3 + - + -
235E PRO 3.4 12.8 - - - -
236E ALA* 3.4 15.8 + - + +
238E ARG* 1.3 74.9 - - - +
240E VAL* 1.3 63.6 + - - +
242E VAL* 3.6 0.3 + - - +
243E ALA* 3.2 18.4 + - - +
269E ARG 5.6 1.1 - - - -
270E LEU* 4.6 2.2 - - + -
273E ALA* 3.6 21.1 - - + -
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Residues in contact with VAL 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E ALA 3.3 12.7 + - - +
237E SER* 3.5 9.9 - - - +
238E ARG 3.2 0.2 - - - -
239E HIS* 1.3 78.4 - - - +
241E GLN* 1.3 64.9 + - - +
243E ALA* 3.2 4.7 + - - +
244E GLU* 3.0 48.1 + - - +
270E LEU* 4.7 3.4 - - - -
273E ALA* 3.9 13.5 - - + -
274E TYR* 3.6 34.0 + - + +
277E VAL* 3.8 23.6 - - + -
296E ARG* 4.0 5.4 - - - +
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Residues in contact with GLN 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E GLU* 3.2 37.5 + - - +
66E ARG* 4.2 4.9 - - - +
72E TYR* 3.6 17.5 + - + +
73E LEU* 4.9 0.9 - - - -
74E ALA* 4.9 7.3 + - - +
237E SER 3.0 18.6 + - - +
238E ARG* 3.0 35.6 + - - +
240E VAL* 1.3 77.7 - - - +
242E VAL* 1.3 56.3 + - - +
244E GLU* 3.1 7.1 + - - +
245E MET* 2.9 36.1 + - + +
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Residues in contact with VAL 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E SER 3.8 5.6 - - - +
72E TYR* 5.2 0.9 - - - -
207E LEU* 3.5 23.6 - - + -
209E ILE* 4.8 1.6 - - + -
228E VAL* 3.5 19.6 - - + +
229E ALA 4.4 11.2 - - - +
230E SER* 3.8 20.2 - - - +
238E ARG* 2.9 56.2 + - - +
239E HIS 3.9 4.3 - - - +
241E GLN* 1.3 72.9 - - - +
243E ALA* 1.3 62.3 + - - +
245E MET* 3.5 5.8 + - - +
246E VAL* 3.3 24.8 + - - +
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Residues in contact with ALA 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E LEU* 3.7 11.7 - - + -
209E ILE* 3.8 7.4 - - + +
239E HIS 3.2 7.5 + - - +
240E VAL 3.6 2.9 - - - +
241E GLN 3.2 0.2 - - - -
242E VAL* 1.3 79.6 - - - +
244E GLU* 1.3 61.6 + - - +
246E VAL* 3.4 2.1 + - - +
247E ILE* 3.2 12.1 + - - +
270E LEU* 3.4 42.0 - - + -
274E TYR* 4.7 3.4 - - - +
300E PHE* 3.1 27.5 - - + -
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Residues in contact with GLU 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E VAL* 3.0 26.2 + - - +
241E GLN* 3.7 5.6 - - - +
243E ALA* 1.3 73.4 - - - +
245E MET* 1.3 68.6 + - + +
247E ILE* 3.5 10.1 - - + +
248E GLU* 3.2 36.8 + - + +
274E TYR* 3.1 20.2 + - - +
296E ARG* 2.6 36.5 + - - -
300E PHE* 5.4 0.2 - - - -
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Residues in contact with MET 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E VAL* 4.2 11.2 - - + +
55E LEU 4.0 13.0 - - - +
56E GLU* 3.2 54.5 - - + +
66E ARG* 5.6 0.7 - - - -
72E TYR* 3.6 48.3 - - + -
93E THR* 5.5 3.6 - - - -
94E GLY* 4.7 2.9 - - - -
241E GLN* 2.9 25.1 + - + +
242E VAL 3.8 2.7 - - - +
244E GLU* 1.3 80.0 - - + +
246E VAL* 1.3 56.4 + - - +
248E GLU* 4.3 2.5 - - - +
249E LYS* 3.2 28.9 + - - +
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Residues in contact with VAL 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E TYR* 4.3 4.3 - - + -
205E MET* 3.7 26.5 - - + +
206E VAL 6.3 0.2 - - - -
207E LEU* 3.7 34.3 - - + -
228E VAL* 3.8 26.5 - - + -
242E VAL 3.3 17.1 + - - +
243E ALA 3.7 4.3 - - - +
244E GLU 3.2 0.6 - - - -
245E MET* 1.3 76.0 - - - +
247E ILE* 1.3 54.6 + - - +
249E LYS* 3.2 3.1 + - - +
250E ALA* 2.7 36.0 + - - +
262E ILE* 4.0 24.7 - - + -
300E PHE* 5.1 0.9 - - + -
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Residues in contact with ILE 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243E ALA 3.2 8.5 + - - +
244E GLU* 3.5 17.9 - - + +
246E VAL* 1.3 79.0 - - - +
248E GLU* 1.3 72.1 + - + +
250E ALA* 3.4 4.0 - - - +
251E LYS* 2.8 47.3 + - - +
262E ILE* 3.9 13.0 - - + -
300E PHE* 3.6 52.9 - - + +
303E ALA* 4.2 3.4 - - + -
313E LEU* 3.9 12.1 - - + -
315E ILE* 3.7 19.7 - - + -
