Contacts of the helix formed by residues 455 - 476 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B LEU 4.0 1.8 + - - -
454B PHE* 1.3 77.4 - - - +
456B ALA* 1.3 63.4 + - - +
457B GLU* 4.7 5.8 - - + +
458B THR* 4.1 17.8 + - - +
459B LEU* 3.5 25.0 + - - +
582B LEU* 5.7 3.8 - - - -
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Residues in contact with ALA 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B ALA* 1.3 75.6 - - - +
457B GLU* 1.3 60.4 + - + +
458B THR 2.8 12.1 + - - -
459B LEU* 3.2 16.8 + - - +
460B LEU* 3.2 14.8 + - - +
552B PHE* 5.1 7.0 - - + -
582B LEU* 5.1 15.7 - - + +
584B SER* 5.5 5.6 - - - +
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Residues in contact with GLU 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B ALA* 4.7 5.1 - - + +
456B ALA* 1.3 76.2 - - + +
458B THR* 1.3 58.8 + - - +
460B LEU* 4.3 9.4 - - - +
461B GLY* 3.4 17.8 + - - -
616B ALA* 5.0 18.0 - - + +
618B SER 5.1 8.1 + - - +
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Residues in contact with THR 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B PHE* 5.6 4.5 - - + -
455B ALA* 4.1 25.4 + - - +
456B ALA 2.8 3.0 - - - -
457B GLU* 1.3 79.0 + - - +
459B LEU* 1.3 66.6 + - - -
460B LEU 3.2 0.7 - - - -
461B GLY* 3.0 10.1 + - - +
462B MET* 3.0 32.8 - - + +
494B GLN* 4.0 30.5 - - + +
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Residues in contact with LEU 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B LEU* 4.7 2.7 - - + -
454B PHE* 3.7 21.1 - - + -
455B ALA 3.5 19.5 + - - +
456B ALA* 3.2 6.0 + - - +
458B THR* 1.3 76.0 - - - +
460B LEU* 1.3 55.5 + - - +
462B MET* 2.8 53.3 + - + +
463B CYS* 3.3 9.2 + - - -
551B VAL* 3.1 33.9 - - + +
552B PHE* 4.1 29.6 - - + -
554B GLU* 5.4 1.8 - - + -
582B LEU* 3.7 29.8 - - + -
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Residues in contact with LEU 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B ALA 3.2 14.1 + - - +
457B GLU* 4.3 6.3 - - - +
459B LEU* 1.3 79.9 - - - +
461B GLY* 1.3 50.6 + - - +
462B MET 2.7 11.1 + - - -
463B CYS* 3.3 16.6 + - + -
464B LEU* 3.4 18.5 + - + +
548B MET* 6.2 0.4 - - + -
552B PHE* 4.5 18.4 - - + -
587B VAL* 5.2 6.5 - - + -
612B LEU* 3.4 38.6 - - + +
615B ILE* 3.7 16.4 - - + +
616B ALA* 3.1 48.9 - - + +
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Residues in contact with GLY 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B GLU 3.4 11.9 + - - -
458B THR* 3.0 16.7 + - - +
460B LEU* 1.3 74.1 - - - +
462B MET* 1.3 56.0 + - - +
464B LEU* 4.8 7.9 - - - -
465B ASP* 2.7 20.8 - - - +
494B GLN* 4.3 9.2 - - - +
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Residues in contact with MET 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B LEU* 4.6 22.4 - - + -
446B TYR* 5.9 2.7 - - - -
447B LEU* 4.8 2.0 - - - -
454B PHE* 4.0 14.4 - - + -
458B THR* 3.0 25.1 - - + +
459B LEU* 2.9 53.4 - - + +
460B LEU 2.7 2.4 + - - -
461B GLY* 1.3 80.7 - - - +
463B CYS* 1.3 53.7 + - - +
464B LEU 2.7 4.0 + - - -
