Contacts of the helix formed by residues 472 - 490 (chain A) in PDB entry 3BZI
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 LEU 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442A LEU* 4.4 7.4 - - + -
451A LEU* 5.4 1.1 - - + -
453A TYR* 3.7 58.3 - - + +
463A LEU* 3.9 28.7 - - + -
469A PRO* 2.9 21.6 + - + +
471A SER* 1.3 91.7 + - - +
473A MET* 1.3 57.3 - - - +
474A LYS 3.2 2.5 - - - -
475A LYS* 3.1 17.8 + - + +
476A ILE* 2.8 36.3 + - + +
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Residues in contact with MET 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A VAL* 5.0 6.5 - - + +
468A HIS* 3.8 42.2 - - + +
469A PRO* 3.4 24.5 - - - +
470A ASN* 3.5 21.4 + - - +
471A SER 3.5 0.6 - - - -
472A LEU* 1.3 77.5 - - - +
474A LYS* 1.3 60.7 + - + +
476A ILE* 3.4 18.8 + - + +
477A THR* 3.0 29.2 + - - -
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Residues in contact with LYS 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A ASN 5.1 0.4 + - - -
471A SER 5.0 2.4 + - - +
472A LEU 3.2 0.6 - - - -
473A MET* 1.3 78.9 - - + +
475A LYS* 1.3 60.6 + - + +
477A THR* 3.2 9.6 + - - +
478A LEU* 3.0 36.0 + - + +
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Residues in contact with LYS 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A PHE* 3.5 47.0 - - + -
438A ASP* 2.8 30.8 + - - -
440A THR* 3.0 10.3 + - - +
442A LEU* 3.8 8.5 - - + +
453A TYR* 2.8 31.7 + - + +
471A SER 5.2 5.1 + - - +
472A LEU* 3.1 23.9 + - + +
474A LYS* 1.3 79.0 - - + +
476A ILE* 1.3 57.7 + - - +
478A LEU* 3.4 7.5 + - + +
479A LEU* 3.0 25.6 + - - +
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Residues in contact with ILE 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A LEU* 3.8 20.4 - - + -
451A LEU* 3.9 25.4 - - + -
465A VAL* 4.2 22.2 - - + -
469A PRO* 4.2 17.7 - - + -
472A LEU* 2.8 27.1 + - + +
473A MET* 3.4 22.9 - - + +
475A LYS* 1.3 75.4 - - - +
477A THR* 1.3 68.2 + - - +
479A LEU* 3.3 5.6 + - + +
480A LYS* 2.9 47.4 + - + +
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Residues in contact with THR 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A MET 3.0 16.8 + - - -
474A LYS* 3.2 12.0 + - - +
476A ILE* 1.3 74.9 - - - +
478A LEU* 1.3 63.7 + - + +
480A LYS* 3.1 11.0 + - - +
481A TYR* 2.9 52.6 + - + -
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Residues in contact with LEU 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A TYR* 3.6 54.3 - - + +
436A PHE* 3.9 25.6 - - + -
474A LYS* 3.0 21.3 + - + +
475A LYS* 3.6 11.7 - - + +
477A THR* 1.3 82.8 - - + +
479A LEU* 1.3 63.9 + - - +
481A TYR* 3.0 12.8 + - + +
482A PHE* 2.9 33.5 + - + -
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Residues in contact with LEU 479 (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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432A VAL* 3.6 27.5 - - + +
433A GLY* 4.4 1.1 - - - +
434A VAL* 3.8 25.7 - - + +
442A LEU* 3.5 41.7 - - + +
444A LEU* 3.7 39.3 - - + +
451A LEU* 5.1 2.0 - - + -
475A LYS 3.0 18.2 + - - +
476A ILE* 3.3 6.0 + - + +
478A LEU* 1.3 75.3 - - - +
480A LYS* 1.3 66.5 + - + +
482A PHE* 3.2 4.4 + - - +
483A ARG* 2.9 26.3 + - + +
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Residues in contact with LYS 480 (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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444A LEU* 5.0 5.6 - - - -
448A GLY 4.7 10.3 + - - -
465A VAL* 4.3 22.8 - - - +
476A ILE* 2.9 35.8 + - + +
477A THR* 3.4 11.2 - - - +
479A LEU* 1.3 85.8 - - + +
481A TYR* 1.3 60.0 + - + +
483A ARG* 3.4 36.0 + - - +
484A ASN* 3.0 29.5 + - - +
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Residues in contact with TYR 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A THR* 2.9 47.8 + - + -
478A LEU* 3.0 13.4 + - + +
480A LYS* 1.3 73.4 - - + +
482A PHE* 1.3 62.5 + - + +
484A ASN* 3.6 11.0 + - + +
