Contacts of the helix formed by residues 351 - 373 (chain A) in PDB entry 3DRW
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 351 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A PRO 3.8 1.8 + - - -
350A LEU* 1.3 74.6 - - - +
352A GLU* 1.3 64.6 + - - +
353A GLU* 3.5 10.1 + - - +
354A GLU* 3.1 37.6 + - - +
355A LEU* 3.0 23.3 + - - +
413A LYS* 4.4 4.9 - - - +
450A HIS* 4.8 0.8 + - - -
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Residues in contact with GLU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A SER* 1.3 74.6 - - - +
353A GLU* 1.3 57.5 + - - +
355A LEU* 3.5 3.0 + - + +
356A ALA* 2.9 29.3 + - - +
404A LYS* 5.9 0.5 + - - -
412A TYR 5.0 0.9 - - - +
413A LYS* 3.8 38.5 - - + +
414A VAL 4.0 15.3 + - - +
415A VAL* 3.9 21.5 - - + +
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Residues in contact with GLU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A SER* 3.1 9.9 + - - +
352A GLU* 1.3 79.2 - - - +
354A GLU* 1.3 57.5 + - + +
356A ALA* 3.3 9.2 + - - +
357A LYS* 2.9 63.7 + - - +
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Residues in contact with GLU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU* 3.5 14.0 - - + +
351A SER* 3.1 30.7 + - - +
353A GLU* 1.3 73.0 - - + +
355A LEU* 1.3 64.5 + - - +
357A LYS* 3.2 18.9 + - - +
358A SER* 3.0 19.4 + - - -
446A PHE* 3.2 33.0 - - + -
449A ARG* 3.3 28.6 + - - -
450A HIS* 2.8 31.2 + - - -
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Residues in contact with LEU 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A ILE* 3.7 20.9 - - + -
342A TYR* 3.4 30.4 - - + -
344A THR* 4.0 17.9 - - + +
348A ASN* 4.5 1.6 - - - +
350A LEU* 3.8 31.2 - - + +
351A SER 3.0 26.0 + - - +
352A GLU* 3.8 7.9 - - - +
354A GLU* 1.3 74.3 - - - +
356A ALA* 1.3 63.8 + - - +
358A SER* 3.4 1.8 + - - -
359A LEU* 3.1 27.7 + - - +
413A LYS* 4.2 21.1 - - + +
415A VAL* 4.1 15.0 - - + -
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Residues in contact with ALA 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A GLU 2.9 19.3 + - - +
353A GLU* 3.6 13.2 - - - +
354A GLU 3.3 0.2 - - - -
355A LEU* 1.3 77.2 - - - +
357A LYS* 1.3 56.6 + - + +
359A LEU* 3.3 2.9 + - - +
360A GLU* 2.7 30.6 + - - +
415A VAL* 3.8 19.6 - - + +
417A ILE* 4.2 15.4 - - + +
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Residues in contact with LYS 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.9 23.4 - - + +
353A GLU* 2.9 59.5 + - - +
354A GLU* 3.2 22.3 + - - +
356A ALA* 1.3 77.4 - - - +
358A SER* 1.3 58.0 + - - +
360A GLU* 3.3 13.5 + - - +
361A PHE* 2.8 30.0 + - - +
442A THR* 5.4 0.2 - - - -
446A PHE* 3.9 23.8 - - + -
449A ARG* 5.4 3.6 - - - +
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Residues in contact with SER 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A TYR* 2.6 20.5 + - - -
350A LEU* 5.3 1.1 - - - -
354A GLU 3.0 16.1 + - - -
355A LEU* 3.6 5.8 - - - -
357A LYS* 1.3 76.0 - - - +
359A LEU* 1.3 62.7 + - - +
361A PHE 3.2 1.2 + - - -
362A GLY 3.1 17.2 + - - -
439A ALA* 2.6 34.1 + - - -
442A THR* 3.1 23.4 + - - -
443A TYR* 3.7 5.5 + - - -
446A PHE* 3.8 9.8 - - - -
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Residues in contact with LEU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A GLN* 4.0 21.1 - - + -
