Contacts of the helix formed by residues 392 - 418 (chain B) in PDB entry 2KWI
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 SER 392 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B GLY* 1.3 76.5 - - - -
393B GLU* 1.3 66.0 + - - +
394B THR 3.4 1.6 - - - -
395B GLN* 3.9 18.2 - - - -
396B ALA* 2.8 39.8 + - - +
399B LYS* 5.3 9.6 - - - -
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Residues in contact with GLU 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B GLY* 3.5 10.3 - - - -
392B SER* 1.3 105.4 + - - +
394B THR* 1.3 65.9 + - - +
396B ALA* 3.7 11.1 - - - +
397B GLY 4.3 1.7 + - - -
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Residues in contact with THR 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B GLU* 1.3 77.9 - - - +
395B GLN* 1.3 66.1 + - - +
396B ALA 3.1 2.7 + - - -
397B GLY* 3.3 10.6 + - - -
398B ILE* 3.4 18.5 + - + +
446B ALA* 4.0 22.0 - - + -
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Residues in contact with GLN 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B GLY 4.8 9.2 - - - +
392B SER* 3.4 14.7 + - - +
394B THR* 1.3 75.5 - - - +
396B ALA* 1.3 54.1 + - - +
398B ILE* 3.1 9.6 + - - +
399B LYS* 2.7 54.2 + - - +
443B LEU* 3.0 36.3 + - + +
444B ARG* 5.2 0.6 - - - +
446B ALA* 3.4 30.2 + - + +
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Residues in contact with ALA 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B SER* 2.8 25.2 + - - +
393B GLU* 3.7 9.2 - - - +
394B THR 3.1 0.2 - - - -
395B GLN* 1.3 77.4 - - - +
397B GLY* 1.3 62.8 + - - +
399B LYS* 3.3 8.3 + - - +
400B GLU* 3.0 37.6 + - - +
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Residues in contact with GLY 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B GLU 4.3 2.0 + - - -
394B THR 3.3 7.8 + - - -
396B ALA* 1.3 78.8 - - - +
398B ILE* 1.3 58.2 + - - +
400B GLU* 3.5 10.1 + - - +
401B GLU* 3.0 28.5 + - - +
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Residues in contact with ILE 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B THR* 3.4 23.8 + - + +
395B GLN* 3.1 13.4 + - - +
397B GLY* 1.3 75.6 - - - +
399B LYS* 1.3 54.8 + - - +
401B GLU* 3.0 7.7 + - + +
402B ILE* 2.7 39.5 + - + +
439B LEU* 3.8 15.3 - - + +
442B LYS* 3.7 39.0 - - + +
443B LEU* 3.4 39.0 - - + +
446B ALA* 4.9 2.0 - - + -
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Residues in contact with LYS 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B SER* 5.3 9.8 - - - -
395B GLN* 2.7 38.2 + - - +
396B ALA* 3.7 7.9 - - - +
398B ILE* 1.3 72.2 - - - +
400B GLU* 1.3 58.6 + - + +
402B ILE* 3.3 12.3 + - + +
403B ARG* 2.9 37.6 + - - +
443B LEU* 3.7 26.7 - - + -
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Residues in contact with GLU 400 (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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396B ALA* 3.0 31.2 + - - +
397B GLY* 3.9 7.5 + - - +
399B LYS* 1.3 76.6 - - + +
401B GLU* 1.3 58.3 + - - +
403B ARG* 3.4 17.6 + - - +
404B ARG* 3.0 29.0 + - - +
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Residues in contact with GLU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B GLY 3.0 19.0 + - - +
398B ILE* 3.0 7.2 + - + +
400B GLU* 1.3 74.3 - - - +
402B ILE* 1.3 59.6 + - - +
404B ARG* 2.7 53.0 + - - +
405B GLN* 2.9 49.8 + - - +
439B LEU* 3.6 22.7 - - + -
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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
