Contacts of the helix formed by residues 426 - 448 (chain A) in PDB entry 5TBY
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 ALA 426 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A TYR* 3.5 4.6 + - - -
423A ALA* 2.7 43.7 - - - +
425A GLY 1.3 61.2 + - - +
427A LEU* 1.3 63.7 + - + +
429A LYS* 2.9 31.6 - - - +
430A ALA 2.9 9.9 + - - -
600A PRO 4.7 1.1 + - - -
601A LEU* 3.3 33.8 - - - +
602A ASN* 4.2 6.1 - - - +
605A VAL* 5.2 1.1 - - + -
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Residues in contact with LEU 427 (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 PHE* 3.3 32.1 - - + -
395A LEU* 4.8 14.6 - - + -
424A THR* 2.9 10.8 + - - +
426A ALA* 1.3 78.3 - - - +
428A ALA* 1.3 57.9 + - - +
429A LYS 3.1 0.3 + - - -
430A ALA* 3.3 7.6 + - + +
431A VAL* 2.9 31.7 + - + +
601A LEU* 4.7 0.9 - - + -
605A VAL* 3.4 41.6 - - + +
609A TYR* 3.3 34.1 - - + +
621A PHE* 4.3 18.8 - - + -
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Residues in contact with ALA 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A VAL* 4.1 20.2 - - + +
274A ILE* 5.3 3.1 - - + -
286A PHE* 5.9 0.4 - - + -
356A ILE* 4.2 23.3 - - + +
359A PHE* 4.5 7.1 - - + -
424A THR 3.2 5.1 + - - +
425A GLY* 3.6 15.3 - - - -
427A LEU* 1.3 76.6 - - - +
429A LYS* 1.3 56.2 + - - +
431A VAL* 3.0 13.0 - - + -
432A TYR* 2.8 34.3 + - - +
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Residues in contact with LYS 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LYS* 4.0 40.0 + - + +
271A SER 5.3 0.7 - - - +
273A VAL* 5.9 1.1 - - - -
422A TYR* 5.8 9.3 - - + -
425A GLY* 3.3 8.2 - - - +
426A ALA* 2.9 34.6 + - - +
428A ALA* 1.3 76.1 - - - +
430A ALA* 1.3 62.2 + - - +
431A VAL 3.2 0.7 - - - -
432A TYR* 5.0 1.6 - - - -
433A GLU* 3.2 28.9 + - - +
599A ASP* 2.7 39.2 + - - +
600A PRO* 2.8 33.6 + - - +
601A LEU* 4.6 2.5 - - + -
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Residues in contact with ALA 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LYS* 5.5 2.2 - - - +
426A ALA 2.9 5.9 + - - -
427A LEU* 3.6 7.4 - - + +
429A LYS* 1.3 75.3 - - - +
431A VAL* 1.3 58.9 + - - +
433A GLU* 4.3 1.7 - - - +
434A ARG* 3.1 32.8 + - - +
601A LEU* 3.2 35.6 - - + +
621A PHE* 3.9 21.3 - - + -
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Residues in contact with VAL 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LEU* 3.3 40.6 - - + -
356A ILE* 3.3 18.6 - - + -
359A PHE* 5.4 4.9 - - + -
427A LEU* 2.9 13.0 + - + +
428A ALA* 3.0 33.9 - - - +
430A ALA* 1.3 75.1 - - - +
432A TYR* 1.3 60.9 + - - +
434A ARG* 2.8 11.0 + - - +
435A MET* 2.7 31.9 + - - -
620A LEU* 4.8 6.6 - - + +
621A PHE* 4.7 14.6 - - + -
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Residues in contact with TYR 432 (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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230A PHE* 3.0 61.4 + + + -
231A GLY* 3.6 2.4 + - - -
268A LEU* 4.6 19.7 - - + -
270A LYS* 4.9 8.1 - - + -
273A VAL* 5.0 8.3 - - + -
283A TYR* 3.2 47.8 - + - -
285A ILE* 5.0 2.7 - - + -
352A LEU* 5.9 0.4 - - - -
356A ILE* 4.0 26.2 - - + -
428A ALA 2.8 24.5 + - - +
429A LYS* 4.7 1.3 - - - +
431A VAL* 1.3 75.6 - - + +
433A GLU* 1.3 60.2 + - - +
435A MET* 3.1 11.1 + - + +
436A PHE* 2.9 29.5 + + + +
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Residues in contact with GLU 433 (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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268A LEU* 3.0 38.4 - - - +
