Contacts of the helix formed by residues 436 - 459 (chain A) in PDB entry 1PG0
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 GLU 436 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A SER* 3.6 11.5 - - - +
365A SER* 2.7 39.3 + - - -
431A ALA* 2.9 14.9 + - - +
434A SER* 3.3 24.0 - - - +
435A ARG* 1.3 73.8 - - - +
437A PHE* 1.3 63.8 + - - +
438A GLY 3.3 3.1 - - - -
439A LYS* 3.1 27.9 + - + +
440A ALA 3.1 16.3 + - - -
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Residues in contact with PHE 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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30A GLN* 3.6 43.3 - - + -
33A VAL* 3.7 22.2 - - + -
34A TRP* 3.9 13.2 - + + -
360A THR* 3.2 32.3 - - + +
363A LEU* 3.6 26.5 + - + +
432A TRP* 3.4 47.8 - + + -
435A ARG* 3.0 24.7 + - + -
436A GLU* 1.3 76.0 - - - +
438A GLY* 1.3 63.8 + - - +
440A ALA* 3.1 3.1 + - - +
441A VAL* 2.9 27.4 + - - +
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Residues in contact with GLY 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A THR 3.5 1.7 + - - -
361A ALA* 3.5 25.3 - - - +
362A LYS 5.0 0.7 - - - -
363A LEU 2.8 20.2 + - - -
364A SER* 5.6 0.2 - - - -
436A GLU 3.3 0.2 - - - -
437A PHE* 1.3 73.4 - - - +
439A LYS* 1.3 56.2 + - - +
441A VAL* 3.5 1.9 + - - +
442A ARG* 3.0 47.3 + - - +
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Residues in contact with LYS 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A VAL* 3.2 36.4 + - - +
431A ALA* 4.4 8.3 - - + -
436A GLU* 3.1 29.7 + - + +
438A GLY* 1.3 75.1 - - - +
440A ALA* 1.3 66.7 + - - +
442A ARG* 3.4 18.9 + - - +
443A GLU* 3.0 31.2 + - + +
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Residues in contact with ALA 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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428A ILE* 4.3 7.5 - - + +
431A ALA* 3.6 23.9 - - + +
432A TRP* 3.6 36.3 - - + -
436A GLU 3.1 6.7 + - - +
437A PHE 3.1 9.1 + - - +
439A LYS* 1.3 76.6 - - - +
441A VAL* 1.3 57.7 + - - +
443A GLU* 3.2 8.4 + - - +
444A ILE* 2.9 34.5 + - - +
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Residues in contact with VAL 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A TYR* 3.3 39.7 - - + +
360A THR* 3.8 24.7 - - + -
361A ALA* 3.9 23.1 - - + +
380A ARG* 5.1 3.8 - - - +
432A TRP* 4.1 7.9 - - + -
437A PHE 2.9 19.0 + - - +
438A GLY 3.9 4.0 - - - +
440A ALA* 1.3 76.2 - - - +
442A ARG* 1.3 58.2 + - + +
444A ILE* 3.1 8.2 + - - +
445A MET* 2.8 35.7 + - + +
491A LEU* 5.2 4.5 - - + -
494A VAL* 5.5 0.2 - - + -
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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
----------------------------------------------------------
361A ALA 4.3 8.1 + - - -
380A ARG* 5.6 11.3 - - - +
438A GLY* 3.0 40.9 + - - +
439A LYS* 3.4 15.1 + - - +
441A VAL* 1.3 77.1 - - + +
443A GLU* 1.3 58.0 + - - +
445A MET* 3.8 5.3 - - - +
446A ALA* 2.9 31.2 + - - +
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Residues in contact with GLU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A ALA* 4.9 7.5 - - + +
427A VAL* 3.9 26.4 - - + +
428A ILE* 3.4 29.4 - - + -
439A LYS* 3.0 21.1 + - + +
440A ALA* 3.4 10.3 - - - +
442A ARG* 1.3 78.0 - - - +
444A ILE* 1.3 62.1 + - - +
446A ALA* 3.3 10.7 + - - +
447A LEU* 3.1 29.3 + - + +
