Contacts of the helix formed by residues 397 - 420 (chain B) in PDB entry 2CT8
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 397 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B PHE* 6.3 0.4 - - - -
327B PRO* 5.5 1.4 - - - +
328B PHE* 5.3 4.5 + - - -
392B TYR* 2.7 35.4 + - + +
393B MET* 4.1 2.0 - - - -
395B LYS* 3.0 8.9 - - + +
396B VAL* 1.3 70.6 - - - +
398B PHE* 1.3 60.2 + - - +
399B TYR* 3.5 9.7 + - - +
400B LYS* 3.0 38.7 + - - +
401B ALA* 3.0 22.7 + - - +
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Residues in contact with PHE 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA* 3.6 44.0 - - + -
33B THR* 4.0 20.2 - - + -
34B ILE* 4.4 17.0 - - + -
255B LEU* 5.7 0.7 - - + -
323B LEU* 3.7 34.1 - - + +
328B PHE* 3.7 33.2 - + + +
393B MET* 3.1 27.8 - - + -
396B VAL* 3.0 33.1 + - + -
397B ASN* 1.3 70.7 - - - +
399B TYR* 1.3 54.5 + - - +
401B ALA* 3.1 1.7 + - - +
402B ILE* 2.8 39.6 + - + +
454B ILE* 6.1 2.2 - - + -
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Residues in contact with TYR 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B LEU 3.9 6.2 + - - -
324B ARG* 3.1 43.9 + - - +
325B GLU 3.7 14.4 + - - -
326B VAL 3.5 14.6 - - - +
327B PRO* 3.5 43.3 - - + +
328B PHE 4.4 2.0 - - - +
397B ASN* 3.3 7.1 + - - +
398B PHE* 1.3 78.8 - - - +
400B LYS* 1.3 76.9 + - + +
402B ILE* 3.6 3.7 + - - +
403B GLU* 3.0 33.4 + - + +
13D C 4.9 10.5 + - - -
14D A 6.2 2.9 - - - -
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Residues in contact with LYS 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B TYR* 3.3 59.1 + - + +
397B ASN* 3.0 19.7 + - - +
399B TYR* 1.3 97.3 - - + +
401B ALA* 1.3 65.0 + - - +
403B GLU* 2.6 36.5 + - - +
404B GLU* 3.0 19.6 + - - +
407B LYS* 5.5 1.2 - - - +
14D A 5.5 16.0 + - - -
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Residues in contact with ALA 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B TYR* 3.6 18.6 - - + +
392B TYR* 3.8 15.9 - - + +
393B MET* 3.3 32.8 - - + -
397B ASN 3.0 19.3 + - - +
398B PHE 3.1 2.0 + - - +
400B LYS* 1.3 77.8 - - - +
402B ILE* 1.3 61.3 + - + +
404B GLU* 3.2 6.6 + - - +
405B ILE* 3.1 22.3 + - - +
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Residues in contact with ILE 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B TYR* 3.7 17.3 - - + +
323B LEU* 3.2 40.4 - - + +
324B ARG* 3.4 28.9 - - + -
393B MET* 6.1 0.7 - - + -
398B PHE* 2.8 20.7 + - + +
399B TYR 4.0 2.9 - - - +
401B ALA* 1.3 70.8 - - + +
403B GLU* 1.3 66.1 + - - +
405B ILE* 3.0 15.6 + - + +
406B LEU* 2.9 45.3 + - + +
454B ILE* 4.6 26.9 - - + -
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Residues in contact with GLU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B TYR* 5.1 1.4 + - - -
399B TYR* 3.0 23.7 + - + +
400B LYS* 2.6 49.5 + - - +
401B ALA 3.1 0.2 - - - -
402B ILE* 1.3 77.7 - - - +
404B GLU* 1.3 63.4 + - - +
406B LEU* 3.1 12.1 + - + +
407B LYS* 2.9 52.9 + - + +
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Residues in contact with GLU 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B GLU* 5.4 0.3 - - - +
385B SER* 3.8 22.1 + - - +
388B ASN* 3.5 42.8 + - + +
389B TYR* 4.1 13.5 - - + +
392B TYR* 3.8 14.6 + - + -
400B LYS 3.0 14.9 + - - +
401B ALA 3.2 9.4 + - - +
403B GLU* 1.3 76.4 - - + +
405B ILE* 1.3 63.4 + - - +
407B LYS* 3.7 31.8 + - - +
408B PHE* 3.1 24.9 + - - +
450B LEU* 5.5 1.7 - - - +