270A LYS* 3.4 34.6 - - + +
429A LYS 3.2 18.5 + - - +
430A ALA* 4.3 2.2 - - - +
432A TYR* 1.3 81.2 - - - +
434A ARG* 1.3 51.5 + - + +
436A PHE* 3.3 12.8 + - - +
437A ASN* 2.8 60.8 + - - +
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Residues in contact with ARG 434 (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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430A ALA* 3.1 23.3 + - + +
431A VAL* 2.8 8.7 + - - +
433A GLU* 1.3 77.3 - - + +
435A MET* 1.3 53.1 + - - -
437A ASN* 3.7 19.4 - - - +
438A TRP* 2.7 33.2 + - - +
619A THR 4.3 2.8 + - - -
620A LEU* 2.7 56.8 + - + +
621A PHE* 5.9 4.7 - - + -
623A ASN* 2.6 46.7 - - - +
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Residues in contact with MET 435 (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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230A PHE* 4.1 28.9 - - + -
349A MET* 4.1 21.8 - - - +
352A LEU* 3.4 50.3 - - + -
353A THR* 4.4 5.2 - - - +
431A VAL 2.7 14.0 + - - +
432A TYR* 3.1 17.5 + - + +
434A ARG* 1.3 68.5 - - - +
436A PHE* 1.3 60.8 + - - +
438A TRP* 3.1 29.8 + - - +
439A MET* 2.9 40.9 + - + +
616A LEU* 5.9 1.8 - - + -
620A LEU* 4.8 4.0 - - + +
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Residues in contact with PHE 436 (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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227A LEU* 3.9 33.4 - - + -
230A PHE* 3.5 36.1 - - + -
231A GLY* 5.3 1.3 - - - -
244A PHE* 5.1 16.6 - + + -
265A THR* 4.1 35.2 - - + -
266A TYR 6.1 0.2 - - - -
268A LEU* 4.6 22.2 - - + -
432A TYR* 2.9 15.3 + + + +
433A GLU* 3.3 25.8 - - - +
435A MET* 1.3 76.6 - - - +
437A ASN* 1.3 60.5 + - - +
439A MET* 3.3 10.1 + - + +
440A VAL* 2.9 37.9 + - + +
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Residues in contact with ASN 437 (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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265A THR* 5.5 1.7 + - - -
433A GLU* 2.8 46.8 + - - +
434A ARG* 3.9 24.5 - - - +
436A PHE* 1.3 76.8 - - - +
438A TRP* 1.3 58.3 + - - +
440A VAL* 3.6 10.8 - - - +
441A THR* 2.8 36.4 + - - +
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Residues in contact with TRP 438 (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* 4.0 21.5 - + - -
345A GLU* 5.7 10.3 - - + -
349A MET* 5.1 12.6 - - + -
434A ARG* 2.7 24.1 + - - +
435A MET* 3.1 26.4 + - + +
437A ASN* 1.3 72.7 - - - +
439A MET* 1.3 76.6 + - - +
441A THR* 3.3 7.2 + - + -
442A ARG* 2.8 80.7 + - + +
616A LEU* 4.8 19.2 - - + +
619A THR* 4.9 9.5 + - - -
620A LEU* 3.8 22.0 - - + -
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Residues in contact with MET 439 (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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226A ALA* 5.0 12.6 - - + -
227A LEU* 5.6 8.1 - - + -
230A PHE* 5.8 11.4 - - + -
336A PHE* 3.8 24.5 - - + -
339A LEU* 6.0 1.8 - - + -
341A PHE* 3.7 35.7 - - + -
349A MET* 5.9 1.6 - - - +
435A MET* 2.9 26.5 + - + +
436A PHE* 3.4 11.7 - - + +
438A TRP* 1.3 90.2 - - + +
440A VAL* 1.3 58.0 + - + +
442A ARG* 2.9 4.0 + - - -
443A ILE* 2.7 55.5 + - + +
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Residues in contact with VAL 440 (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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227A LEU* 5.3 4.5 - - + -
263A ILE* 4.8 11.9 - - + +
265A THR* 4.5 17.0 - - + +
436A PHE* 2.9 48.0 + - + +
437A ASN* 3.2 13.2 + - - +
