Contacts of the helix formed by residues 345 - 365 (chain A) in PDB entry 5NTI
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 CYS 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A LEU* 1.3 79.8 - - - +
346A GLN* 1.3 67.2 + - - +
347A ASN 4.1 1.8 - - - -
348A ASP* 3.2 44.1 + - - -
349A GLN* 3.2 17.3 + - - +
434A GLN* 4.1 18.6 - - - +
435A GLU* 3.8 28.8 + - - +
438A LYS* 3.7 7.3 - - - +
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Residues in contact with GLN 346 (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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344A LEU 3.9 0.4 + - - -
345A CYS* 1.3 72.2 - - - +
347A ASN* 1.3 64.9 + - - +
349A GLN* 3.1 28.6 + - - +
350A ILE* 3.2 20.8 + - + +
502P GLN* 5.8 4.5 - - - +
506P GLY 4.6 16.5 + - - -
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Residues in contact with ASN 347 (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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345A CYS* 3.4 2.1 - - - -
346A GLN* 1.3 77.5 - - - +
348A ASP* 1.3 81.3 + - - +
350A ILE* 3.3 11.3 + - - +
351A VAL* 3.0 30.9 + - - +
432A GLY 3.2 22.0 + - - +
434A GLN* 3.4 42.5 + - - +
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Residues in contact with ASP 348 (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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344A LEU* 4.6 8.3 - - + +
345A CYS* 3.2 24.0 + - - +
347A ASN* 1.3 87.5 + - - +
349A GLN* 1.3 61.3 + - - +
351A VAL* 3.9 0.7 - - - +
352A LEU* 3.0 38.5 + - + +
433A LEU* 3.6 20.4 - - + -
434A GLN* 2.8 26.4 + - - +
435A GLU* 2.9 33.3 + - - +
439A VAL* 4.2 10.5 - - + +
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Residues in contact with GLN 349 (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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341A PHE* 3.5 48.3 + - + +
342A MET* 3.3 38.5 + - - +
344A LEU* 3.0 23.5 + - + +
345A CYS 3.2 11.5 + - - +
346A GLN* 3.1 19.4 + - - +
348A ASP* 1.3 77.4 - - - +
350A ILE* 1.3 64.0 + - - +
352A LEU* 3.4 0.6 + - - -
353A LEU* 3.0 26.8 + - - +
505P LEU* 4.0 21.3 - - + +
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Residues in contact with ILE 350 (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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346A GLN* 3.2 17.0 + - + +
347A ASN* 3.4 10.5 - - - +
349A GLN* 1.3 77.1 - - - +
351A VAL* 1.3 55.4 + - + +
353A LEU* 3.4 0.7 + - - -
354A LYS* 2.8 47.1 + - + +
499P THR* 5.1 5.6 - - + +
501P LEU* 3.8 20.3 - - + +
502P GLN* 3.7 45.8 - - + +
505P LEU* 3.8 17.9 - - + -
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Residues in contact with VAL 351 (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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347A ASN* 3.0 27.7 + - - +
348A ASP* 3.9 4.5 - - - +
349A GLN 3.4 0.2 - - - -
350A ILE* 1.3 79.5 - - + +
352A LEU* 1.3 62.8 + - - +
354A LYS* 4.0 4.1 - - - +
355A ALA* 3.1 26.0 + - + +
430A ARG* 3.8 14.4 - - + -
431A PRO 3.6 20.9 - - - +
432A GLY* 3.9 20.6 - - - +
433A LEU* 3.7 20.6 - - + -
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Residues in contact with LEU 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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341A PHE* 4.2 10.8 - - + -
344A LEU* 3.6 28.9 - - + -
348A ASP 3.0 23.2 + - - +
349A GLN 4.0 2.7 - - - +
351A VAL* 1.3 75.6 - - - +
353A LEU* 1.3 57.7 + - - +
355A ALA* 3.8 0.5 - - - +
356A GLY* 2.8 29.3 + - - -
425A LEU* 3.4 27.6 - - + +
426A ILE* 3.9 17.0 - - + -
427A ASN 3.5 29.6 - - - +