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398B ILE* 2.7 25.9 + - + +
399B LYS* 3.4 14.4 - - + +
401B GLU* 1.3 71.2 - - - +
403B ARG* 1.3 52.0 + - + +
405B GLN* 3.0 5.6 + - - +
406B GLU* 2.7 58.8 + - - +
436B LEU* 4.0 11.7 - - + -
439B LEU* 3.7 31.1 - - + +
440B LYS* 4.8 13.7 - - + +
443B LEU* 3.7 42.6 - - + -
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Residues in contact with ARG 403 (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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399B LYS* 2.9 24.6 + - + +
400B GLU* 3.6 18.5 - - - +
402B ILE* 1.3 76.4 - - + +
404B ARG* 1.3 57.8 + - - +
406B GLU* 3.6 17.1 - - - +
407B PHE* 2.8 30.4 + - - +
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Residues in contact with ARG 404 (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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400B GLU 3.0 16.7 + - - +
401B GLU* 2.7 54.0 + - - +
403B ARG* 1.3 76.8 - - - +
405B GLN* 1.3 64.6 + - - +
407B PHE* 3.3 11.0 + - + +
408B LEU* 2.9 41.9 + - + +
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Residues in contact with GLN 405 (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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401B GLU* 2.9 48.2 + - - +
402B ILE 3.5 4.5 - - - +
404B ARG* 1.3 80.4 - - - +
406B GLU* 1.3 59.9 + - - +
408B LEU* 3.3 12.2 + - - +
409B LEU* 2.9 30.1 + - - +
432B VAL* 3.4 23.4 - - + +
435B ILE* 3.4 28.1 - - + +
436B LEU* 3.7 23.9 - - + +
439B LEU* 4.0 15.9 - - + -
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Residues in contact with GLU 406 (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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402B ILE* 2.7 38.5 + - + +
403B ARG* 3.6 20.2 - - - +
405B GLN* 1.3 74.7 - - - +
407B PHE* 1.3 51.9 + - - +
409B LEU* 3.3 5.1 + - - +
410B ASN* 2.6 39.3 + - + +
436B LEU* 3.6 19.1 - - + -
440B LYS* 5.6 4.6 - - - -
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Residues in contact with PHE 407 (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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403B ARG 2.8 18.5 + - - +
404B ARG* 3.3 12.6 - - + +
405B GLN 3.2 0.2 - - - -
406B GLU* 1.3 73.4 - - - +
408B LEU* 1.3 75.1 + - + +
410B ASN* 3.7 10.0 - - - +
411B SER* 2.8 44.9 + - - -
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Residues in contact with LEU 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B ARG* 2.9 25.7 + - + +
405B GLN* 3.5 28.0 - - - +
407B PHE* 1.3 89.3 - - + +
409B LEU* 1.3 64.0 + - - +
411B SER* 4.0 3.8 - - - -
412B LEU* 3.1 34.4 + - + +
428B ARG* 3.9 25.1 - - - +
432B VAL* 3.5 20.0 - - + -
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Residues in contact with LEU 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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48A ALA* 3.9 9.9 - - + -
82A TYR* 3.0 23.3 - - - +
405B GLN 2.9 16.2 + - - +
406B GLU* 3.7 5.2 - - - +
408B LEU* 1.3 73.9 - - - +
410B ASN* 1.3 60.9 + - - +
412B LEU* 3.4 3.1 + - - +
413B HIS* 2.8 58.0 + - + +
429B LEU* 3.5 7.4 - - + +
432B VAL* 3.5 25.3 - - + +
433B GLN* 3.6 28.5 - - + +
436B LEU* 4.9 11.4 - - + -
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Residues in contact with ASN 410 (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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406B GLU 2.6 24.0 + - - +
407B PHE* 3.7 10.4 - - - +
409B LEU* 1.3 74.4 - - - +
411B SER* 1.3 57.0 + - - +
413B HIS* 3.1 9.8 + - - +
414B ARG* 2.8 74.0 + - - +
