Contacts of the helix formed by residues 367 - 389 (chain A) in PDB entry 3NGN
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 TYR 367 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A ARG* 3.4 41.0 + - + -
323A LYS* 4.3 20.4 + - - -
362A HIS* 3.8 19.3 - + + -
364A ASP* 2.8 46.5 + - + +
366A GLU* 1.3 94.4 + - + +
368A SER* 1.3 63.7 + - - +
369A ASP* 3.0 7.6 - - - -
370A VAL* 3.0 29.9 + - + +
371A LYS* 3.2 13.7 + - - +
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Residues in contact with SER 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ASP 4.3 0.4 + - - -
365A PRO 3.9 10.0 + - - -
366A GLU 3.7 2.6 + - - -
367A TYR* 1.3 75.1 - - - +
369A ASP* 1.3 56.3 + - - +
371A LYS* 3.5 16.3 + - - +
372A LEU* 3.0 28.4 + - - +
419A VAL* 5.0 2.5 - - - +
434A ASP* 3.0 47.4 + - - +
436A LYS* 3.4 13.4 - - - +
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Residues in contact with ASP 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ALA* 5.5 2.8 - - - +
319A ARG* 2.6 50.0 + - - +
320A VAL* 5.6 0.7 - - - +
367A TYR* 3.2 10.4 - - - +
368A SER* 1.3 70.1 + - - +
370A VAL* 1.3 72.4 + - - +
372A LEU* 3.3 3.9 + - - +
373A ILE* 2.9 46.3 + - + +
434A ASP 3.1 19.7 + - - +
435A PHE* 3.9 20.1 - - + +
436A LYS* 3.9 7.7 - - + +
437A GLU* 5.7 2.6 - - + +
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Residues in contact with VAL 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ARG* 3.7 27.8 - - + +
320A VAL* 4.2 15.7 - - + -
323A LYS* 3.8 17.0 - - + -
362A HIS* 4.0 8.3 - - + -
367A TYR* 3.0 34.0 + - + +
369A ASP* 1.3 84.8 - - - +
371A LYS* 1.3 53.1 + - - +
373A ILE* 3.2 1.7 + - - +
374A GLN* 2.7 62.0 + - + +
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Residues in contact with LYS 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A MET* 4.0 4.2 - - + +
362A HIS* 3.1 31.6 - - + +
363A TRP 2.8 25.7 + - - -
364A ASP 3.4 18.5 + - - -
365A PRO* 3.7 9.3 - - + +
367A TYR* 3.2 12.2 + - + +
368A SER* 3.7 16.2 - - - +
370A VAL* 1.3 74.9 - - - +
372A LEU* 1.3 62.1 + - - +
374A GLN* 3.4 9.7 + - - +
375A THR* 2.9 29.8 + - - -
411A LEU 4.4 5.8 - - - +
412A ASN* 2.9 28.2 + - - +
413A SER* 4.2 15.9 - - - +
419A VAL* 4.2 4.5 - - + -
556A AMP 3.5 9.5 + - - -
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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 SER 3.0 18.2 + - - +
369A ASP* 3.7 5.2 - - - +
371A LYS* 1.3 76.8 - - - +
373A ILE* 1.3 63.5 + - - +
375A THR* 3.1 6.3 + - - -
376A MET* 2.9 36.8 + - + +
418A GLY* 3.8 12.3 - - - +
419A VAL* 3.8 32.0 - - + +
422A TYR* 4.1 18.2 - - + -
428A VAL* 4.5 8.7 - - + -
432A HIS* 4.9 3.6 - - + -
434A ASP* 4.5 16.6 - - + -
435A PHE* 3.6 35.4 - - + -
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Residues in contact with ILE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A MET* 3.9 27.4 - - + -
320A VAL* 4.0 17.9 - - + -
369A ASP* 2.9 30.3 + - + +
370A VAL 3.9 2.0 - - - +
372A LEU* 1.3 77.8 - - - +
374A GLN* 1.3 57.1 + - - +
376A MET* 3.1 22.5 + - + +
377A MET* 2.9 57.4 + - + +
435A PHE* 4.0 17.3 - - + -
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Residues in contact with GLN 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A PHE* 3.7 29.1 - - + +
320A VAL* 4.9 2.8 + - + -
323A LYS* 3.7 10.5 + - - +
325A ASN* 2.8 32.8 - - - +
361A MET* 3.4 17.1 - - + +
362A HIS* 2.9 25.5 + - - +
370A VAL* 2.7 42.6 + - + +