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Residues in contact with ILE 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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389A VAL* 5.4 0.9 - - + -
428A ILE* 3.8 22.7 - - + -
432A TRP* 3.8 14.1 - - + -
440A ALA 2.9 18.8 + - - +
441A VAL* 3.5 7.9 - - - +
443A GLU* 1.3 76.8 - - - +
445A MET* 1.3 64.7 + - + +
447A LEU* 3.2 9.3 + - - +
448A ALA* 3.0 24.4 + - - +
487A LEU* 3.7 18.5 - - + +
490A TYR* 3.5 31.4 - - + +
491A LEU* 3.7 43.1 - - + -
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Residues in contact with MET 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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357A TYR* 3.4 39.7 - - + +
380A ARG* 5.1 2.9 - - - +
384A ASP* 3.8 25.6 - - + +
385A ILE* 4.7 1.1 - - + -
388A LYS* 4.1 23.6 - - - +
389A VAL* 3.8 30.3 - - + -
441A VAL* 2.8 25.8 + - + +
442A ARG* 4.0 5.4 - - - +
444A ILE* 1.3 77.3 - - + +
446A ALA* 1.3 60.8 + - - +
448A ALA* 3.3 5.2 + - - +
449A ASP* 3.0 32.9 + - - +
491A LEU* 4.3 12.3 - - + -
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Residues in contact with ALA 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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442A ARG 2.9 19.0 + - - +
443A GLU* 3.5 11.9 - - - +
444A ILE 3.2 0.2 - - - -
445A MET* 1.3 73.5 - - - +
447A LEU* 1.3 67.1 + - + +
449A ASP* 3.2 13.6 + - - +
450A LEU* 3.2 24.3 + - - +
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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
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420A THR* 4.2 16.2 - - + +
421A PHE* 3.0 50.9 - - + +
424A ALA* 3.8 26.0 - - + -
428A ILE* 3.9 19.1 - - + -
443A GLU* 3.1 17.7 + - + +
444A ILE* 3.2 7.4 + - - +
446A ALA* 1.3 78.7 - - - +
448A ALA* 1.3 62.6 + - - +
450A LEU* 3.1 10.8 + - + +
451A ALA 2.9 17.8 + - - -
487A LEU* 3.9 9.6 - - + -
490A TYR* 3.9 15.3 - - + -
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Residues in contact with ALA 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LYS* 4.2 24.2 - - + -
389A VAL* 4.6 3.1 - - + -
444A ILE 3.0 14.6 + - - +
445A MET* 3.5 17.3 - - - +
446A ALA 3.2 0.2 - - - -
447A LEU* 1.3 78.3 - - - +
449A ASP* 1.3 62.1 + - - +
451A ALA* 3.1 3.5 + - - +
452A ASN* 2.9 31.8 + - - +
487A LEU* 3.8 25.1 - - + +
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Residues in contact with ASP 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LYS* 3.3 37.3 + - - +
445A MET 3.0 17.8 + - - +
446A ALA* 3.5 13.6 - - - +
447A LEU 3.2 0.4 - - - -
448A ALA* 1.3 75.8 - - - +
450A LEU* 1.3 58.1 + - - +
452A ASN* 3.2 7.5 + - - +
453A ARG* 2.9 40.0 + - - +
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Residues in contact with LEU 450 (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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417A LEU* 4.7 13.6 - - + +
420A THR* 4.2 25.4 - - + -
421A PHE* 4.1 10.3 - - + -
446A ALA 3.2 10.9 + - - +
447A LEU* 3.1 22.8 + - + +
449A ASP* 1.3 80.1 - - - +
451A ALA* 1.3 56.8 + - - +
453A ARG* 3.2 17.6 + - - +
454A TYR* 2.9 28.5 + - - +
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Residues in contact with ALA 451 (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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392A LEU* 3.5 28.5 - - + -
421A PHE* 3.7 13.4 - - + -
447A LEU 2.9 6.9 + - - +
448A ALA* 3.1 8.9 + - - +
450A LEU* 1.3 76.8 - - - +
452A ASN* 1.3 57.3 + - - +
454A TYR* 3.3 4.0 + - - +