430A ARG* 3.9 12.8 + - + -
433A LEU* 4.3 9.4 - - + -
439A VAL* 4.3 15.9 - - + -
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Residues in contact with LEU 353 (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 VAL* 4.4 12.6 - - + +
332A VAL* 4.0 28.7 - - + -
335A ALA* 3.8 15.3 - - + -
341A PHE* 3.8 15.7 - - + -
349A GLN 3.0 10.8 + - - +
350A ILE 3.9 2.2 - - - +
352A LEU* 1.3 75.2 - - - +
354A LYS* 1.3 59.9 + - - +
357A ALA* 2.8 38.8 + - + +
425A LEU* 3.8 18.6 - - + -
505A LEU* 5.3 0.2 - - - -
501P LEU* 4.0 18.8 - - + -
505P LEU* 3.8 39.5 - - + -
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Residues in contact with LYS 354 (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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350A ILE* 2.8 30.9 + - + +
351A VAL* 4.0 4.5 - - - +
353A LEU* 1.3 74.0 - - - +
355A ALA* 1.3 60.7 + - - +
357A ALA* 4.6 2.6 + - - +
358A MET* 5.4 1.4 + - - +
504A GLU* 3.7 26.3 + - + +
505A LEU* 3.9 40.3 - - + +
506A PHE* 5.4 5.7 - - - -
501P LEU* 3.9 8.2 - - + +
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Residues in contact with ALA 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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351A VAL* 3.1 18.6 + - + +
354A LYS* 1.3 78.4 - - - +
356A GLY* 1.3 59.7 + - - +
357A ALA 3.7 0.2 - - - -
358A MET* 4.9 2.1 + - - +
359A GLU* 3.9 19.6 + - - +
430A ARG* 3.6 33.4 - - + +
431A PRO* 6.3 0.9 - - + -
476A CYS* 4.8 6.2 - - - +
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Residues in contact with GLY 356 (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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352A LEU 2.8 22.3 + - - -
355A ALA* 1.3 74.5 - - - +
357A ALA* 1.3 64.5 + - - +
358A MET 3.4 2.0 - - - -
359A GLU* 3.3 5.6 + - - +
360A VAL* 3.0 30.1 + - - +
424A VAL* 4.5 3.1 - - - +
425A LEU* 4.7 7.6 - - - -
430A ARG* 3.7 17.0 - - - +
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Residues in contact with ALA 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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328A ILE* 3.9 27.6 - - + -
331A VAL* 4.0 17.7 - - + +
332A VAL* 5.8 0.9 - - + -
353A LEU* 2.8 30.6 + - + +
354A LYS 4.6 1.7 + - - +
355A ALA 3.7 0.4 - - - -
356A GLY* 1.3 73.4 - - - +
358A MET* 1.3 63.2 + - - +
360A VAL* 3.3 3.6 + - - +
361A VAL* 3.2 26.3 + - - +
425A LEU* 5.0 0.2 - - - +
505A LEU* 4.4 11.7 - - + -
506A PHE* 5.7 0.2 - - + -
501P LEU* 6.4 0.9 - - + -
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Residues in contact with MET 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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324A LEU* 3.8 46.7 - - + -
328A ILE* 5.1 1.6 - - - -
354A LYS 5.4 1.9 + - - +
355A ALA 4.9 2.6 + - - +
356A GLY 3.4 0.2 - - - -
357A ALA* 1.3 78.8 - - - +
359A GLU* 1.3 63.0 + - - +
361A VAL* 3.4 6.5 + - - +
362A LEU* 3.0 47.1 + - + +
400A ILE* 5.1 4.7 - - + -
475A LEU 5.8 0.2 - - - +
476A CYS* 3.8 24.5 - - + -
479A HIS* 4.0 26.7 - - + +
506A PHE* 3.7 29.9 - - + -
601A C3S 4.9 8.7 - - + -
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Residues in contact with GLU 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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355A ALA 3.9 7.2 + - - +
356A GLY 3.3 11.0 + - - +
358A MET* 1.3 78.1 - - - +
360A VAL* 1.3 62.0 + - - +
362A LEU* 3.4 3.9 + - - +
363A VAL* 3.2 26.7 + - - +
424A VAL* 3.6 19.7 - - + +
427A ASN* 5.2 1.2 + - - -
430A ARG* 2.8 42.6 + - - -
469A LYS 5.3 1.0 - - - +
472A LEU* 3.7 34.5 - - + +
