Contacts of the helix formed by residues 455 - 476 (chain A) in PDB entry 1SNX
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 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453A LEU 3.6 3.7 + - - +
454A PHE* 1.3 76.9 - - - +
456A ALA* 1.3 61.6 + - - +
457A GLU* 3.9 3.6 - - + +
458A THR* 4.0 16.8 - - - +
459A LEU* 3.5 26.0 + - - +
582A LEU* 5.8 1.8 - - - -
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Residues in contact with ALA 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A ALA* 1.3 72.9 - - - +
457A GLU* 1.3 65.7 + - + +
458A THR 2.8 7.0 + - - -
459A LEU* 4.0 8.5 - - + +
460A LEU* 3.0 25.5 + - - +
552A PHE* 5.5 5.2 - - + -
582A LEU* 4.9 16.4 - - + +
584A SER* 5.3 5.8 - - - +
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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
----------------------------------------------------------
455A ALA* 3.9 2.6 - - + +
456A ALA* 1.3 77.1 - - + +
458A THR* 1.3 57.5 + - - +
460A LEU* 4.0 7.8 - - - +
461A GLY* 3.1 17.8 + - - -
616A ALA* 4.9 17.7 - - - +
618A SER 5.1 12.3 + - - +
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Residues in contact with THR 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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454A PHE* 5.5 3.8 - - + -
455A ALA* 4.0 21.0 + - - +
456A ALA 2.8 1.8 - - - +
457A GLU* 1.3 78.8 - - - +
459A LEU* 1.3 59.3 + - - +
460A LEU 2.9 1.3 - - - -
461A GLY* 2.6 25.7 + - - +
462A MET* 3.0 30.8 - - + +
494A GLN* 3.5 29.8 - - + +
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Residues in contact with LEU 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LEU* 4.5 4.5 - - + -
454A PHE* 4.2 18.4 - - + -
455A ALA 3.5 17.4 + - - +
456A ALA* 3.3 8.3 + - - +
458A THR* 1.3 78.6 - - - +
460A LEU* 1.3 61.9 + - - +
462A MET* 3.2 25.2 + - + +
463A CYS* 3.1 21.7 + - - -
551A VAL* 3.4 37.7 - - + +
552A PHE* 4.0 21.8 - - + +
554A GLU* 5.3 1.3 - - + -
582A LEU* 3.1 42.6 - - + -
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Residues in contact with LEU 460 (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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456A ALA 3.0 17.3 + - - +
457A GLU* 4.0 6.5 - - - +
458A THR 2.9 0.4 - - - -
459A LEU* 1.3 74.7 - - - +
461A GLY* 1.3 55.4 + - - +
462A MET 2.9 11.1 + - - -
463A CYS* 3.4 15.7 + - + +
464A LEU* 3.6 16.7 + - + +
548A MET* 5.3 1.8 - - + -
552A PHE* 4.1 21.5 - - + -
587A VAL* 5.0 8.1 - - + -
590A ILE* 5.8 0.2 - - + -
612A LEU* 3.9 32.1 - - + +
615A ILE* 3.7 15.7 - - + +
616A ALA* 3.2 46.3 - - + +
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Residues in contact with GLY 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A GLU 3.1 12.7 + - - -
458A THR* 2.6 24.4 + - - +
460A LEU* 1.3 70.3 - - - +
462A MET* 1.3 58.5 + - - +
464A LEU* 4.9 3.8 - - - -
465A ASP* 2.8 18.3 - - - +
494A GLN* 4.3 7.4 - - - +
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Residues in contact with MET 462 (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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443A LEU* 4.5 22.0 - - + -
446A TYR* 5.7 3.8 - - + -
447A LEU* 4.8 4.0 - - - -
454A PHE* 4.3 13.5 - - + -
458A THR* 3.0 39.7 - - + +
459A LEU* 3.2 37.5 - - + +
460A LEU 2.9 0.6 + - - -
461A GLY* 1.3 80.3 - - - +
463A CYS* 1.3 63.5 + - - +
