Contacts of the helix formed by residues 466 - 475 (chain A) in PDB entry 1B0K
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 PRO 466 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355A ILE* 3.8 25.3 - - + +
360A ASN* 3.2 30.7 - - + +
365A ASP* 3.5 36.8 - - + +
366A MET* 5.6 0.7 - - + -
369A SER* 3.2 18.8 + - - +
444A SER* 3.9 4.7 - - - +
465A SER* 1.4 83.6 - - - +
467A GLU* 1.3 71.3 + - - +
469A VAL 3.7 0.3 + - - -
470A THR* 2.9 27.7 + - - -
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Residues in contact with GLU 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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214A TRP* 3.7 33.7 - - + +
216A SER* 3.0 23.1 + - - -
365A ASP* 5.1 1.0 - - - +
368A ARG* 2.8 57.3 + - - +
369A SER* 3.9 4.6 + - - +
372A VAL* 3.8 9.7 - - + +
465A SER* 4.1 7.6 - - - +
466A PRO* 1.3 91.5 - - - +
468A ILE* 1.3 59.7 + - + +
470A THR* 3.6 8.2 + - - -
471A ALA 3.3 18.2 + - - -
500A PRO* 4.0 11.4 - - + -
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Residues in contact with ILE 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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214A TRP* 3.5 33.2 - - + +
320A PRO* 4.5 24.7 - - + -
321A HIS 5.8 0.2 - - - +
334A VAL* 4.3 16.8 - - + -
464A THR* 3.7 17.5 - - + +
465A SER* 3.1 23.1 + - - +
467A GLU* 1.3 74.4 - - + +
469A VAL* 1.4 67.6 + - - +
470A THR 3.2 0.9 - - - -
471A ALA* 3.2 3.8 + - - +
472A LEU* 2.9 44.7 + - + +
482A PRO* 4.1 20.6 - - + -
483A GLU* 6.4 0.7 - - + -
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Residues in contact with VAL 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A GLY* 3.9 12.3 - - - -
354A LEU 3.7 21.3 - - - +
355A ILE* 3.7 19.3 - - + -
387A PHE* 4.5 5.2 - - + -
442A VAL* 4.1 14.6 - - + +
443A THR* 3.7 22.2 - - - -
444A SER* 3.9 5.2 - - - +
464A THR* 3.5 24.5 - - + -
465A SER 3.1 11.7 + - - +
466A PRO 3.8 7.2 - - - +
468A ILE* 1.4 75.9 - - - +
470A THR* 1.3 57.8 + - - +
472A LEU* 3.7 2.2 - - - +
473A ALA* 2.9 27.7 + - - +
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Residues in contact with THR 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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355A ILE* 4.3 1.7 - - - +
369A SER* 3.8 30.0 + - - +
372A VAL* 4.3 5.4 - - + -
373A ALA* 4.1 20.0 - - + +
387A PHE* 3.9 33.2 - - + -
409A LEU* 5.3 0.2 - - + -
412A VAL* 5.6 0.7 - - + -
466A PRO 2.9 14.8 + - - -
467A GLU* 3.7 8.5 - - - -
468A ILE 3.2 0.2 - - - -
469A VAL* 1.3 77.1 - - - +
471A ALA* 1.3 61.9 + - - +
473A ALA* 3.3 2.8 + - + +
474A ILE* 3.2 33.0 + - + +
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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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214A TRP* 4.4 2.9 - - + -
372A VAL* 3.9 17.2 - - + +
467A GLU 3.3 10.7 + - - +
468A ILE* 3.2 7.0 + - - +
470A THR* 1.3 76.8 - - - +
472A LEU* 1.3 62.5 + - - +
474A ILE* 3.3 7.8 + - - +
475A ALA* 3.2 21.5 + - - +
480A PHE* 4.0 7.0 - - + -
482A PRO* 3.6 34.5 - - + -
497A LEU* 4.2 9.4 - - + +
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Residues in contact with LEU 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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322A ILE* 4.3 22.4 - - + -
334A VAL* 5.0 7.4 - - + -
337A VAL* 6.1 1.8 - - + -
350A ILE* 3.8 16.0 - - + +
442A VAL* 4.4 17.0 - - + -
464A THR* 5.2 0.7 - - + -
468A ILE* 2.9 37.5 + - + +
469A VAL* 3.9 3.8 - - - +
471A ALA* 1.3 78.5 - - + +
473A ALA* 1.4 50.5 + - - +
475A ALA* 3.4 4.7 + - - +
476A GLY* 2.7 33.8 + - - -
477A THR 3.7 17.6 + - - +
478A LEU* 4.7 9.4 - - + +
480A PHE* 3.4 31.9 - - + +
482A PRO* 5.0 2.7 - - + -
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Residues in contact with ALA 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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350A ILE* 5.5 1.8 - - - -
353A GLY* 4.7 9.9 - - - -
383A CYS* 3.7 9.8 - - - -
384A LYS 3.1 2.8 + - - -
385A SER* 3.0 45.4 + - - -
387A PHE* 4.1 27.4 - - + -
442A VAL* 5.5 0.8 - - - +
469A VAL 2.9 17.6 + - - +
470A THR 3.3 4.7 + - - +
472A LEU* 1.4 73.1 - - - +
474A ILE* 1.3 65.1 + - - +
475A ALA 3.5 0.2 + - - -
476A GLY 3.7 0.7 + - - -
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Residues in contact with ILE 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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372A VAL* 4.5 9.6 - - + -
373A ALA* 4.4 10.3 - - - -
376A ALA* 3.7 31.0 - - + -
381A LEU* 4.9 12.8 - - + +
382A LYS 4.1 5.0 - - - +
383A CYS* 4.1 24.2 - - - +
384A LYS* 3.6 16.8 + - - +
412A VAL* 4.8 4.9 - - + -
470A THR* 3.2 30.7 + - + +
471A ALA* 3.5 8.1 - - - +
473A ALA* 1.3 75.5 - - - +
475A ALA* 1.4 57.6 + - - +
487A LEU* 3.7 29.2 - - + +
497A LEU* 6.0 2.9 - - + -
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Residues in contact with ALA 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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384A LYS* 3.8 13.1 - - - +
471A ALA 3.2 16.0 + - - +
472A LEU 3.8 3.6 - - - +
474A ILE* 1.4 79.2 - - - +
476A GLY* 1.3 58.9 + - - +
477A THR* 3.4 12.2 + - + +
480A PHE* 3.7 36.3 - - + -
487A LEU* 4.7 11.0 - - + -
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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
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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