371A LYS* 3.7 4.8 - - - +
373A ILE* 1.3 71.2 - - - +
375A THR* 1.3 56.8 + - - +
377A MET* 3.5 19.3 + - + +
378A PHE* 2.9 30.0 + - - +
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Residues in contact with THR 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A MET* 3.7 18.4 - - + +
371A LYS 2.9 15.2 + - - -
372A LEU* 3.1 8.9 + - - -
374A GLN* 1.3 76.6 - - - +
376A MET* 1.3 56.4 + - - +
378A PHE* 3.2 2.4 + - + +
379A VAL* 2.9 30.0 + - + +
407A LEU* 6.1 0.4 - - + -
411A LEU* 4.0 6.3 - - + +
419A VAL* 3.6 20.4 - - + +
422A TYR* 3.9 12.3 - - + -
423A LEU* 3.8 40.6 - - + -
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Residues in contact with MET 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LEU* 2.9 23.4 + - + +
373A ILE* 3.1 49.1 + - + +
375A THR* 1.3 71.5 - - - +
377A MET* 1.3 66.4 + - + +
379A VAL* 3.9 0.9 - - - +
380A SER* 3.0 27.2 + - - -
422A TYR* 3.7 37.0 + - + +
428A VAL* 5.4 0.7 - - - -
435A PHE* 3.5 25.6 - - + -
460A ILE* 3.9 25.8 - - + -
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Residues in contact with MET 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A PHE* 3.8 26.9 - - + +
305A VAL* 3.8 24.2 - - + +
306A ALA* 3.7 29.6 - - - -
309A ASN* 5.7 1.3 - - + +
316A MET* 4.7 3.4 - - + -
320A VAL* 3.6 27.6 - - + -
373A ILE* 2.9 26.1 + - + +
374A GLN* 3.6 24.9 - - + +
376A MET* 1.3 77.9 - - + +
378A PHE* 1.3 58.5 + - - +
380A SER* 4.1 4.9 - - - -
381A GLU* 2.7 37.2 + - + +
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Residues in contact with PHE 378 (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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300A VAL* 4.2 17.7 - - + -
302A PHE* 3.6 26.6 - + + -
327A GLY* 3.6 19.7 - - - -
328A VAL 3.7 13.7 - - - -
329A ALA* 5.4 0.4 - - + -
357A ALA* 3.7 21.8 - - + -
358A ASN 3.7 9.2 - - - -
359A ALA* 3.6 16.2 - - + -
361A MET* 4.2 6.7 - - + -
374A GLN 2.9 19.8 + - - +
375A THR* 3.6 4.0 - - + +
377A MET* 1.3 78.3 - - - +
379A VAL* 1.3 59.7 + - + +
381A GLU* 3.7 2.0 - - - -
382A VAL* 2.9 44.6 + - + +
407A LEU* 3.4 34.5 - - + -
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Residues in contact with VAL 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A THR* 2.9 22.0 + - + +
378A PHE* 1.3 80.2 - - + +
380A SER* 1.3 57.6 + - - +
382A VAL* 3.1 8.1 + - - +
383A LYS* 2.8 28.8 + - - +
405A LEU* 6.4 1.3 - - + -
407A LEU* 4.8 9.0 - - + -
422A TYR* 3.8 20.4 - - + +
423A LEU* 3.5 31.0 - - + -
462A HIS* 3.9 15.7 - - + -
464A PHE* 3.7 29.2 - - + -
466A LEU* 5.4 2.0 - - + -
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Residues in contact with SER 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A MET 3.0 20.0 + - - -
377A MET* 3.8 5.9 + - - -
379A VAL* 1.3 74.5 - - - +
381A GLU* 1.3 67.3 + - - +
383A LYS* 2.3 51.4 - - - +
384A ASN* 3.4 5.7 - - - +
422A TYR* 5.1 0.6 + - - -
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Residues in contact with GLU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A VAL* 3.9 35.1 - - + +
305A VAL* 4.0 28.2 - - + +
309A ASN* 5.2 2.6 + - - -
377A MET* 2.7 28.2 + - - +
378A PHE 3.9 2.5 - - - +
380A SER* 1.3 79.5 + - - +
382A VAL* 1.3 62.1 + - - +
384A ASN* 3.1 27.5 + - - +
385A ILE* 3.4 16.2 + - - +
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Residues in contact with VAL 382 (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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300A VAL* 5.8 0.2 - - + -