464A LEU 3.1 1.3 - - - -
465A ASP* 2.5 33.3 + - - +
466A VAL* 2.8 14.5 + - - +
494A GLN* 4.2 11.0 - - - +
496A ILE* 3.6 23.6 - - + -
551A VAL* 5.0 8.1 - - + -
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Residues in contact with CYS 463 (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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459A LEU 3.1 19.1 - - - -
460A LEU* 3.8 12.3 - - + +
462A MET* 1.3 77.8 - - - +
464A LEU* 1.3 50.7 + - - +
466A VAL* 2.9 14.2 + - - +
467A CYS* 2.7 33.3 + - - +
544A PHE* 3.7 4.8 - - + -
547A LEU* 6.4 0.2 - - - -
548A MET* 4.1 19.1 - - + -
551A VAL* 3.6 29.4 - - - +
552A PHE* 3.7 15.7 - - - -
612A LEU* 4.1 17.5 - - + -
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Residues in contact with LEU 464 (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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460A LEU* 3.6 11.7 + - + +
461A GLY* 5.6 2.2 - - - -
462A MET 3.1 1.5 - - - +
463A CYS* 1.3 74.1 - - - +
465A ASP* 1.3 60.3 + - - +
467A CYS* 2.9 2.0 + - - -
468A GLU* 2.4 50.1 + - - +
609A LEU* 3.3 35.4 - - + +
612A LEU* 3.1 52.5 - - + +
613A ALA* 4.0 10.3 - - + +
616A ALA* 4.7 8.3 - - + -
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Residues in contact with ASP 465 (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 LYS* 3.3 32.9 + - + +
461A GLY 2.8 25.2 - - - +
462A MET 2.5 15.3 + - - +
464A LEU* 1.3 75.5 - - - +
466A VAL* 1.3 61.1 + - - +
468A GLU* 3.5 9.3 - - - +
469A GLY 3.0 15.4 + - - -
494A GLN 3.4 6.8 - - - +
495A VAL* 4.0 4.2 - - - +
496A ILE* 3.3 45.1 + - + +
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Residues in contact with VAL 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LEU* 5.0 4.3 - - + -
462A MET 2.8 16.7 + - - +
463A CYS* 3.2 11.7 - - - +
465A ASP* 1.3 75.4 - - - +
467A CYS* 1.3 52.2 + - - +
469A GLY* 3.0 5.4 + - - -
470A MET* 2.7 40.3 + - + +
483A LEU* 3.9 22.0 - - + -
488A CYS* 4.4 9.4 - - + -
496A ILE* 4.2 19.5 - - + -
498A VAL* 4.1 15.6 - - + +
544A PHE* 3.4 26.5 - - + -
547A LEU* 4.2 14.6 - - + -
551A VAL* 5.8 0.4 - - + -
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Residues in contact with CYS 467 (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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463A CYS 2.7 16.8 + - - +
464A LEU* 2.9 12.5 + - + +
466A VAL* 1.3 68.7 - - - +
468A GLU* 1.3 72.4 + - - +
470A MET* 2.5 19.3 + - - +
471A ALA* 2.8 9.6 + - - -
544A PHE* 3.7 23.3 - - + -
605A PHE* 3.9 14.8 - - - -
608A LEU* 3.8 29.6 - - - -
609A LEU* 3.5 22.0 - - + -
612A LEU* 4.2 3.6 - - + -
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Residues in contact with GLU 468 (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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415A HIS* 4.4 18.4 + - + -
417A LYS* 2.6 36.8 + - + +
464A LEU* 2.4 43.1 + - + +
465A ASP* 3.5 12.5 + - - +
467A CYS* 1.3 68.0 - - - +
469A GLY* 1.3 67.2 + - - +
471A ALA* 3.1 8.8 + - - +
472A TYR* 3.3 9.5 + - - +
609A LEU* 3.3 31.7 - - + +
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Residues in contact with GLY 469 (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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415A HIS* 5.0 1.8 - - - -
417A LYS* 3.6 21.2 - - - +
418A LEU* 3.9 20.4 - - - +
465A ASP 3.0 4.8 + - - -
