Contacts of the helix formed by residues 344 - 367 (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 GLN 344 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B LEU* 4.0 2.4 - - - +
253B THR* 2.9 29.8 + - + +
256B ASP* 3.2 14.4 + - - +
342B LEU* 4.9 0.7 - - - -
343B GLU* 1.3 81.1 - - + +
345B PRO* 1.3 64.4 - - - +
346B ASP* 3.1 3.4 - - + +
347B ARG* 3.0 59.7 + - + +
348B VAL* 3.3 14.5 + - - +
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Residues in contact with PRO 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A LYS* 5.2 2.5 - - - +
337B GLY* 3.8 18.9 - - - +
342B LEU* 3.5 24.4 - - + +
343B GLU 3.1 14.8 - - - +
344B GLN* 1.3 84.7 - - - +
346B ASP* 1.3 68.9 + - - +
348B VAL* 3.1 12.4 + - + +
349B ASP* 2.9 28.8 + - - +
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Residues in contact with ASP 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ASP* 5.5 3.6 - - - +
344B GLN* 3.1 2.2 - - + -
345B PRO* 1.3 83.6 - - + +
347B ARG* 1.3 65.2 + - + +
349B ASP* 3.2 13.4 + - - +
350B MET* 2.9 32.5 + - + +
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Residues in contact with ARG 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B GLY 5.0 0.8 + - - -
251B THR* 3.0 40.6 + - - -
252B LEU* 4.2 15.2 - - + +
253B THR 4.9 0.4 - - - +
344B GLN* 3.0 57.7 + - + +
346B ASP* 1.3 78.4 - - + +
348B VAL* 1.3 62.0 + - - +
350B MET* 3.4 9.9 + - - +
351B LEU* 3.1 27.2 + - - +
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Residues in contact with VAL 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LEU* 4.2 18.8 - - + -
256B ASP* 4.8 1.6 - - - +
260B LEU* 4.2 13.2 - - + -
335B ILE* 3.7 20.5 - - + +
336B CYS 3.3 10.8 - - - +
337B GLY* 3.2 28.0 - - - +
342B LEU* 4.1 20.2 - - + -
344B GLN 3.5 14.8 - - - +
345B PRO 3.1 7.8 + - - +
347B ARG* 1.3 75.3 - - - +
349B ASP* 1.3 65.8 + - - +
351B LEU* 2.9 18.2 + - - +
352B GLN* 3.1 11.5 + - - +
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Residues in contact with ASP 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A LYS* 3.6 22.1 + - - +
422A LYS* 5.5 10.2 + - - -
426A ARG* 5.8 2.4 + - - -
337B GLY* 3.6 19.0 + - - -
338B ASP* 5.2 0.5 - - - +
345B PRO* 2.9 18.4 + - - +
346B ASP* 3.2 15.8 + - - +
348B VAL* 1.3 76.3 - - - +
350B MET* 1.3 75.3 + - + +
352B GLN* 3.5 14.9 + - - +
353B GLU* 3.3 21.5 + - - +
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Residues in contact with MET 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LYS* 5.8 2.2 - - - -
346B ASP* 2.9 21.0 + - + +
347B ARG* 3.4 13.5 - - - +
348B VAL 3.0 0.2 - - - -
349B ASP* 1.3 91.9 - - + +
351B LEU* 1.3 59.6 + - - +
353B GLU* 3.1 32.2 - - - +
354B PRO* 3.3 18.0 - - - +
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B PRO 3.1 23.1 - - - +
248B GLY* 3.5 32.3 - - - +
249B PHE* 3.8 5.2 - - - +
252B LEU* 3.7 22.2 - - + -
335B ILE* 3.7 24.7 - - + -
347B ARG* 3.1 16.9 + - - +
348B VAL* 2.9 10.4 + - - +
350B MET* 1.3 77.9 - - - +
352B GLN* 1.3 55.8 + - - +
353B GLU 3.5 0.2 - - - -
354B PRO* 3.3 16.6 - - + +
355B LEU* 3.6 12.5 - - + +
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Residues in contact with GLN 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A LEU* 3.6 27.2 - - - +
332B ILE* 2.8 43.4 + - - +
335B ILE* 3.1 23.6 + - - +
336B CYS* 3.8 12.4 - - - +
337B GLY 4.8 1.8 + - - -
348B VAL 3.1 9.7 + - - +
349B ASP* 3.9 17.7 - - - +