340A LEU* 3.4 34.3 - - + +
341A MET 4.0 4.7 - - - -
342A TYR* 3.5 34.1 - - + +
355A LEU 3.1 18.5 + - - +
356A ALA 3.6 6.3 - - - +
358A SER* 1.3 73.8 - - - +
360A GLU* 1.3 66.5 + - - +
362A GLY 3.0 2.3 + - - +
363A THR 3.0 19.1 + - - -
415A VAL* 3.7 35.9 - - + +
417A ILE* 3.5 19.0 - - + +
439A ALA* 4.6 4.0 - - + -
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Residues in contact with GLU 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A ALA 2.7 21.4 + - - +
357A LYS* 3.3 12.6 + - - +
359A LEU* 1.3 74.5 - - - +
361A PHE* 1.3 59.4 + - - +
363A THR* 3.4 1.8 + - - +
364A THR* 2.6 40.6 + - - +
381A TYR* 4.7 3.2 + - - +
385A LEU* 4.1 11.4 - - - +
389A PHE* 4.0 18.1 - - + -
417A ILE* 3.4 14.1 - - + +
420A ARG* 2.9 26.1 + - - -
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Residues in contact with PHE 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.7 28.3 - - + -
2A ILE* 3.8 26.9 - - + -
3A PRO* 4.3 4.5 - - + -
108A LEU* 4.6 9.9 - - + -
357A LYS 2.8 17.5 + - - +
358A SER 3.6 4.7 - - - +
359A LEU 3.1 0.6 - - - -
360A GLU* 1.3 76.7 - - - +
362A GLY* 1.3 62.4 + - - +
365A LEU* 2.9 32.6 + - + +
381A TYR* 3.3 48.4 - + - +
438A GLY* 3.3 33.0 - - - -
441A LEU* 4.6 7.9 - - + -
442A THR* 3.3 21.1 - - + -
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Residues in contact with GLY 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A SER 3.1 8.4 + - - -
359A LEU 3.0 6.9 + - - -
361A PHE* 1.3 77.8 - - - +
363A THR* 1.3 61.9 + - - +
365A LEU* 3.8 1.7 - - - +
366A ALA 3.0 18.0 + - - -
435A ILE* 3.6 42.3 - - - +
438A GLY* 4.2 4.0 - - - -
439A ALA* 3.8 9.4 - - - +
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Residues in contact with THR 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A LEU* 4.0 15.1 - - - +
359A LEU 3.0 13.4 + - - +
360A GLU* 3.5 10.1 - - - +
362A GLY* 1.3 75.4 - - - +
364A THR* 1.3 61.1 - - - +
366A ALA* 3.4 2.6 + - - +
367A ALA* 2.8 29.6 + - - +
389A PHE* 4.4 2.0 - - + -
417A ILE* 3.9 18.4 - - + -
418A PRO 4.1 4.7 - - - +
419A THR* 3.4 14.3 - - - +
420A ARG* 2.9 42.5 + - + +
435A ILE* 4.3 10.2 - - - +
1484A AMP 5.1 3.6 + - - -
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Residues in contact with THR 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A GLU* 2.6 28.3 + - - +
363A THR* 1.3 76.7 - - - +
365A LEU* 1.3 59.8 + - - +
367A ALA* 3.2 1.2 + - - -
368A ALA* 2.9 26.0 + - - +
381A TYR* 3.4 32.0 + - + +
384A GLY* 3.5 31.0 - - - +
385A LEU* 3.5 14.4 - - + +
420A ARG* 2.9 25.6 + - - +
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Residues in contact with LEU 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A THR* 4.1 9.0 - - + -
105A LEU* 6.0 0.7 - - + -
108A LEU* 3.9 42.0 - - + -
361A PHE* 2.9 21.7 + - + +
362A GLY 3.8 3.4 - - - +
364A THR* 1.3 75.0 - - - +
366A ALA* 1.3 65.0 + - - +
368A ALA* 3.3 5.0 + - + +
369A ARG* 2.9 22.5 + - - +
375A ILE* 4.4 19.1 - - + -
381A TYR* 3.8 18.8 - - + -
434A THR* 3.6 30.1 - - + +
437A ALA* 5.1 1.3 - - + -
438A GLY* 3.9 18.4 - - - +
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Residues in contact with ALA 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A GLY 3.0 7.2 + - - +
363A THR* 3.7 7.0 - - - +
