Contacts of the helix formed by residues 379 - 402 (chain B) in PDB entry 1DKF
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 MET 379 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A ARG* 4.9 9.1 + - - +
402A TYR* 3.1 30.7 - - + +
424A LEU* 3.6 24.9 - - + +
427A LEU* 3.6 37.0 - - + -
428A PRO* 4.3 14.1 - - + -
375B PRO 2.8 20.9 + - - +
376B LYS* 3.8 6.1 - - - +
377B MET 3.2 0.4 - - - -
378B LEU* 1.3 102.3 - - + +
380B LYS* 1.3 63.2 + - - +
381B ILE 3.1 1.3 - - - -
382B THR* 3.2 24.1 + - - +
383B ASP* 3.9 6.6 + - - +
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Residues in contact with LYS 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ASP* 5.3 5.7 + - - -
395A GLU* 5.6 1.0 + - - -
312B PHE* 3.9 15.0 - - + -
315B GLN* 3.8 40.9 + - - +
316B LEU* 4.1 9.4 - - + -
319B LEU* 3.9 24.5 - - + -
329B LEU* 4.6 10.5 - - + -
376B LYS* 3.5 28.3 + - - +
377B MET 3.0 16.6 + - - +
378B LEU 2.9 0.8 + - - -
379B MET* 1.3 73.6 - - - +
381B ILE* 1.3 67.0 + - - +
382B THR 2.9 2.2 - - - -
383B ASP* 2.9 24.7 + - - +
384B LEU* 2.8 24.2 + - + +
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Residues in contact with ILE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A LEU* 4.9 6.5 - - + -
428A PRO* 4.2 16.4 - - + -
329B LEU* 3.5 24.7 - - + +
332B ILE* 3.5 31.9 - - + -
333B CYS* 4.1 21.3 - - + -
378B LEU* 3.0 20.2 + - + +
380B LYS* 1.3 79.7 - - - +
382B THR* 1.3 56.0 + - - +
384B LEU* 3.6 11.4 - - + +
385B ARG* 2.9 58.7 + - - +
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Residues in contact with THR 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU* 5.9 0.4 - - - +
427A LEU* 4.1 6.3 - - + +
428A PRO* 3.6 32.4 - - + +
431A ARG* 3.6 45.9 + - + +
379B MET* 3.2 25.6 + - - -
380B LYS 2.9 1.0 - - - -
381B ILE* 1.3 79.6 - - - +
383B ASP* 1.3 64.5 + - - +
385B ARG* 3.2 13.4 + - - +
386B SER* 3.2 12.6 + - - -
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Residues in contact with ASP 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ASP* 4.3 15.1 - - - +
431A ARG* 4.3 14.3 + - - +
312B PHE* 3.8 18.4 - - + -
315B GLN* 3.9 13.0 - - - +
379B MET 4.0 4.9 - - - +
380B LYS* 2.9 33.7 + - - +
382B THR* 1.3 76.7 - - - +
384B LEU* 1.3 66.0 + - - +
386B SER* 3.1 10.1 + - - -
387B ILE* 3.1 26.5 + - + +
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Residues in contact with LEU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ASP* 3.2 45.1 - - + +
270B ILE* 3.8 26.0 - - + -
271B LEU* 3.6 28.3 - - + +
312B PHE* 3.9 20.5 - - + -
329B LEU* 5.5 3.4 - - + -
333B CYS* 4.8 11.2 - - + -
380B LYS 2.8 14.1 + - - +
381B ILE* 3.6 13.5 - - + +
383B ASP* 1.3 77.0 - - - +
385B ARG* 1.3 57.8 + - - +
387B ILE* 3.4 3.6 + - + +
388B SER* 3.0 28.6 + - - -
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Residues in contact with ARG 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A PRO* 4.4 22.3 - - + +
429A ALA* 5.6 0.6 - - - +
431A ARG* 5.8 1.8 - - + -
432A SER* 4.0 23.1 + - - +
435A LEU* 5.5 0.6 - - - +
267B ASP* 4.0 11.5 + - - -
332B ILE 5.7 0.2 + - - -
333B CYS* 3.3 30.3 + - - +
336B CYS* 3.5 31.3 - - - +
338B ASP* 5.7 0.8 + - - +
339B ARG* 3.1 27.4 - - - +
381B ILE* 2.9 29.7 + - - +
382B THR* 3.3 13.0 - - - +
383B ASP 3.2 0.4 - - - -
384B LEU* 1.3 78.9 - - - +
386B SER* 1.3 61.7 + - - +
388B SER* 3.1 7.0 + - - +
389B ALA* 3.1 24.3 + - - +
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Residues in contact with SER 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ARG* 3.3 24.1 + - - +