465B ASP* 2.4 39.5 + - - +
466B VAL* 2.9 8.2 + - - +
494B GLN* 4.4 13.7 - - + +
496B ILE* 3.8 22.9 - - + -
551B VAL* 4.7 7.4 - - + -
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Residues in contact with CYS 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B LEU 3.4 18.2 - - - -
460B LEU* 3.9 12.3 - - + +
462B MET* 1.3 73.4 - - - +
464B LEU* 1.3 50.4 + - - +
466B VAL* 4.3 9.6 - - - -
467B CYS* 2.7 37.7 + - - +
544B PHE* 3.7 8.3 - - + -
547B LEU* 6.2 0.2 - - - -
548B MET* 4.0 25.6 - - + -
551B VAL* 3.7 31.6 - - - -
552B PHE* 4.3 5.8 - - - -
612B LEU* 4.0 12.8 - - + -
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Residues in contact with LEU 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B LEU* 3.4 15.8 + - + +
461B GLY* 5.2 4.5 - - - -
462B MET 2.9 1.7 - - - +
463B CYS* 1.3 76.2 - - - +
465B ASP* 1.3 60.2 + - - +
466B VAL 3.1 0.2 - - - -
467B CYS* 3.8 1.3 - - - -
468B GLU* 2.3 57.3 + - - +
609B LEU* 3.2 26.0 - - + +
612B LEU* 3.0 48.0 - - + +
613B ALA* 4.2 11.0 - - - +
616B ALA* 4.7 11.2 - - + -
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Residues in contact with ASP 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B LYS* 3.0 43.1 + - - +
461B GLY 2.7 29.9 - - - +
462B MET* 2.4 18.5 + - - +
464B LEU* 1.3 74.0 - - - +
466B VAL* 1.3 54.0 + - - +
468B GLU* 3.8 4.8 + - - +
469B GLY 3.0 19.4 + - - -
494B GLN 4.3 1.4 - - - +
495B VAL* 4.2 6.9 - - - +
496B ILE* 3.3 38.7 + - + +
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Residues in contact with VAL 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B LEU* 5.2 6.3 - - + -
462B MET* 2.9 12.0 + - + +
463B CYS* 3.9 10.1 - - - +
465B ASP* 1.3 73.5 - - - +
467B CYS* 1.3 57.4 + - - +
469B GLY* 3.0 2.4 + - - -
470B MET* 2.6 40.9 + - + +
483B LEU* 3.8 15.9 - - + -
488B CYS* 3.8 27.4 - - - -
496B ILE* 4.0 23.8 - - + -
498B VAL* 3.8 15.3 - - + +
544B PHE* 4.2 16.2 - - + -
547B LEU* 4.4 7.4 - - + -
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Residues in contact with CYS 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B CYS 2.7 26.0 + - - +
464B LEU* 3.6 8.1 - - - +
466B VAL* 1.3 69.4 - - - +
468B GLU* 1.3 70.8 + - - +
470B MET* 3.3 1.9 + - - +
471B ALA* 2.8 21.1 + - - +
544B PHE* 3.9 14.1 - - + -
605B PHE* 3.8 20.3 - - - -
608B LEU* 3.7 29.8 - - - -
609B LEU* 3.9 17.9 - - + -
612B LEU* 3.9 10.8 - - + -
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Residues in contact with GLU 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415B HIS* 4.6 13.2 - - + +
417B LYS* 3.0 29.8 + - + -
464B LEU* 2.3 57.2 + - - +
465B ASP* 3.8 6.5 + - - +
467B CYS* 1.3 70.3 - - - +
469B GLY* 1.3 69.2 + - - +
471B ALA* 2.7 16.1 + - - +
472B TYR* 3.3 3.8 + - - +
609B LEU* 3.2 34.4 - - + +
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Residues in contact with GLY 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415B HIS* 5.2 2.9 - - - -
417B LYS* 3.4 23.9 - - - +
418B LEU* 3.9 25.0 - - - +
465B ASP 3.0 7.7 + - - -
