Contacts of the helix formed by residues 455 - 472 (chain B) in PDB entry 1B3U
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 TYR 455 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453B HIS 3.7 1.8 + - - -
454B VAL* 1.3 71.4 - - - +
456B ALA* 1.3 59.1 + - - +
458B ARG* 3.2 44.5 - - - +
459B GLU* 2.9 55.6 + - + +
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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
----------------------------------------------------------
416B TRP* 5.1 14.6 - - + -
420B LEU* 4.8 11.2 - - + +
454B VAL* 2.9 13.6 + - + +
455B TYR* 1.3 81.0 - - + +
457B ILE* 1.3 61.5 + - + +
459B GLU* 3.6 6.5 + - - +
460B ALA* 3.1 26.3 + - - +
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Residues in contact with ILE 457 (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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416B TRP* 3.7 20.6 - - + +
419B ARG* 3.1 54.5 - - + +
420B LEU* 4.6 11.9 - - + +
423B ILE* 3.8 17.7 - - + +
449B TRP* 4.0 15.0 - - + +
452B ASP* 3.4 23.8 - - + +
454B VAL* 2.8 20.0 + - + +
456B ALA* 1.3 71.2 - - + +
458B ARG* 1.3 59.3 + - - +
460B ALA* 3.1 6.3 + - - +
461B ALA* 2.8 28.6 + - - +
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Residues in contact with ARG 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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449B TRP 3.5 8.7 - - - -
450B LEU* 3.3 22.2 - - - +
451B VAL* 3.9 4.0 - - - +
452B ASP 2.7 45.2 + - - +
453B HIS* 4.4 6.3 + - - +
454B VAL 3.2 1.7 + - - +
455B TYR* 3.2 55.9 - - - +
457B ILE* 1.3 77.5 - - - +
459B GLU* 1.3 62.4 + - - +
461B ALA* 3.4 2.1 + - - +
462B THR* 3.0 28.4 + - - +
502B PHE* 6.1 2.0 - - - -
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Residues in contact with GLU 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B TYR* 2.9 55.9 + - + +
456B ALA* 3.7 7.1 - - - +
457B ILE 3.1 0.2 - - - -
458B ARG* 1.3 78.4 - - - +
460B ALA* 1.3 60.9 + - - +
462B THR* 3.3 9.1 + - - -
463B SER* 3.2 21.7 + - - -
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Residues in contact with ALA 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B LEU* 4.2 16.6 - - + -
423B ILE* 4.0 23.1 - - + +
424B GLU* 5.6 2.7 - - - +
456B ALA 3.1 15.0 + - - +
457B ILE 3.1 5.3 + - - +
459B GLU* 1.3 78.4 - - - +
461B ALA* 1.3 61.0 + - - +
462B THR 3.2 0.2 + - - -
463B SER* 3.3 5.9 + - - -
464B ASN* 2.9 30.1 + - - +
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Residues in contact with ALA 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B ILE* 4.1 6.6 - - + +
446B CYS* 4.3 6.2 - - - +
449B TRP* 3.2 48.0 - - + +
450B LEU* 3.9 8.1 - - + +
457B ILE 2.8 16.8 + - - +
458B ARG 3.7 3.1 - - - +
460B ALA* 1.3 71.8 - - - +
462B THR* 1.3 57.8 + - - +
464B ASN* 3.4 8.0 - - - +
465B LEU* 2.9 30.8 + - - +
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Residues in contact with THR 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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450B LEU* 3.4 18.9 - - - +
458B ARG 3.0 14.9 + - - -
459B GLU* 3.4 12.2 - - - +
460B ALA 3.1 0.2 - - - -
461B ALA* 1.3 78.7 - - - +
463B SER* 1.3 65.6 + - - +
464B ASN 3.2 0.3 + - - -
465B LEU* 3.2 3.2 + - - +
466B LYS* 3.1 22.7 + - + +
506B VAL* 3.6 26.4 - - + +
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Residues in contact with SER 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 GLU 3.2 8.8 + - - -
460B ALA* 3.8 7.6 - - - -
462B THR* 1.3 81.3 - - - +
464B ASN* 1.3 62.9 + - - +
466B LYS* 3.4 8.7 + - - +
467B LYS* 3.0 47.2 + - - +
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Residues in contact with ASN 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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423B ILE* 4.1 17.0 - - + +
426B MET* 3.2 38.4 - - - +
427B PRO* 4.2 11.3 - - - +
446B CYS* 4.3 11.6 - - - +