435A LEU* 3.3 31.0 - - - +
308B LEU* 5.5 0.7 - - - -
382B THR 3.2 7.2 + - - -
383B ASP* 3.1 11.6 + - - -
385B ARG* 1.3 79.1 - - - +
387B ILE* 1.3 61.4 + - - +
389B ALA* 3.4 13.7 - - - +
390B LYS* 3.4 17.9 - - - +
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Residues in contact with ILE 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ILE* 3.5 26.2 - - + -
305B LEU* 5.1 4.3 - - + +
308B LEU* 3.4 33.4 - - + +
309B VAL* 4.1 22.7 - - + -
312B PHE* 3.5 44.0 - - + -
383B ASP* 3.1 15.3 + - + +
384B LEU* 3.8 6.7 - - - +
385B ARG 3.3 0.2 - - - -
386B SER* 1.3 74.0 - - - +
388B SER* 1.3 62.3 + - - +
389B ALA 3.0 2.5 + - - -
390B LYS* 3.2 5.2 + - - +
391B GLY* 2.7 24.9 + - - -
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Residues in contact with SER 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LEU* 3.6 23.2 - - - +
267B ASP* 2.6 39.2 + - - -
270B ILE* 4.0 11.2 - - - +
384B LEU 3.0 8.3 + - - -
385B ARG* 3.1 14.4 + - - +
387B ILE* 1.3 77.1 - - - +
389B ALA* 1.3 55.4 + - - +
391B GLY 3.5 1.1 - - - +
392B ALA* 2.9 27.9 + - - +
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Residues in contact with ALA 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A SER* 5.8 3.1 - - - +
435A LEU* 5.0 10.5 - - + -
385B ARG 3.1 18.2 + - - +
386B SER* 3.4 10.1 - - - +
387B ILE 3.0 0.4 - - - -
388B SER* 1.3 81.5 + - - +
390B LYS* 1.3 64.8 + - + +
392B ALA* 3.3 11.2 + - - +
393B GLU* 3.4 18.5 + - - +
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Residues in contact with LYS 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A LEU* 6.4 0.7 - - + -
305B LEU* 3.8 27.8 - - + +
308B LEU* 4.1 33.6 - - + +
386B SER 3.4 15.3 - - - +
387B ILE 3.2 4.6 + - - +
389B ALA* 1.3 73.8 - - + +
391B GLY* 1.3 67.6 + - - +
393B GLU* 2.9 28.7 + - + +
394B ARG* 3.0 10.4 + - - +
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Residues in contact with GLY 391 (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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266B LEU* 3.6 5.6 - - - -
270B ILE* 5.4 2.2 - - - -
305B LEU* 3.7 9.8 - - - +
387B ILE* 2.7 17.0 + - - -
388B SER* 3.3 3.3 + - - -
390B LYS* 1.3 77.5 - - - +
392B ALA* 1.3 55.9 + - - +
394B ARG* 3.1 2.4 + - - +
395B VAL* 2.9 23.7 + - - +
600B BMS 3.2 31.4 - - - +
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Residues in contact with ALA 392 (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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266B LEU* 3.5 8.8 - - + +
388B SER 2.9 15.4 + - - +
389B ALA* 3.7 6.3 - - - +
390B LYS 3.2 0.4 - - - -
391B GLY* 1.3 76.3 - - - +
393B GLU* 1.3 62.7 + - - +
395B VAL* 3.3 14.2 - - + +
396B ILE* 3.2 23.7 + - - +
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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
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439A GLU* 4.7 12.0 - - - +
389B ALA 3.4 15.9 + - - +
390B LYS* 2.9 23.0 + - + +
392B ALA* 1.3 76.7 - - - +
394B ARG* 1.3 59.7 + - - +
396B ILE* 2.6 38.4 - - + +
397B THR* 3.3 5.8 + - - -
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Residues in contact with ARG 394 (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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219B SER 4.2 14.3 + - - -
220B LEU* 4.7 2.8 - - - +
301B GLY* 2.6 31.2 + - - +
302B PHE 3.6 15.5 + - - -
303B GLY* 3.7 11.9 - - - +
304B PRO* 3.6 24.0 - - - +