439A MET* 1.3 70.9 - - + +
441A THR* 1.3 61.8 + - - +
443A ILE* 3.4 15.9 - - + +
444A ASN* 3.1 41.0 + - - +
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Residues in contact with THR 441 (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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437A ASN* 2.8 16.4 + - - +
438A TRP* 3.4 12.4 - - + -
440A VAL* 1.3 79.1 - - - +
442A ARG* 1.3 79.0 + - - +
444A ASN* 3.9 2.4 - - - +
445A ALA* 3.0 27.3 + - + +
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Residues in contact with ARG 442 (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* 4.9 12.1 - - + -
438A TRP* 2.8 79.8 + - + +
439A MET* 2.9 7.6 + - - +
441A THR* 1.3 83.6 - - - +
443A ILE* 1.3 59.3 + - + +
445A ALA* 3.3 11.7 - - - +
446A THR* 2.9 35.6 + - + +
619A THR* 5.6 6.9 + - - +
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Residues in contact with ILE 443 (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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223A ALA* 5.7 7.6 - - + -
227A LEU* 4.9 14.8 - - + -
263A ILE* 4.0 21.8 - - + -
339A LEU* 5.1 13.9 - - + -
341A PHE* 5.4 4.0 - - + -
439A MET* 2.7 46.5 + - + +
440A VAL* 3.4 21.3 - - + +
442A ARG* 1.3 72.7 - - + +
444A ASN* 1.3 73.8 + - - +
446A THR* 3.0 8.4 + - - +
447A LEU* 2.6 50.1 + - + +
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Residues in contact with ASN 444 (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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261A ALA 4.7 2.8 - - - +
262A ASP* 2.6 33.1 + - - -
263A ILE* 3.7 21.8 + - - +
440A VAL* 3.1 25.9 + - - +
441A THR* 3.4 2.8 + - - +
443A ILE* 1.3 87.9 - - - +
445A ALA* 1.3 60.8 + - - +
447A LEU 4.4 0.2 - - - +
448A GLU* 2.9 53.3 + - - +
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Residues in contact with ALA 445 (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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441A THR* 3.0 22.3 + - + +
442A ARG* 3.3 15.3 - - - +
444A ASN* 1.3 78.6 - - - +
446A THR* 1.3 60.9 + - + +
448A GLU 4.1 8.5 - - - +
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Residues in contact with THR 446 (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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216A LEU* 5.0 1.4 - - - +
219A GLN* 5.6 1.1 + - - -
339A LEU* 5.5 8.9 + - - +
442A ARG* 2.9 21.5 + - + +
443A ILE* 3.0 15.1 + - - +
445A ALA* 1.3 82.8 - - + +
447A LEU* 1.3 69.1 + - - +
448A GLU 3.5 1.7 + - - -
449A THR* 4.3 13.9 - - - +
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Residues in contact with LEU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LEU* 3.9 26.9 - - + +
219A GLN* 3.8 34.3 - - + +
220A ILE* 4.5 18.4 - - + +
223A ALA* 4.4 15.7 - - + -
260A SER* 3.6 4.7 + - - -
261A ALA* 3.3 26.4 + - + +
339A LEU* 3.9 23.3 - - + +
443A ILE* 2.6 30.5 + - + +
446A THR* 1.3 82.0 - - - +
448A GLU* 1.3 61.8 + - - +
449A THR 3.7 2.7 + - - -
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Residues in contact with GLU 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A HIS* 5.7 0.9 - - - -
260A SER* 2.7 15.9 - - - +
261A ALA 3.0 22.2 - - - +
262A ASP* 2.9 36.4 + - - +
444A ASN* 2.9 30.7 + - - +
445A ALA 4.1 10.2 - - - +
446A THR 4.9 0.4 - - - -
447A LEU* 1.3 73.3 - - - +
449A THR* 1.3 63.5 + - - +
450A LYS 3.4 2.0 + - - +
451A GLN* 5.1 16.0 + - + +
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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