466B VAL 3.2 5.2 - - - -
468B GLU* 1.3 81.7 - - - +
470B MET* 1.3 61.8 + - - +
472B TYR* 3.4 17.4 - - - +
473B LEU* 3.7 2.4 + - - +
498B VAL* 4.4 2.2 - - - -
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Residues in contact with MET 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B VAL* 2.6 32.2 + - + +
468B GLU 2.9 1.6 + - - -
469B GLY* 1.3 68.6 - - - -
471B ALA* 1.3 67.4 + - - +
473B LEU* 2.6 34.1 + - + +
474B GLU* 2.5 23.7 + - - -
480B HIS* 3.7 28.0 - - + -
483B LEU* 3.8 30.1 - - + -
498B VAL* 3.9 12.3 - - + -
540B ASP* 5.3 4.7 - - - +
605B PHE* 3.2 36.8 - - + -
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Residues in contact with ALA 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467B CYS 2.8 12.4 + - - +
468B GLU* 2.7 19.6 + - - +
470B MET* 1.3 70.0 - - - +
472B TYR* 1.3 52.7 + - - +
474B GLU* 2.8 6.5 + - - +
475B GLU* 2.7 36.8 + - - +
605B PHE* 3.6 22.3 - - + +
606B SER* 4.5 10.8 - - - +
609B LEU* 4.3 13.2 - - + -
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Residues in contact with TYR 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B LYS 3.9 3.8 + - - -
413B LEU* 3.1 47.1 - - + +
414B SER 3.1 22.4 + - - -
415B HIS* 4.3 24.9 - + + -
418B LEU* 3.3 21.5 - - + -
468B GLU 3.3 3.6 + - - +
469B GLY 3.4 11.0 - - - +
470B MET 2.8 2.6 + - - -
471B ALA* 1.3 75.2 - - - +
473B LEU* 1.3 53.4 + - + +
475B GLU* 2.7 11.8 + - + +
476B ALA* 2.3 46.1 + - + +
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Residues in contact with LEU 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B LEU* 3.6 31.2 - - + -
418B LEU* 3.7 30.3 - - + -
469B GLY 4.2 2.2 - - - +
470B MET* 2.6 37.1 + - + +
472B TYR* 1.3 78.7 - - + +
474B GLU* 1.3 60.4 + - - +
476B ALA* 3.8 0.4 - - - -
477B CYS 2.8 3.1 + - - -
478B VAL* 2.4 54.2 + - + +
480B HIS* 4.8 4.5 - - + -
501B PHE* 3.4 33.0 - - + -
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Residues in contact with GLU 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470B MET 2.5 16.2 + - - +
471B ALA* 2.9 16.1 - - - +
473B LEU* 1.3 75.5 - - - +
475B GLU* 1.3 56.0 + - + +
477B CYS* 3.1 18.9 - - - -
478B VAL 4.0 6.0 + - - -
537B SER* 3.7 21.8 + - - +
538B LYS* 5.7 1.0 - - - -
541B VAL* 4.6 0.9 - - - +
604B ALA* 3.5 15.9 - - - +
605B PHE* 2.7 42.2 + - + +
606B SER* 2.9 32.2 + - - -
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Residues in contact with GLU 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471B ALA 2.7 15.2 + - - +
472B TYR* 2.7 10.1 + - + +
474B GLU* 1.3 72.9 - - + +
476B ALA* 1.3 53.0 + - - +
477B CYS* 2.4 35.4 + - - -
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Residues in contact with ALA 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B LEU* 3.9 22.9 - - + +
472B TYR* 2.3 44.0 + - + +
473B LEU* 3.8 3.4 - - - -
475B GLU* 1.3 68.7 + - - +
477B CYS* 1.3 72.4 + - - +
478B VAL* 3.1 20.3 - - + +
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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