Contacts of the helix formed by residues 388 - 409 (chain E) in PDB entry 2I2X
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 ASN 388 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385E ASP* 3.2 7.4 + - + +
387E ASP* 1.3 78.0 - - - +
389E ILE* 1.3 65.5 + - - +
390E TYR* 3.4 11.1 + - - +
391E LEU* 2.8 47.0 + - + +
392E ARG* 3.1 25.9 + - - +
434E ASP 5.5 2.0 + - - -
436E MET* 3.8 25.6 - - - +
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Residues in contact with ILE 389 (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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5E ARG* 3.1 37.5 - - - +
189E GLY 4.1 12.1 - - - +
190E CYS* 4.3 12.1 - - + +
193E SER* 4.1 19.1 - - - +
194E ILE* 4.1 27.6 - - + +
252E PRO* 5.1 0.9 - - - +
387E ASP 3.7 2.5 + - - +
388E ASN* 1.3 72.1 + - - +
390E TYR* 1.3 65.7 + - - +
392E ARG* 3.4 33.2 + - - +
393E ALA* 3.5 11.1 - - - +
436E MET* 4.0 25.4 - - + -
440E MET* 5.5 0.2 - - + -
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Residues in contact with TYR 390 (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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185E LEU* 3.5 25.1 - - + -
190E CYS* 3.7 18.2 - - - -
388E ASN* 3.2 5.7 + - - +
389E ILE* 1.3 78.6 - - - +
391E LEU* 1.3 74.5 + - + +
393E ALA* 3.1 7.5 + - - +
394E LYS* 2.9 40.6 + - + +
432E LEU* 3.8 9.7 - - - +
433E PRO 2.6 30.4 + - - -
434E ASP 3.9 8.5 - - - -
435E ASP 3.6 13.5 - - - -
436E MET* 3.6 35.9 - - + -
439E PHE* 3.4 42.7 - + + +
440E MET* 5.4 0.2 - - - -
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Residues in contact with LEU 391 (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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385E ASP* 3.3 31.9 - - + +
388E ASN* 2.8 32.3 + - + +
390E TYR* 1.3 75.3 - - + +
392E ARG* 1.3 57.9 + - - +
394E LYS* 2.9 32.9 + - - +
395E ASN* 2.8 39.9 + - - +
434E ASP* 3.7 40.2 - - + +
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Residues in contact with ARG 392 (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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5E ARG* 3.9 4.6 - - - +
6E TYR 4.8 1.0 + - - +
193E SER* 5.0 1.0 + - - -
252E PRO* 3.1 40.3 + - + +
255E LEU* 4.3 9.3 - - - +
256E VAL* 3.2 10.9 - - - +
259E GLU* 2.7 44.0 + - - -
381E SER 3.9 4.4 - - - +
382E ILE* 3.4 41.1 - - + +
385E ASP* 3.7 11.3 + - - +
386E GLY* 3.1 25.1 + - - -
388E ASN 3.1 23.7 + - - +
389E ILE* 3.4 26.1 + - - +
391E LEU* 1.3 75.9 - - - +
393E ALA* 1.3 60.6 + - - +
395E ASN 3.6 0.3 + - - -
396E ALA* 3.0 28.8 + - - +
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Residues in contact with ALA 393 (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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185E LEU* 3.8 17.9 - - + -
189E GLY* 4.1 16.2 - - - -
249E ILE* 4.2 8.3 - - + +
252E PRO* 3.7 22.4 - - + -
389E ILE 3.5 11.9 - - - +
390E TYR* 3.1 9.1 + - - +
392E ARG* 1.3 81.8 - - - +
394E LYS* 1.3 57.5 + - - +
396E ALA* 3.2 4.0 - - - +
397E ALA* 3.0 28.2 + - - +
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Residues in contact with LYS 394 (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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185E LEU* 4.1 17.9 - - + +
390E TYR* 2.9 44.3 + - + +
391E LEU* 2.9 27.5 + - - +
393E ALA* 1.3 73.4 - - - +
395E ASN* 1.3 61.5 + - - +
397E ALA* 3.2 6.3 + - - +
398E ILE* 2.9 48.3 + - + +
429E LEU* 4.0 19.8 + - + +
430E GLU* 5.6 1.0 + - - +
432E LEU* 4.0 14.5 + - + -