305B LEU* 3.9 21.3 - - + -
390B LYS 3.0 5.6 + - - +
391B GLY 3.5 7.4 - - - +
393B GLU* 1.3 76.5 - - - +
395B VAL* 1.3 57.9 + - - +
397B THR* 3.0 25.8 + - - +
398B LEU* 2.8 61.2 + - + +
401B GLU* 5.4 2.0 + - - -
600B BMS 4.4 6.1 - - + -
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Residues in contact with VAL 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LEU* 4.8 4.9 - - + -
391B GLY 2.9 15.5 + - - +
392B ALA* 3.3 19.1 - - + +
394B ARG* 1.3 77.7 - - - +
396B ILE* 1.3 63.9 + - + +
398B LEU* 3.6 7.2 + - - +
399B LYS* 2.9 39.2 + - + +
406B MET* 3.2 33.1 - - + +
600B BMS 3.9 28.5 - - + -
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Residues in contact with ILE 396 (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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392B ALA 3.2 9.1 + - - +
393B GLU* 2.6 37.7 - - + +
395B VAL* 1.3 83.8 - - + +
397B THR* 1.3 84.8 + - - +
399B LYS* 3.1 12.6 + - + +
400B MET* 3.1 25.5 + - + +
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Residues in contact with THR 397 (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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393B GLU 3.4 9.4 + - - -
394B ARG* 3.0 29.1 + - - +
396B ILE* 1.3 88.0 - - - +
398B LEU* 1.3 59.3 + - + +
400B MET* 2.8 45.4 + - + +
401B GLU* 3.1 29.8 + - + +
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Residues in contact with LEU 398 (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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220B LEU* 4.6 13.5 - - + -
225B TRP* 3.7 34.3 - - + -
301B GLY 4.3 2.0 - - - +
394B ARG* 2.8 65.1 + - + +
395B VAL* 3.9 4.7 - - - +
397B THR* 1.3 68.5 - - + +
399B LYS* 1.3 62.5 + - - +
400B MET 2.8 6.5 + - - -
401B GLU* 4.3 12.8 - - + +
402B ILE* 3.0 43.9 + - + +
405B SER* 3.3 7.3 + - - +
406B MET* 4.8 1.1 - - - -
600B BMS 3.9 14.1 - - + -
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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
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395B VAL* 2.9 31.3 + - + +
396B ILE* 3.1 14.1 + - + +
398B LEU* 1.3 75.1 - - - +
400B MET* 1.3 57.6 + - - +
402B ILE 3.3 13.1 - - - +
403B PRO* 5.2 0.5 - - - +
404B GLY 5.1 1.6 + - - -
405B SER* 2.8 27.0 + - - +
406B MET* 3.3 36.9 + - - +
408B PRO* 4.8 14.8 - - - +
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Residues in contact with MET 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ILE* 3.1 13.4 + - + +
397B THR* 2.8 34.5 + - + +
399B LYS* 1.3 80.0 - - - +
401B GLU* 1.3 79.1 + - + +
402B ILE 3.0 12.2 + - - -
403B PRO* 4.6 2.1 - - - +
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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
----------------------------------------------------------
220B LEU* 6.0 3.2 - - + +
394B ARG* 5.4 2.3 + - - -
397B THR* 3.1 33.8 + - + +
398B LEU* 3.2 11.0 + - + +
400B MET* 1.3 88.4 - - - +
402B ILE* 1.3 68.7 + - + +
403B PRO* 4.0 6.3 - - - +
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Residues in contact with ILE 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU* 3.8 28.5 - - + -
222B ILE* 4.5 13.0 - - + -
225B TRP* 3.7 38.1 - - + +
226B ASP* 6.0 0.4 - - - +
398B LEU* 3.0 27.4 + - + +
399B LYS 3.3 12.7 - - - +
400B MET 3.0 2.6 - - - -
401B GLU* 1.3 90.0 - - + +
403B PRO* 1.3 75.6 - - + +
405B SER* 3.0 30.8 + - - -
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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