365A LEU* 1.3 76.3 - - - +
367A ALA* 1.3 57.1 + - - +
369A ARG* 3.2 3.3 + - - +
370A ALA* 2.8 31.7 + - - +
431A LEU* 3.7 20.8 - - + +
434A THR* 3.8 12.6 - - + +
435A ILE* 3.5 32.8 - - + -
1484A AMP 4.4 11.0 - - - +
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Residues in contact with ALA 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A THR 2.8 21.0 + - - +
364A THR 3.2 6.0 + - - +
366A ALA* 1.3 70.9 - - - +
368A ALA* 1.3 55.7 + - - +
370A ALA 3.4 0.5 + - - -
371A SER* 2.7 38.4 + - - -
384A GLY* 4.0 6.3 - - - +
387A VAL* 4.0 18.2 - - + -
420A ARG* 3.6 30.5 - - + +
422A VAL* 3.4 10.9 - - + +
1484A AMP 4.3 3.5 - - - -
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Residues in contact with ALA 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A THR 2.9 13.6 + - - +
365A LEU* 3.5 9.2 - - - +
367A ALA* 1.3 76.5 - - - +
369A ARG* 1.3 56.2 + - - +
371A SER* 3.1 5.7 + - - -
372A LEU* 2.9 34.8 + - + +
375A ILE* 4.1 13.7 - - + -
380A ASP 3.4 27.8 - - - +
381A TYR* 4.3 4.9 - - - -
383A VAL* 4.5 1.8 - - + -
384A GLY* 3.7 13.8 - - - +
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Residues in contact with ARG 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ARG* 4.8 6.5 - - - +
100A ILE* 3.9 24.2 - - - +
104A THR* 4.0 4.9 + - - -
365A LEU 2.9 16.4 + - - +
366A ALA* 3.6 4.9 - - - +
368A ALA* 1.3 75.6 - - - +
370A ALA* 1.3 57.7 + - - +
372A LEU* 5.1 0.7 - - - -
373A GLY* 2.7 43.1 + - - +
374A ASP 5.1 0.9 - - - +
375A ILE* 4.0 15.2 - - + +
427A LEU* 3.7 30.6 - - + +
429A VAL 3.0 26.7 + - - -
430A GLY* 3.5 12.5 + - - -
431A LEU* 3.9 6.2 - - + +
434A THR* 3.0 35.4 + - + -
1485A NA 3.3 26.0 - - - -
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Residues in contact with ALA 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A ALA 2.8 20.2 + - - +
367A ALA 3.7 4.5 - - - +
369A ARG* 1.3 73.3 - - - +
371A SER* 1.3 58.5 + - - +
422A VAL* 4.0 11.4 - - + -
425A PRO* 3.6 13.6 - - + +
426A VAL* 2.8 33.6 + - - +
427A LEU 3.4 20.7 + - - +
431A LEU* 3.9 18.5 - - + +
1484A AMP 4.1 4.7 - - - +
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Residues in contact with SER 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A ALA 2.7 21.1 + - - -
368A ALA 3.1 3.8 + - - -
370A ALA* 1.3 79.4 - - - +
372A LEU* 1.3 60.0 + - - +
383A VAL* 3.9 19.7 - - - -
387A VAL* 3.9 10.2 - - - +
422A VAL* 3.2 23.6 - - - +
426A VAL* 3.3 13.3 + - - +
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Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ALA 2.9 19.8 + - - +
371A SER* 1.3 79.1 - - - +
373A GLY* 1.3 56.0 + - - +
374A ASP* 3.3 23.3 + - - +
375A ILE* 4.7 1.3 - - + -
380A ASP* 3.4 46.4 - - + +
383A VAL* 4.0 32.8 - - + -
426A VAL* 3.5 8.2 - - - +
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Residues in contact with GLY 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ARG* 3.4 21.5 + - - -
369A ARG* 2.7 28.1 + - - +
372A LEU* 1.3 71.0 - - - +
374A ASP* 1.3 62.4 + - - +
426A VAL* 3.3 16.2 - - - +
427A LEU* 3.6 22.4 - - - +
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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
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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