449B TRP* 4.5 4.9 - - - -
460B ALA 2.9 18.5 + - - +
461B ALA* 3.4 7.0 - - - +
463B SER* 1.3 76.9 - - - +
465B LEU* 1.3 63.1 + - - +
467B LYS* 3.2 8.1 + - - +
468B LEU* 2.8 45.6 + - - +
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Residues in contact with LEU 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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446B CYS* 5.4 13.7 - - + +
447B MET* 5.1 9.9 - - + +
450B LEU* 4.2 24.2 - - + -
461B ALA 2.9 16.9 + - - +
462B THR* 3.7 5.4 - - - +
464B ASN* 1.3 75.9 - - - +
466B LYS* 1.3 65.2 + - - +
468B LEU* 3.4 17.3 + - + +
469B VAL* 3.3 23.8 + - + +
481B ILE* 3.9 29.8 - - + -
503B CYS* 4.6 16.2 - - + +
506B VAL* 4.3 19.5 - - + -
507B LEU* 4.9 7.0 - - + -
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Residues in contact with LYS 466 (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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462B THR* 3.1 14.6 + - + +
463B SER* 3.6 12.8 - - - +
464B ASN 3.2 0.2 - - - -
465B LEU* 1.3 80.2 - - - +
467B LYS* 1.3 74.1 + - + +
469B VAL* 3.2 6.0 + - - +
470B GLU* 3.0 51.7 + - + +
506B VAL* 3.8 14.1 - - + +
509B GLU* 3.4 43.4 + - - +
510B VAL* 4.8 7.6 - - + -
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Residues in contact with LYS 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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427B PRO* 6.1 4.7 - - + -
463B SER* 3.0 33.6 + - - +
464B ASN* 3.6 8.5 - - - +
466B LYS* 1.3 89.9 - - - +
468B LEU* 1.3 67.9 + - + +
470B GLU* 3.0 28.1 + - - +
471B LYS* 2.8 25.8 + - - +
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Residues in contact with LEU 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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426B MET* 5.1 2.2 - - + +
427B PRO* 5.6 2.0 - - + -
430B ALA* 5.4 6.7 - - + -
438B PHE* 3.8 39.0 - - + -
443B ASN* 5.6 0.4 - - - +
446B CYS* 4.5 15.5 - - + -
464B ASN* 2.8 44.2 + - - +
465B LEU* 3.4 20.2 - - + +
467B LYS* 1.3 74.9 - - + +
469B VAL* 1.3 53.5 + - - +
471B LYS* 2.8 10.5 + - - +
472B PHE* 2.6 46.8 + - + +
476B TRP* 4.2 21.1 - - + -
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Residues in contact with VAL 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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465B LEU* 3.5 18.4 - - + +
466B LYS* 3.2 7.7 + - - +
468B LEU* 1.3 73.8 - - - +
470B GLU* 1.3 59.8 + - - +
473B GLY* 2.6 47.0 + - - +
474B LYS* 4.5 1.8 - - - -
476B TRP* 4.4 14.3 - - + -
477B ALA* 4.1 17.9 - - + -
481B ILE* 4.6 0.2 - - + -
506B VAL* 6.1 0.9 - - + -
507B LEU* 4.1 24.5 - - + -
510B VAL* 3.4 32.5 - - + +
511B CYS* 4.9 4.0 - - - -
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Residues in contact with GLU 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 LYS* 3.0 38.2 + - - +
467B LYS* 3.0 42.7 + - - +
469B VAL* 1.3 76.2 - - - +
471B LYS* 1.3 59.2 + - - +
473B GLY* 4.6 1.4 + - - -
510B VAL* 3.8 25.8 - - + +
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Residues in contact with LYS 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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430B ALA* 4.2 23.8 - - + -
431B GLY* 4.2 14.3 - - - -
434B GLY* 6.0 0.4 - - - -
467B LYS 2.8 11.5 + - - +
468B LEU* 2.8 10.5 + - - +
470B GLU* 1.3 79.9 - - - +
472B PHE* 1.3 88.6 + - + +
473B GLY 3.6 0.3 + - - -
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Residues in contact with PHE 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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430B ALA* 4.2 7.6 - - + -
434B GLY* 3.8 4.0 - - - -
435B VAL* 3.6 39.5 - - + -
438B PHE* 3.5 42.8 - + - -
468B LEU* 2.6 25.0 + - + +
471B LYS* 1.3 105.0 - - + +
473B GLY* 1.3 58.3 + - - +
476B TRP* 3.8 53.5 + + + +
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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