329A ALA* 4.9 2.9 - - + -
355A ILE* 4.1 18.6 - - + -
357A ALA* 4.2 20.4 - - + -
378A PHE* 2.9 35.6 + - + +
379A VAL* 3.1 9.6 + - - +
381A GLU* 1.3 74.7 - - + +
383A LYS* 1.3 58.7 + - - +
384A ASN 2.9 8.8 + - - -
385A ILE* 3.1 16.4 + - + +
386A LEU* 3.0 19.7 + - + +
405A LEU* 4.0 32.8 - - + -
407A LEU* 6.0 0.2 - - + -
464A PHE* 4.5 4.9 - - + -
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Residues in contact with LYS 383 (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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379A VAL* 2.8 16.3 + - - +
380A SER* 2.3 42.1 - - - +
382A VAL* 1.3 68.4 - - - +
384A ASN* 1.3 72.1 + - - +
386A LEU* 4.2 8.1 - - + -
387A GLU* 4.6 14.3 - - + +
422A TYR* 5.5 0.2 + - - -
461A THR 5.0 2.2 + - - -
462A HIS* 4.1 14.5 - - - +
463A GLY* 3.6 31.6 - - - +
464A PHE* 3.6 22.1 - - + -
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Residues in contact with ASN 384 (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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380A SER 3.4 6.1 - - - +
381A GLU* 3.1 27.7 + - - +
382A VAL 2.9 1.6 + - - -
383A LYS* 1.3 85.1 - - - +
385A ILE* 1.3 67.8 + - - +
386A LEU* 3.0 5.6 - - - +
387A GLU* 3.1 37.8 + - - +
388A LYS* 3.1 16.6 + - - +
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Residues in contact with ILE 385 (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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296A GLN* 4.4 1.0 - - - +
298A HIS* 3.5 57.0 - - + +
300A VAL* 4.7 11.2 - - + -
329A ALA* 4.2 16.4 - - + -
331A VAL* 4.0 19.9 - - + +
355A ILE* 4.7 12.6 - - + -
381A GLU 3.5 17.0 - - - +
382A VAL* 3.1 15.4 + - + +
384A ASN* 1.3 82.0 - - + +
386A LEU* 1.3 64.0 + - - +
387A GLU 3.2 0.3 + - - -
388A LYS* 3.5 5.6 + - - +
389A ALA* 3.4 21.5 + - - +
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Residues in contact with LEU 386 (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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355A ILE* 3.6 30.1 - - + -
382A VAL* 3.0 16.5 + - + +
383A LYS* 4.2 6.7 - - + -
384A ASN 3.9 4.7 - - - +
385A ILE* 1.3 79.4 - - - +
387A GLU* 1.3 67.7 + - + +
389A ALA* 3.7 11.7 - - - -
402A SER* 3.8 24.5 - - - +
403A ILE* 3.8 32.4 - - + +
405A LEU* 5.5 2.7 - - + -
464A PHE* 3.6 29.8 - - + -
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Residues in contact with GLU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LYS* 4.6 13.6 - - + +
384A ASN* 3.1 36.7 + - - +
386A LEU* 1.3 81.1 - - + +
388A LYS* 1.3 69.2 + - - +
389A ALA 2.8 10.3 + - - +
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Residues in contact with LYS 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLN* 4.5 15.9 - - - +
298A HIS* 6.2 2.2 - - + +
384A ASN 3.1 12.4 + - - +
385A ILE* 4.0 5.4 - - - +
387A GLU* 1.3 77.8 - - - +
389A ALA* 1.3 57.7 + - + +
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Residues in contact with ALA 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A VAL* 5.8 3.1 - - + -
296A GLN* 3.1 37.7 - - - +
331A VAL* 4.9 13.7 - - + -
353A LEU* 4.9 11.0 - - + +
385A ILE 3.4 7.4 + - - +
386A LEU 3.7 12.1 - - - -
387A GLU 2.8 14.6 + - - +
388A LYS* 1.3 76.3 - - - +
403A ILE* 4.3 16.5 - - + +
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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