466A VAL 3.0 8.0 + - - -
467A CYS 2.7 4.0 + - - -
468A GLU* 1.3 82.0 - - - +
470A MET* 1.3 56.5 + - - -
472A TYR* 3.0 24.2 + - - +
473A LEU* 3.5 6.4 + - - +
498A VAL* 4.9 0.9 - - - -
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Residues in contact with MET 470 (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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418A LEU* 4.9 0.2 - - + -
466A VAL* 2.7 23.8 + - + +
467A CYS 2.5 10.7 + - - +
469A GLY* 1.3 67.4 - - - -
471A ALA* 1.3 58.9 + - - +
473A LEU* 3.9 27.2 - - + +
474A GLU* 2.8 29.7 + - - +
480A HIS* 3.4 36.8 - - + -
483A LEU* 3.4 38.8 - - + -
498A VAL* 3.7 20.9 - - + -
540A ASP* 5.5 2.9 - - - +
605A PHE* 3.5 31.3 - - + -
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Residues in contact with ALA 471 (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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467A CYS 2.8 13.1 + - - +
468A GLU 3.7 7.4 - - - +
470A MET* 1.3 72.1 - - - +
472A TYR* 1.3 54.1 + - - +
474A GLU* 3.0 4.4 - - - +
475A GLU* 2.7 35.7 + - - +
605A PHE* 3.4 35.1 - - + +
606A SER* 4.1 7.2 - - - +
609A LEU* 4.2 17.0 - - + -
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Residues in contact with TYR 472 (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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412A LYS 4.1 2.9 + - - -
413A LEU* 3.2 37.9 - - + +
414A SER 2.8 35.9 + - - -
415A HIS* 4.0 25.6 - + + +
418A LEU* 3.5 23.3 - - + -
468A GLU 3.3 6.1 + - - +
469A GLY 3.0 10.7 + - - +
471A ALA* 1.3 79.8 - - - +
473A LEU* 1.3 53.1 + - + +
475A GLU* 3.0 9.2 + - + +
476A ALA* 2.4 36.9 + - + +
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Residues in contact with LEU 473 (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 LEU* 3.1 35.9 - - + -
418A LEU* 3.4 33.2 - - + -
469A GLY 3.5 4.1 + - - +
470A MET* 3.9 30.7 - - + +
471A ALA 3.4 0.4 - - - -
472A TYR* 1.3 82.9 - - + +
474A GLU* 1.3 62.6 + - - +
476A ALA* 3.3 4.7 - - + -
477A CYS 3.0 2.8 + - - -
478A VAL* 2.8 49.3 + - + +
480A HIS* 4.9 4.5 - - + -
501A PHE* 3.5 28.0 - - + -
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Residues in contact with GLU 474 (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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470A MET 2.8 21.8 + - - +
471A ALA* 3.0 8.4 - - - +
473A LEU* 1.3 79.1 - - - +
475A GLU* 1.3 58.9 + - - +
477A CYS* 3.1 19.2 + - - -
478A VAL 4.2 3.1 + - - -
537A SER* 4.0 22.2 + - - +
541A VAL* 4.9 1.2 - - - +
604A ALA* 3.3 10.8 - - - +
605A PHE* 2.4 44.3 + - + +
606A SER* 2.6 36.9 + - - -
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Residues in contact with GLU 475 (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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471A ALA 2.7 13.3 + - - +
472A TYR* 3.6 9.3 - - + +
474A GLU* 1.3 77.6 - - + +
476A ALA* 1.3 53.7 + - - +
477A CYS* 2.5 24.3 + - - +
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Residues in contact with ALA 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A LEU* 3.8 22.1 - - + +
472A TYR* 2.4 35.8 + - + +
473A LEU* 3.1 18.1 + - + +
475A GLU* 1.3 68.1 - - - +
477A CYS* 1.3 72.4 + - - +
478A VAL* 2.9 21.3 - - + +
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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