350B MET 3.3 0.2 - - - -
351B LEU* 1.3 77.4 - - - +
353B GLU* 1.3 65.2 + - - +
354B PRO 3.3 0.7 - - - -
355B LEU* 3.0 22.4 + - + +
356B LEU* 3.1 21.8 + - + +
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Residues in contact with GLU 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A GLY* 6.2 4.5 - - - -
422A LYS* 2.7 35.8 + - - +
349B ASP 3.3 8.7 + - - +
350B MET* 3.1 39.5 - - - +
352B GLN* 1.3 79.3 - - - +
354B PRO* 1.3 68.7 - - + +
356B LEU* 3.4 11.5 + - - +
357B GLU* 3.3 23.1 + - - +
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Residues in contact with PRO 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B VAL* 5.2 1.0 - - - +
187B LEU* 3.6 20.0 - - + +
350B MET 3.3 9.4 - - - +
351B LEU* 3.3 20.6 - - + +
353B GLU* 1.3 94.3 - - + +
355B LEU* 1.3 53.0 + - - +
357B GLU* 3.1 7.9 + - + +
358B ALA* 2.8 35.9 + - - +
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Residues in contact with LEU 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LEU* 4.3 16.4 - - + -
191B VAL* 4.4 12.3 - - + -
246B LEU* 5.7 1.6 - - + -
247B PRO* 5.8 1.8 - - + -
328B LEU* 4.0 18.5 - - + +
331B ALA* 4.0 33.0 - - + +
332B ILE* 3.7 19.0 - - + +
335B ILE* 4.1 24.0 - - + -
351B LEU* 3.6 21.1 - - + +
352B GLN* 3.0 16.0 + - - +
354B PRO* 1.3 75.2 - - + +
356B LEU* 1.3 57.0 + - - +
358B ALA* 3.2 3.9 + - - +
359B LEU* 2.8 31.0 + - - +
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Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A GLY* 5.5 2.2 - - - +
421A ALA* 4.0 26.7 - - + -
422A LYS* 4.6 11.9 - - - +
425A LEU* 3.5 29.4 - - + -
332B ILE* 3.7 37.7 - - + -
352B GLN* 3.1 24.3 + - + +
353B GLU* 3.7 10.1 - - - +
355B LEU* 1.3 75.8 - - - +
357B GLU* 1.3 58.7 + - - +
359B LEU* 4.5 1.3 - - - -
360B LYS* 3.0 28.1 + - - +
374B PHE* 3.6 8.1 - - + -
378B LEU* 4.1 14.4 - - + -
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Residues in contact with GLU 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A PRO* 4.0 15.7 - - + +
418A GLY* 3.6 25.1 + - - -
184B VAL* 4.8 3.8 - - + -
353B GLU* 3.3 11.5 + - - +
354B PRO* 3.1 11.7 + - + +
356B LEU* 1.3 76.9 - - - +
358B ALA* 1.3 67.7 + - - +
360B LYS* 2.7 39.0 + - - +
361B VAL* 3.0 35.9 + - + +
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Residues in contact with ALA 358 (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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184B VAL* 3.5 28.2 - - + +
187B LEU* 4.2 12.6 - - + -
188B ILE* 3.7 16.4 - - + +
328B LEU* 4.2 9.4 - - + -
354B PRO 2.8 17.0 + - - +
355B LEU 3.5 4.3 - - - +
357B GLU* 1.3 76.3 - - - +
359B LEU* 1.3 62.3 + - - +
361B VAL* 3.2 2.5 - - - +
362B TYR* 3.0 29.1 + - - +
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Residues in contact with LEU 359 (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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325B GLU* 4.3 11.4 - - + +
328B LEU* 3.8 30.7 - - + +
329B LEU* 4.7 9.4 - - + -
332B ILE* 3.7 23.6 - - + -
355B LEU 2.8 16.7 + - - +
356B LEU 3.9 3.6 - - - +
358B ALA* 1.3 75.6 - - - +
360B LYS* 1.3 65.0 + - - +
362B TYR* 4.6 1.1 - - + -
363B VAL* 2.9 51.8 + - + +
374B PHE* 3.9 16.8 - - + -
377B MET* 4.2 20.2 - - + -
378B LEU* 4.2 13.7 - - + -
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Residues in contact with LYS 360 (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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406A GLU* 4.0 10.7 + - - +