485A TYR* 3.1 24.3 + - - +
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Residues in contact with PHE 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A VAL* 3.8 34.5 - - + -
417A TYR* 3.9 19.1 - + + -
421A TYR* 4.4 22.7 - + + -
422A GLY 3.9 19.3 - - - -
424A GLY* 3.7 26.9 - - - -
432A VAL* 6.4 0.2 - - + -
433A GLY 5.5 0.2 - - - +
434A VAL* 3.7 32.1 - - + -
436A PHE* 5.1 0.2 - + - -
478A LEU* 2.9 31.2 + - + -
479A LEU* 3.5 7.4 - - + +
481A TYR* 1.3 73.8 - - + +
483A ARG* 1.3 65.4 + - - +
485A TYR* 3.2 6.1 + - + +
486A MET* 3.1 37.6 + - + +
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Residues in contact with ARG 483 (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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430A ASN 6.0 0.4 - - - -
432A VAL* 4.1 22.7 - - + -
444A LEU* 3.4 31.2 - - - +
448A GLY* 4.4 14.6 + - - -
479A LEU* 2.9 19.2 + - + +
480A LYS* 3.4 38.6 + - - +
482A PHE* 1.3 73.3 - - - +
484A ASN* 1.3 65.6 + - - +
486A MET* 3.4 13.2 + - - +
487A SER* 3.0 26.3 + - - -
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Residues in contact with ASN 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LYS 3.0 17.0 + - - +
481A TYR* 3.8 12.5 - - + +
483A ARG* 1.3 79.4 - - - +
485A TYR* 1.3 60.0 + - - +
487A SER* 3.2 6.8 + - - -
488A GLU* 2.8 57.7 + - - +
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Residues in contact with TYR 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A VAL* 3.9 21.5 - - + -
481A TYR 3.1 16.3 + - - +
482A PHE* 3.2 8.0 + - + +
484A ASN* 1.3 81.1 + - - +
486A MET* 1.3 57.2 + - - +
488A GLU* 4.6 0.2 - - - -
489A HIS* 2.9 72.7 + + + +
490A LEU* 4.6 5.3 - - + +
1E LEU* 3.4 30.3 - - + +
3E CYS* 3.7 22.3 - - - +
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Residues in contact with MET 486 (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 LYS* 3.1 40.1 + - + +
415A VAL* 3.6 22.0 - - + -
424A GLY 4.1 5.4 - - - +
425A TYR* 3.5 48.7 - - - +
426A GLN* 3.7 9.2 - - + +
432A VAL* 4.1 12.8 - - + -
433A GLY 5.3 0.4 - - - +
482A PHE* 3.1 33.6 + - + +
483A ARG* 3.9 9.9 - - - +
485A TYR* 1.3 73.2 - - - +
487A SER* 1.3 66.9 + - - +
490A LEU* 3.1 31.0 + - + +
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Residues in contact with SER 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A LYS* 3.9 12.5 + - - +
426A GLN* 6.1 0.9 - - - +
483A ARG* 3.0 21.3 + - - -
484A ASN* 3.6 7.4 - - - -
486A MET* 1.3 79.4 - - - +
488A GLU* 1.3 63.6 + - - +
490A LEU 4.7 1.7 + - - +
7E ASN* 4.8 2.3 + - - -
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Residues in contact with GLU 488 (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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484A ASN* 2.8 44.2 + - - +
485A TYR 3.7 3.6 - - - +
487A SER* 1.3 80.7 + - - +
489A HIS* 1.3 83.9 + - + +
7E ASN* 3.1 14.3 + - - -
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Residues in contact with HIS 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A TYR* 2.9 61.9 + + + +
488A GLU* 1.3 100.9 + - + +
490A LEU* 1.3 69.9 + - + +
6E PRO* 3.3 10.1 - - + +
7E ASN* 3.0 31.5 + - - +
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Residues in contact with LEU 490 (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 LYS* 3.0 35.9 + - + -
414A TRP 3.5 24.9 - - - +
415A VAL* 3.7 18.4 - - + -
485A TYR* 4.5 5.4 - - + +
486A MET* 3.1 24.8 + - + +
487A SER 4.8 1.0 - - - +
488A GLU 3.9 0.2 - - - -
489A HIS* 1.3 94.1 - - + +
491A LEU* 1.3 60.8 + - - +
3E CYS* 4.0 12.6 - - + -
4E SER* 3.6 29.8 - - - +
5E TPO 3.7 2.9 - - - +
6E PRO* 4.0 9.6 - - + -
7E ASN* 3.4 10.4 + - - +
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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
------------------------------------------------------------
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