473A ARG* 4.0 18.0 + - - +
476A CYS* 3.6 21.2 - - - +
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Residues in contact with VAL 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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331A VAL* 3.7 30.7 - - + -
334A PHE* 5.1 6.5 - - + -
356A GLY 3.0 17.9 + - - +
357A ALA 3.3 6.9 + - - +
359A GLU* 1.3 75.9 - - - +
361A VAL* 1.3 52.5 + - - +
363A VAL* 3.1 7.3 + - - +
364A ARG* 2.8 50.3 + - - +
421A THR* 3.8 36.3 - - - +
424A VAL* 3.9 10.3 - - + -
425A LEU* 4.3 13.5 - - + -
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Residues in contact with VAL 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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324A LEU* 3.8 24.7 - - + -
327A ALA* 4.1 21.3 - - + -
328A ILE* 3.9 22.0 - - + -
331A VAL* 3.7 17.5 - - + -
357A ALA 3.2 15.6 + - - +
358A MET* 3.4 9.2 + - - +
360A VAL* 1.3 74.1 - - - +
362A LEU* 1.3 59.9 + - + +
364A ARG* 3.3 9.5 + - - +
365A MET* 2.9 29.3 + - - +
601A C3S 4.2 20.0 - - + +
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Residues in contact with LEU 362 (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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358A MET* 3.0 44.6 + - + +
359A GLU 3.7 4.9 - - - +
360A VAL 3.3 0.2 - - - -
361A VAL* 1.3 77.8 - - + +
363A VAL* 1.3 61.5 + - - +
365A MET* 3.5 19.1 - - - +
366A CYS 4.5 0.9 + - - -
400A ILE* 3.8 41.9 - - + +
403A PHE* 3.6 20.3 - - + -
404A SER* 4.8 2.3 + - - -
407A LEU* 4.5 1.4 - - - +
472A LEU* 4.2 12.6 - - + -
475A LEU* 3.8 34.1 - - + -
476A CYS* 4.3 9.0 - - - -
601A C3S 5.7 6.1 - - + -
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Residues in contact with VAL 363 (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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359A GLU 3.2 16.0 + - - +
360A VAL* 3.1 7.1 + - - +
362A LEU* 1.3 73.5 - - - +
364A ARG* 1.3 63.1 + - - +
365A MET 3.0 5.4 + - - -
366A CYS* 3.2 29.3 + - - +
403A PHE* 4.4 4.9 - - + -
407A LEU* 3.9 13.3 - - + +
412A PHE* 5.2 2.0 - - + -
417A ILE* 4.5 8.2 - - + +
420A TYR* 3.7 36.6 - - + -
421A THR* 3.6 20.4 - - + -
424A VAL* 4.2 13.9 - - + -
472A LEU* 4.3 13.5 - - + -
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Residues in contact with ARG 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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281A TYR* 4.0 28.4 - - + +
284A THR* 2.9 48.5 + - - -
285A CYS* 4.6 2.0 - - - -
327A ALA* 4.6 1.9 + - - -
330A TYR* 3.8 14.3 + - - +
331A VAL* 4.3 14.9 - - - +
334A PHE* 3.7 21.2 - - - +
360A VAL* 2.8 40.8 + - + +
361A VAL* 3.7 7.6 - - - +
363A VAL* 1.3 72.8 - - - +
365A MET* 1.3 61.1 + - - +
366A CYS 3.2 0.7 + - - -
367A ARG* 3.3 28.9 + - - +
417A ILE* 4.9 3.4 - - - -
421A THR* 4.4 10.0 + - + -
601A C3S 3.4 41.9 + - + +
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Residues in contact with MET 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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361A VAL 2.9 16.6 + - - +
362A LEU* 3.5 14.6 - - - +
363A VAL 3.0 0.8 + - - -
364A ARG* 1.3 77.4 - - - +
366A CYS* 1.3 56.2 + - - +
368A ALA* 2.8 20.8 + - - -
369A TYR* 3.2 12.1 + - + +
376A VAL* 3.8 30.1 - - + -
400A ILE* 3.5 34.1 - - + +
401A PHE* 4.3 17.7 - - + -
404A SER* 3.8 21.1 - - - +
601A C3S 3.7 42.8 - - + -
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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
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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