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Residues in contact with GLU 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E THR* 3.9 28.7 + - - +
94E GLY* 3.8 7.0 - - - +
133E PHE* 4.8 4.3 - - - -
244E GLU* 3.2 25.5 + - + +
245E MET* 4.3 2.9 - - - +
247E ILE* 1.3 79.2 - - + +
249E LYS* 1.3 65.4 + - - +
250E ALA 3.1 0.9 - - - -
251E LYS* 3.1 28.6 + - - +
252E ARG* 2.7 59.3 + - - +
299E ARG* 5.1 5.0 + - - -
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Residues in contact with LYS 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E VAL* 3.5 19.5 - - + +
72E TYR* 3.3 20.2 - - - +
94E GLY* 3.3 26.4 - - - +
96E THR* 3.1 29.1 + - - +
121E PHE* 5.0 6.3 - - - -
203E VAL* 6.3 1.1 - - - -
205E MET* 3.7 15.5 - - + -
226E GLU* 3.6 24.1 + - - -
245E MET 3.2 19.9 + - - +
246E VAL 3.6 3.1 - - - +
248E GLU* 1.3 77.8 - - - +
250E ALA* 1.3 59.4 + - - +
252E ARG* 3.7 2.3 + - - +
253E LEU* 3.4 39.3 + - + +
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Residues in contact with ALA 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E MET* 4.1 8.0 - - - -
246E VAL 2.7 20.7 + - - +
247E ILE* 3.4 6.7 - - - +
249E LYS* 1.3 72.2 - - - +
251E LYS* 1.3 64.3 + - - +
253E LEU* 3.4 3.7 + - - +
254E VAL* 3.3 29.4 + - - +
260E VAL* 4.1 11.3 - - + +
262E ILE* 3.8 15.0 - - + -
313E LEU* 3.7 26.9 - - + -
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Residues in contact with LYS 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E LEU* 3.5 44.1 - - + +
133E PHE* 3.4 35.9 - - + -
247E ILE* 2.8 36.3 + - + +
248E GLU* 3.1 37.6 + - - +
250E ALA* 1.3 76.9 - - - +
252E ARG* 1.3 68.5 + - - +
254E VAL 3.4 1.2 + - - -
255E GLU* 3.1 31.8 + - - +
299E ARG* 5.2 5.0 + - - +
303E ALA* 3.8 14.7 - - - +
313E LEU* 5.1 3.1 - - + -
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Residues in contact with ARG 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E ARG* 3.6 22.3 - - - +
93E THR* 3.5 12.7 + - - +
94E GLY 3.8 18.2 - - - +
95E ASP* 3.6 20.4 - - - +
120E ASN* 3.9 13.2 + - - +
131E ILE* 3.3 21.2 - - - +
133E PHE* 3.9 19.4 - - - -
248E GLU* 2.7 44.4 + - - +
249E LYS 4.1 4.5 - - - +
251E LYS* 1.3 82.0 - - - +
253E LEU* 1.3 60.8 + - + +
255E GLU* 2.8 56.5 + - - +
256E HIS* 3.6 14.7 + - - -
28F ARG* 3.7 11.9 - - - +
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Residues in contact with LEU 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E THR* 5.2 6.3 - - - +
120E ASN* 5.1 11.9 - - + +
121E PHE* 4.2 17.5 - - + -
203E VAL* 4.3 20.4 - - + -
205E MET* 5.1 2.2 - - - -
249E LYS* 3.4 38.6 + - + +
250E ALA* 3.8 1.8 - - - +
251E LYS 3.2 0.4 - - - -
252E ARG* 1.3 76.4 - - + +
254E VAL* 1.3 59.9 + - - +
255E GLU 3.1 1.3 - - - -
256E HIS* 3.0 20.2 + - + +
258E LYS* 3.2 50.8 + - + +
260E VAL* 3.7 25.4 - - + -
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Residues in contact with VAL 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E LEU* 3.7 16.6 - - + -
135E ASN* 4.3 6.6 + - - +
250E ALA 3.3 16.0 + - - +
253E LEU* 1.3 71.4 - - - +
255E GLU* 1.3 56.8 + - - +
256E HIS 3.1 5.6 - - - -
257E LYS* 3.0 18.1 + - - +
258E LYS 3.6 10.3 - - - +
260E VAL* 3.9 10.1 - - + -
307E VAL* 3.7 23.6 - - + -
310E GLY 3.9 4.2 - - - +
311E GLY 4.1 1.1 - - - -
312E SER 3.5 47.3 - - - +
313E LEU* 4.0 12.6 - - + +
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Residues in contact with GLU 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E ASN* 4.1 19.7 - - + +
130E LYS 3.4 25.4 + - - +
131E ILE* 3.4 7.3 - - - +
132E LEU* 3.1 27.6 + - - +
135E ASN* 4.7 4.3 - - - +
251E LYS 3.1 17.9 + - - +
252E ARG* 2.8 57.4 + - - +
253E LEU 3.1 0.2 - - - -
254E VAL* 1.3 77.1 - - - +
256E HIS* 1.3 64.9 + - + +
257E LYS* 3.3 7.2 + - - +
28F ARG* 3.8 15.1 + - - -
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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
------------------------------------------------------------
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