455A VAL* 3.1 32.1 + - - +
483A LEU* 3.4 29.8 - - + -
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Residues in contact with ASN 452 (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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387A ASN 4.3 3.5 + - - -
388A LYS* 3.0 40.4 + - - +
391A ASN* 3.5 12.6 - - - +
392A LEU* 4.0 11.3 + - - +
395A ARG* 3.2 24.7 + - - +
448A ALA* 2.9 26.3 + - - +
449A ASP* 3.8 6.2 + - - +
451A ALA* 1.3 74.3 - - - +
453A ARG* 1.3 63.6 + - - +
455A VAL* 3.6 0.8 + - - -
456A ASP* 2.8 33.8 + - - +
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Residues in contact with ARG 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A ASP* 2.9 25.8 + - - +
450A LEU* 3.5 18.6 - - + +
452A ASN* 1.3 75.8 - - - +
454A TYR* 1.3 65.2 + - - +
456A ASP* 3.1 9.3 + - + +
457A GLU* 2.9 48.7 + - + +
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Residues in contact with TYR 454 (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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413A ALA* 3.7 9.7 - - - +
414A ASP* 4.0 25.6 - - + -
417A LEU* 3.4 33.4 - - + -
450A LEU 2.9 9.1 + - - +
451A ALA* 3.5 8.1 - - - +
453A ARG* 1.3 78.6 - - - +
455A VAL* 1.3 76.3 + - + +
457A GLU* 3.3 12.1 + - - +
458A GLN* 3.0 58.5 + - + +
476A ILE* 3.7 27.3 - - + +
479A MET* 3.4 37.0 - - + +
480A GLY 4.6 1.6 - - - -
483A LEU* 4.5 5.2 - - + -
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Residues in contact with VAL 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A LEU* 3.8 20.6 - - + -
395A ARG* 3.1 44.0 - - + +
396A ASN* 4.1 14.8 - - - +
451A ALA 3.1 16.4 + - - +
452A ASN 3.8 0.4 - - - +
453A ARG 3.2 0.2 - - - -
454A TYR* 1.3 93.5 - - + +
456A ASP* 1.3 56.9 + - - +
458A GLN* 3.6 1.5 + - - -
459A ALA 2.8 22.0 + - - -
460A PRO* 3.3 24.7 - - + +
476A ILE* 5.4 2.7 - - + +
480A GLY* 4.7 3.6 - - - -
483A LEU* 5.7 0.2 - - + -
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Residues in contact with ASP 456 (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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395A ARG* 3.0 23.7 + - - -
452A ASN* 2.8 21.2 + - - +
453A ARG* 3.1 10.6 + - + +
455A VAL* 1.3 73.7 - - - +
457A GLU* 1.3 67.7 + - + +
459A ALA* 3.0 17.8 + - - +
461A TRP* 3.6 16.4 - - + -
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Residues in contact with GLU 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A ARG* 2.9 42.0 + - + +
454A TYR* 3.7 10.2 - - - +
456A ASP* 1.3 77.4 - - + +
458A GLN* 1.3 71.9 + - - +
459A ALA* 3.4 2.6 + - - +
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Residues in contact with GLN 458 (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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414A ASP* 5.8 0.2 + - - -
454A TYR* 3.0 57.2 + - + +
455A VAL 4.0 1.8 - - - +
457A GLU* 1.3 85.5 + - - +
459A ALA* 1.3 71.2 + - - +
462A VAL* 4.7 0.3 - - - +
463A VAL* 3.6 13.3 - - - +
476A ILE* 3.7 36.1 - - + +
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Residues in contact with ALA 459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A VAL 2.8 12.6 + - - -
456A ASP 3.0 13.5 + - - +
457A GLU 4.2 2.7 - - - +
458A GLN* 1.3 82.9 - - - +
460A PRO* 1.3 64.5 - - - +
461A TRP* 3.4 23.3 - - + +
462A VAL* 2.9 33.8 - - + +
463A VAL* 3.1 5.0 - - - +
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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