433E PRO 3.5 10.0 + - - -
434E ASP* 3.2 20.2 + - - -
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Residues in contact with ASN 395 (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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381E SER* 3.0 34.0 + - - +
384E LYS* 3.4 23.0 - - - +
385E ASP* 2.8 32.4 + - - +
391E LEU* 2.8 27.9 + - - +
392E ARG 4.0 0.2 - - - +
394E LYS* 1.3 73.2 + - - +
396E ALA* 1.3 56.4 + - - +
398E ILE* 4.3 9.8 - - - +
399E GLU* 2.6 38.1 + - - +
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Residues in contact with ALA 396 (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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248E ALA* 3.8 22.8 - - - +
252E PRO* 4.3 1.1 - - + -
378E VAL* 4.3 7.5 - - + +
381E SER* 3.3 12.0 + - - -
382E ILE* 3.7 22.7 - - + -
392E ARG 3.0 15.8 + - - +
393E ALA* 3.2 14.8 + - - +
395E ASN* 1.3 75.5 - - - +
397E ALA* 1.3 56.6 + - - +
399E GLU* 3.3 2.4 + - - +
400E CYS* 2.9 29.3 + - - +
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Residues in contact with ALA 397 (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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185E LEU* 5.5 0.4 - - + -
245E ILE* 3.9 9.9 - - + +
248E ALA* 4.3 5.1 - - - +
249E ILE* 3.8 20.8 - - + +
393E ALA 3.0 12.6 + - - +
394E LYS* 3.6 8.1 - - - +
395E ASN 3.2 0.2 - - - -
396E ALA* 1.3 75.0 - - - +
398E ILE* 1.3 62.3 + - - +
400E CYS* 3.4 8.6 - - - +
401E CYS* 3.2 27.4 + - - -
429E LEU* 3.8 27.1 - - + +
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Residues in contact with ILE 398 (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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394E LYS* 2.9 41.8 + - + +
395E ASN* 3.9 8.1 - - - +
397E ALA* 1.3 73.0 - - - +
399E GLU* 1.3 62.8 + - - +
401E CYS* 3.2 9.2 + - - +
402E ASN* 2.7 44.1 + - - +
426E LYS* 5.9 4.5 - - + +
429E LEU* 4.0 32.1 - - + +
430E GLU* 4.4 23.6 - - + +
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Residues in contact with GLU 399 (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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377E ARG* 2.5 55.9 + - - +
378E VAL* 4.2 3.4 - - - -
381E SER* 3.4 28.0 - - - +
384E LYS* 4.8 6.9 + - - -
395E ASN 2.6 23.0 + - - +
396E ALA 3.4 2.7 - - - +
398E ILE* 1.3 73.5 - - - +
400E CYS* 1.3 53.1 + - - +
402E ASN* 2.9 12.5 + - - +
403E ILE* 2.8 47.7 + - + +
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Residues in contact with CYS 400 (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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244E VAL* 4.0 28.7 - - - -
245E ILE* 4.1 13.9 - - + -
248E ALA* 3.7 13.2 - - + -
369E MET* 3.8 23.8 - - + -
378E VAL* 4.8 1.7 - - + +
396E ALA 2.9 17.6 + - - +
397E ALA* 3.4 8.7 - - - +
399E GLU* 1.3 75.9 - - - +
401E CYS* 1.3 63.0 + - - +
403E ILE* 3.3 11.9 + - - +
404E ILE* 2.9 34.6 + - - +
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Residues in contact with CYS 401 (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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245E ILE* 3.9 17.5 - - - -
397E ALA 3.2 14.0 + - - +
398E ILE* 3.4 10.8 - - - +
399E GLU 3.2 0.8 - - - -
400E CYS* 1.3 79.4 - - - +
402E ASN* 1.3 56.2 - - - +
404E ILE* 3.3 1.7 + - - +
405E GLU* 2.9 33.5 + - - +
422E LEU* 3.8 30.3 - - + +
426E LYS* 4.0 43.7 - - + +
429E LEU* 4.5 4.9 - - - -
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Residues in contact with ASN 402 (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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377E ARG* 4.1 15.5 - - - +