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Residues in contact with ILE 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B ILE* 4.7 6.7 - - + -
389B TYR* 3.8 18.2 - - + -
401B ALA 3.1 15.5 + - - +
402B ILE* 3.0 22.5 + - + +
404B GLU* 1.3 78.4 - - - +
406B LEU* 1.3 61.1 + - + +
408B PHE* 3.7 5.1 - - - +
409B THR* 3.0 28.8 + - - +
447B LEU* 3.7 21.7 - - + +
450B LEU* 3.6 39.0 - - + +
451B LEU* 3.6 31.2 - - + -
454B ILE* 4.6 8.1 - - + -
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Residues in contact with LEU 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B TYR* 3.5 17.7 - - - +
324B ARG* 4.9 7.9 - - + +
346B GLU* 3.8 31.4 - - + +
350B GLU* 3.9 11.2 - - + +
351B ILE* 4.4 19.3 - - + -
402B ILE* 2.9 49.2 + - + +
403B GLU* 3.5 9.6 - - + +
405B ILE* 1.3 75.0 - - + +
407B LYS* 1.3 55.6 + - - +
409B THR* 3.0 7.3 + - - -
410B SER* 2.7 39.1 + - - +
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Residues in contact with LYS 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B SER* 6.1 0.2 - - - +
400B LYS* 5.5 0.8 - - - +
403B GLU* 2.9 49.8 + - + +
404B GLU* 3.4 29.8 + - - +
406B LEU* 1.3 77.1 - - + +
408B PHE* 1.3 58.2 + - - +
410B SER* 3.2 7.8 + - - -
411B TYR* 2.9 26.7 + - - +
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Residues in contact with PHE 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B TYR* 3.7 26.2 - + - -
381B ILE* 4.3 4.0 - - + -
382B ALA* 3.5 26.2 - - + -
385B SER* 3.6 25.2 + - - +
404B GLU 3.1 14.9 + - - +
405B ILE* 3.7 4.3 - - - +
407B LYS* 1.3 75.5 - - - +
409B THR* 1.3 62.7 + - - +
411B TYR* 2.9 36.0 + + - +
412B LEU* 2.9 26.3 + - + +
443B GLY* 3.9 12.6 - - - -
446B VAL* 3.2 35.0 - - + -
447B LEU* 4.2 10.3 - - + -
450B LEU* 4.4 11.4 - - + -
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Residues in contact with THR 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B GLU* 3.4 28.7 - - + +
351B ILE* 3.9 14.0 - - + +
354B LEU* 4.1 13.2 - - + +
405B ILE* 3.0 16.5 + - - +
406B LEU* 3.0 13.0 + - + +
408B PHE* 1.3 79.5 - - - +
410B SER* 1.3 57.3 + - - +
412B LEU* 3.2 4.6 + - - +
413B ASN* 2.9 48.9 + - - +
447B LEU* 3.6 22.5 - - - +
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Residues in contact with SER 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B GLU* 4.3 16.6 + - - -
406B LEU* 2.7 20.2 + - - +
407B LYS* 3.5 8.5 - - - -
409B THR* 1.3 71.2 - - - +
411B TYR* 1.3 65.8 + - - +
413B ASN* 4.0 7.8 + - - +
414B LYS* 3.1 26.6 + - - +
40D U 4.1 14.2 + - - -
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Residues in contact with TYR 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B GLU* 4.1 3.6 - - - +
378B TYR* 3.5 36.4 + + - -
381B ILE* 3.2 46.0 - - + +
407B LYS 2.9 14.1 + - - +
408B PHE* 2.9 19.5 + + + +
410B SER* 1.3 79.0 - - - +
412B LEU* 1.3 78.4 + - + +
414B LYS* 3.3 6.4 + - + +
415B TYR* 2.9 53.9 + + + +
418B GLU* 6.1 1.1 - - - -
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Residues in contact with LEU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B LEU* 3.8 28.9 - - + -
378B TYR* 4.3 18.2 - - + -
408B PHE* 2.9 29.9 + - + +
409B THR* 3.7 5.2 - - - +
411B TYR* 1.3 96.9 - - + +
413B ASN* 1.3 65.1 + - - +
414B LYS 3.1 1.8 - - - -
415B TYR* 3.1 7.2 + - + +
416B VAL* 3.0 28.1 + - - +
439B ALA 5.8 0.2 - - - -
440B LEU* 4.5 19.5 - - + +
443B GLY* 3.9 30.5 - - - -
444B LEU* 4.3 3.8 - - + +