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Residues in contact with SER 411 (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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407B PHE* 2.8 38.0 + - - -
408B LEU* 4.0 4.0 - - - -
410B ASN* 1.3 72.1 - - - +
412B LEU* 1.3 56.5 + - - +
414B ARG* 3.1 6.8 + - - +
415B ASP* 2.7 57.1 + - - +
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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
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77A ALA* 4.5 0.2 - - - +
408B LEU* 3.1 23.2 + - + +
409B LEU 3.7 1.6 - - - +
411B SER* 1.3 79.1 - - - +
413B HIS* 1.3 61.9 + - - +
415B ASP* 4.6 2.5 - - + -
416B LEU* 3.0 39.1 + - + +
425B LYS* 4.0 35.0 - - + +
428B ARG* 3.8 28.3 - - + -
429B LEU* 3.3 27.9 - - + +
432B VAL* 4.2 12.1 - - + -
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Residues in contact with HIS 413 (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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48A ALA* 3.3 33.6 - - + +
75A TYR* 5.3 3.7 - - + -
77A ALA* 3.3 9.2 - - + +
78A ILE* 3.7 25.2 - - + +
82A TYR* 2.8 29.0 + + - -
409B LEU* 2.8 39.4 + - + +
410B ASN* 3.3 11.0 - - - +
411B SER 3.0 0.2 - - - -
412B LEU* 1.3 75.2 - - - +
414B ARG* 1.3 64.7 + - + +
417B GLN* 2.9 38.2 + - - +
429B LEU* 3.6 17.3 - - + -
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Residues in contact with ARG 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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75A TYR* 6.4 0.4 - - + -
410B ASN* 2.8 57.1 + - - +
411B SER* 3.8 5.4 - - - +
413B HIS* 1.3 70.9 - - + +
415B ASP* 1.3 68.5 + - - +
417B GLN* 3.4 24.2 + - - +
418B GLY* 3.6 6.9 + - - -
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Residues in contact with ASP 415 (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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411B SER* 2.7 47.7 + - - +
412B LEU* 4.6 1.8 - - + -
414B ARG* 1.3 75.7 - - - +
416B LEU* 1.3 70.0 - - + +
418B GLY* 3.3 13.3 + - - -
420B ILE* 3.6 21.6 + - + +
425B LYS* 6.2 0.7 - - + +
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Residues in contact with LEU 416 (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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77A ALA* 3.7 4.0 - - + -
81A ASN* 3.4 29.4 + - + +
412B LEU* 3.0 33.4 + - + +
415B ASP* 1.3 82.0 - - + +
417B GLN* 1.3 61.5 + - - +
418B GLY 3.0 5.6 - - - -
419B GLY* 3.0 15.9 + - - -
420B ILE 3.1 20.3 + - - +
421B LYS* 3.6 19.2 - - + +
425B LYS* 3.5 33.4 - - + -
426B GLU* 4.9 2.7 - - + +
429B LEU* 3.5 31.9 - - + -
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Residues in contact with GLN 417 (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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74A ASP* 3.0 39.2 - - - +
75A TYR* 3.3 32.5 - - - -
76A ALA* 5.6 3.6 - - - +
77A ALA* 3.5 19.5 - - + +
81A ASN* 4.9 0.2 - - - +
413B HIS* 2.9 38.1 + - - +
414B ARG* 3.4 17.9 - - - +
415B ASP 3.3 0.4 - - - -
416B LEU* 1.3 76.7 - - - +
418B GLY* 1.3 57.9 + - - +
419B GLY* 3.1 4.5 + - - -
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Residues in contact with GLY 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ARG 3.6 5.0 + - - -
415B ASP 3.3 10.4 + - - -
416B LEU 3.0 1.8 - - - -
417B GLN* 1.3 78.3 - - - +
419B GLY* 1.3 58.6 + - - +
420B ILE* 3.4 8.2 + - - +
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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