398E ILE* 2.7 40.2 + - - +
399E GLU* 2.9 13.6 + - - +
401E CYS* 1.3 73.2 - - - +
403E ILE* 1.3 65.1 + - - +
405E GLU* 3.2 8.6 + - - +
406E GLU* 3.0 32.5 + - - +
426E LYS* 2.9 25.6 + - - +
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Residues in contact with ILE 403 (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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368E TYR* 3.7 15.1 - - + -
369E MET* 4.7 6.1 - - + -
374E ASN* 3.4 56.1 - - + +
377E ARG* 3.9 28.5 - - + +
378E VAL* 3.4 22.2 - - + -
399E GLU* 2.8 30.4 + - + +
400E CYS* 3.5 8.3 - - - +
402E ASN* 1.3 71.0 - - - +
404E ILE* 1.3 66.3 + - + +
406E GLU* 3.0 19.2 + - - +
407E GLY 3.0 10.2 + - - -
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Residues in contact with ILE 404 (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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241E THR* 4.5 2.2 - - + -
244E VAL* 4.4 8.1 - - + -
365E PRO* 3.5 39.9 - - + +
368E TYR* 4.2 15.3 - - + -
369E MET* 3.9 18.4 - - + -
400E CYS* 2.9 25.7 + - - +
401E CYS 3.8 2.9 - - - +
403E ILE* 1.3 74.6 - - + +
405E GLU* 1.3 62.2 + - - +
407E GLY* 3.3 2.4 + - - +
408E ALA* 3.1 22.2 + - - +
412E LEU* 4.2 15.1 - - + +
414E LEU* 4.2 11.7 - - + -
422E LEU* 4.0 26.2 - - + -
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Residues in contact with GLU 405 (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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401E CYS 2.9 16.1 + - - +
402E ASN* 3.2 7.0 + - - +
404E ILE* 1.3 77.5 - - - +
406E GLU* 1.3 62.5 + - + +
408E ALA* 3.3 16.0 + - + +
409E ALA* 3.4 12.1 + - - +
422E LEU* 4.1 22.6 - - + +
423E ALA* 5.3 5.0 - - - +
426E LYS* 3.0 44.6 + - - +
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Residues in contact with GLU 406 (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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368E TYR* 4.4 2.9 - - - +
377E ARG* 2.8 44.1 + - - -
402E ASN* 3.0 19.7 + - + +
403E ILE 3.4 6.5 - - - +
405E GLU* 1.3 76.0 - - + +
407E GLY* 1.3 65.5 + - - +
409E ALA* 3.5 8.9 + - - +
410E GLY* 3.2 15.2 + - - -
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Residues in contact with GLY 407 (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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362E TYR* 5.9 0.4 - - - -
368E TYR* 3.2 34.8 + - - -
403E ILE 3.0 10.9 + - - -
404E ILE 3.3 4.4 + - - -
406E GLU* 1.3 75.8 - - - +
408E ALA* 1.3 53.2 + - - +
410E GLY* 2.8 21.2 + - - -
411E LYS 3.1 0.5 + - - -
412E LEU* 3.0 26.9 + - - -
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Residues in contact with ALA 408 (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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404E ILE 3.1 12.1 + - - +
405E GLU* 3.5 13.5 - - + +
406E GLU 3.2 0.6 - - - -
407E GLY* 1.3 72.0 - - - +
409E ALA* 1.3 57.5 + - - +
410E GLY 3.0 14.5 + - - +
412E LEU* 3.4 20.3 - - - +
414E LEU* 4.3 18.8 - - + +
419E THR* 6.0 3.4 - - + +
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Residues in contact with ALA 409 (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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405E GLU 3.4 8.6 + - - +
406E GLU* 3.9 8.5 - - - +
407E GLY 3.4 0.2 - - - -
408E ALA* 1.3 76.1 - - - +
410E GLY* 1.3 60.5 + - - +
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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