447B LEU* 4.9 3.8 - - + -
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Residues in contact with ASN 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B GLU* 3.0 32.9 + - - +
353B ASN* 5.0 1.2 + - - -
354B LEU* 3.3 23.1 + - - +
357B ARG* 3.1 25.6 + - - +
409B THR* 2.9 32.3 + - - +
410B SER* 4.0 3.9 + - - +
412B LEU* 1.3 76.7 - - - +
414B LYS* 1.3 61.8 + - - +
416B VAL 3.6 0.2 + - - -
417B ASP* 3.4 13.3 + - - +
39D G 3.4 40.8 + - - +
40D U 3.8 6.8 + - - +
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Residues in contact with LYS 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B SER 3.1 18.4 + - - +
411B TYR* 3.5 7.0 - - + +
413B ASN* 1.3 75.5 - - - +
415B TYR* 1.3 59.9 + - - +
417B ASP* 3.2 3.5 + - + +
418B GLU* 2.9 52.9 + - + +
40D U 3.0 31.9 + - - +
41D C 2.7 41.0 + - - +
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Residues in contact with TYR 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ASP* 3.0 37.3 + - - +
377B GLU* 6.1 0.2 - - + -
378B TYR* 4.7 3.4 - + + -
411B TYR* 2.9 45.3 + + - +
412B LEU* 3.1 16.8 + - + +
414B LYS* 1.3 74.5 - - - +
416B VAL* 1.3 59.1 + - - +
418B GLU* 4.0 10.7 + - - +
419B LYS* 2.9 74.7 + - + +
435B LYS* 5.1 0.7 - - - +
436B VAL* 3.8 22.7 - - + +
439B ALA* 3.8 10.5 - - + +
440B LEU* 3.1 28.7 - - + -
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Residues in contact with VAL 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B LEU* 4.4 4.3 - - + -
357B ARG* 3.6 39.7 - - - +
358B VAL* 4.4 2.7 - - + -
361B MET* 4.4 11.9 - - - -
412B LEU 3.0 16.9 + - - +
413B ASN 3.7 7.6 - - - +
415B TYR* 1.3 77.8 - - - +
417B ASP* 1.3 55.2 + - - +
420B GLN* 2.8 32.9 + - - -
421B PRO* 3.6 5.4 - - + +
422B TRP* 3.7 11.8 - - + -
440B LEU* 3.7 28.0 - - + -
34D C 3.8 9.9 - - - +
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Residues in contact with ASP 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ARG* 4.7 2.0 - - - +
413B ASN 3.4 10.2 + - - +
414B LYS* 3.2 10.0 + - + +
415B TYR 3.2 0.2 - - - -
416B VAL* 1.3 82.7 - - - +
418B GLU* 1.3 66.0 + - + +
420B GLN* 3.5 18.0 + - - +
422B TRP* 4.5 8.0 - - - -
32D C 3.7 9.1 + - - +
34D C 4.5 2.1 + - - -
39D G 2.9 34.8 + - - +
40D U 3.2 36.7 + - - +
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Residues in contact with GLU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B TYR* 6.1 1.4 - - - -
414B LYS* 2.9 46.5 + - + +
415B TYR* 4.0 11.5 - - - +
417B ASP* 1.3 74.7 - - + +
419B LYS* 1.3 74.2 + - + +
420B GLN* 3.3 16.6 + - - +
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Residues in contact with LYS 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ASP* 4.2 7.5 + - - +
377B GLU* 5.0 8.3 + - - -
415B TYR* 2.9 57.6 + - + +
418B GLU* 1.3 86.0 - - + +
420B GLN* 1.3 72.6 + - - +
421B PRO* 3.0 2.3 - - + -
424B LEU* 3.7 16.6 - - + +
432B GLU* 5.1 12.1 + - - +
435B LYS* 6.1 1.6 - - - +
436B VAL* 3.5 37.4 - - + +
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Residues in contact with GLN 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B VAL 2.8 15.6 + - - -
417B ASP 3.5 9.7 - - - +
418B GLU* 3.1 14.0 - - - +
419B LYS* 1.3 80.4 - - - +
421B PRO* 1.3 68.1 - - - +
422B TRP* 3.1 38.4 - - + +
423B ALA* 3.1 30.5 + - + +
424B LEU* 3.6 2.5 + - + +
32D C 4.7 8.0 + - - -
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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