410A LYS* 4.4 10.3 - - - +
417A PRO* 3.0 26.3 + - - +
418A GLY* 4.8 1.0 - - - -
420A PHE* 5.8 1.7 - - + +
421A ALA* 6.4 0.2 - - + -
356B LEU 3.0 19.8 + - - +
357B GLU* 2.7 34.9 + - - +
359B LEU* 1.3 77.5 - - - +
361B VAL* 1.3 68.5 + - + +
363B VAL* 4.1 0.9 - - - +
364B ARG* 3.2 56.9 + - - +
374B PHE* 3.4 31.1 - - + -
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Residues in contact with VAL 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B VAL* 4.3 17.0 - - + -
188B ILE* 4.5 5.2 - - + -
357B GLU* 3.0 21.6 + - + +
358B ALA* 3.2 17.0 - - - +
360B LYS* 1.3 83.4 - - + +
362B TYR* 1.3 68.9 + - - +
364B ARG* 3.3 4.4 + - - +
365B LYS* 2.7 37.6 + - - +
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Residues in contact with TYR 362 (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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188B ILE* 3.8 30.1 - - + -
192B ARG* 2.9 29.7 + - - -
322B ASP* 2.7 33.6 + - - -
324B ALA* 3.7 9.6 - - + -
325B GLU* 3.7 19.3 - - + -
328B LEU* 5.0 4.5 - - + -
358B ALA 3.0 16.5 + - - +
359B LEU* 4.0 3.1 - - - +
361B VAL* 1.3 83.2 - - - +
363B VAL* 1.3 63.8 + - + +
365B LYS* 3.2 13.7 + - + +
366B ARG* 3.0 51.4 + - + +
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Residues in contact with VAL 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B GLU* 3.7 20.4 - - - +
359B LEU* 2.9 43.8 + - + +
360B LYS 4.1 1.8 - - - +
362B TYR* 1.3 77.7 - - - +
364B ARG* 1.3 61.0 + - + +
366B ARG 3.3 0.5 + - - -
367B ARG* 3.0 39.0 + - + +
370B ARG 5.5 0.2 - - - +
373B MET* 4.0 13.9 - - + +
374B PHE* 3.8 33.4 - - + +
377B MET* 3.8 17.7 - - + -
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Residues in contact with ARG 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A GLU* 2.8 41.3 + - - -
410A LYS* 4.8 4.2 - - - +
420A PHE* 4.6 1.2 - - - -
360B LYS* 3.2 40.8 + - - +
361B VAL* 3.9 4.3 - - - +
363B VAL* 1.3 79.4 - - + +
365B LYS* 1.3 66.8 + - - +
367B ARG 3.4 5.2 - - - +
368B PRO* 3.3 22.5 - - - +
370B ARG 4.9 1.6 - - - +
371B PRO* 2.9 53.8 + - + +
374B PHE* 3.7 16.1 - - + +
375B PRO* 4.0 13.1 - - - +
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Residues in contact with LYS 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B VAL 2.7 21.7 + - - +
362B TYR* 3.2 15.2 + - + +
364B ARG* 1.3 72.9 - - - +
366B ARG* 1.3 65.8 + - + +
368B PRO* 3.3 14.6 - - - +
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Residues in contact with ARG 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B GLU* 3.7 11.7 + - - +
322B ASP* 3.4 27.0 + - - +
325B GLU* 2.5 44.5 + - - -
362B TYR* 3.0 46.4 + - + +
363B VAL 3.6 7.9 - - - +
365B LYS* 1.3 81.3 - - + +
367B ARG* 1.3 79.9 + - + +
368B PRO* 3.1 7.7 - - - +
370B ARG* 5.1 0.9 + - - -
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Residues in contact with ARG 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU 2.6 30.1 + - - -
320B GLU* 3.2 9.1 + - - +
321B MET* 3.9 0.2 - - - +
325B GLU* 2.7 44.6 + - - -
363B VAL* 3.0 24.3 + - - +
364B ARG* 3.4 9.8 - - - +
366B ARG* 1.3 97.5 - - + +
368B PRO* 1.3 63.3 - - - +
369B SER 3.3 2.9 - - - -
370B ARG* 3.1 66.8 + - - +
371B PRO* 5.0 0.3 - - - +
373B MET* 3.7 25.7 - - - +
377B MET* 4.2 6.7 - - - +
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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