Contacts of the helix formed by residues 472 - 484 (chain A) in PDB entry 2A8B
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 THR 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418A LYS* 3.4 40.4 - - + +
447A ILE* 4.9 5.9 - - - +
466A GLN* 4.3 5.9 + - - -
468A PRO* 3.6 7.0 - - - +
469A MET* 3.0 28.9 + - + +
471A ASN* 1.3 94.4 - - - +
473A VAL* 1.3 60.5 + - - +
474A ASP 3.4 2.0 - - - -
475A ASP* 3.3 16.7 - - - +
476A PHE* 2.9 27.7 + - - +
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Residues in contact with VAL 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A PRO* 4.2 2.7 - - + -
469A MET 3.3 15.0 - - - +
470A ILE* 4.0 11.1 + - - +
471A ASN 3.8 1.2 - - - -
472A THR* 1.3 74.8 - - - +
474A ASP* 1.3 67.7 + - - +
476A PHE* 3.2 8.1 + - - +
477A TRP* 3.1 26.4 + - + -
502A VAL* 3.4 26.2 - - + -
503A LEU 4.9 1.1 - - - +
504A TYR* 3.7 22.7 - - + +
512A TYR* 3.4 35.4 - - + -
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Residues in contact with ASP 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A ASN 5.6 0.4 - - - -
472A THR* 3.4 0.6 - - - +
473A VAL* 1.3 76.6 - - - +
475A ASP* 1.3 56.3 + - - +
477A TRP* 3.3 2.4 + - - +
478A GLN* 2.8 35.7 + - - +
511A ILE 4.7 0.7 - - - +
512A TYR* 3.3 35.5 - - - +
513A GLY* 3.5 27.0 + - - +
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Residues in contact with ASP 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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418A LYS* 2.7 43.0 + - - +
434A LEU* 3.5 33.6 - - + +
446A TYR 4.1 6.9 - - - +
447A ILE* 3.7 12.5 - - + -
472A THR* 3.3 16.8 - - - +
474A ASP* 1.3 76.8 - - - +
476A PHE* 1.3 65.6 + - - +
478A GLN* 3.3 6.2 + - - +
479A MET* 3.0 18.9 + - - +
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Residues in contact with PHE 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ILE* 3.7 11.6 - - + +
465A THR* 4.1 13.2 - - + -
466A GLN 5.1 0.4 - - - -
468A PRO* 3.7 22.2 - - + -
472A THR 2.9 14.4 + - - +
473A VAL* 3.2 9.4 + - - +
475A ASP* 1.3 75.5 - - - +
477A TRP* 1.3 68.7 + + - +
479A MET* 3.1 21.1 + - + +
480A VAL* 2.9 45.5 + - + +
488A ILE* 4.0 24.9 - - + -
504A TYR* 3.3 40.2 - + - -
585A VAL* 3.9 19.3 - - + -
587A HIS* 4.1 8.3 - + - -
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Residues in contact with TRP 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A VAL* 3.1 24.4 + - + +
474A ASP 3.9 2.9 - - - +
476A PHE* 1.3 80.3 - + - +
478A GLN* 1.3 66.1 + - - +
480A VAL* 3.8 8.6 - - + +
481A TRP* 2.9 27.2 + - - +
488A ILE* 3.7 26.7 - - + -
504A TYR* 2.8 48.3 + + - -
505A TRP* 4.0 12.3 - - + -
512A TYR* 3.5 34.9 - + + -
515A VAL* 4.1 14.2 - - + +
517A VAL* 3.9 16.8 - - + -
533A LEU* 3.6 25.6 - - + -
535A LEU* 3.9 37.2 - - + +
546A HIS* 5.4 0.4 - + - -
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Residues in contact with GLN 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A LEU* 4.2 16.8 - - + -
435A ARG* 3.7 20.8 + - - +
436A PRO* 5.1 6.3 - - + -
474A ASP 2.8 19.2 + - - +
475A ASP* 3.4 13.0 - - - +
477A TRP* 1.3 71.5 - - - +
479A MET* 1.3 56.9 + - - +
481A TRP* 3.8 4.9 - - - +
482A GLN* 2.9 66.2 + - - +
514A LYS* 5.2 4.9 + - - +
515A VAL* 4.3 9.7 - - + +
537A GLN* 4.1 18.0 + - - +
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Residues in contact with MET 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A VAL* 3.6 24.0 - - + -
434A LEU* 3.8 10.5 - - + +
447A ILE* 4.1 9.4 - - + -
449A ALA* 3.6 27.4 - - - -
463A ILE* 3.9 11.9 - - + -
465A THR* 4.1 10.3 - - + -
475A ASP 3.0 12.6 + - - +
476A PHE* 3.1 38.8 - - + +
478A GLN* 1.3 74.7 - - - +
480A VAL* 1.3 67.9 + - + +
482A GLN* 3.8 7.2 - - - -
483A GLU* 3.0 36.5 + - + +
585A VAL* 4.0 26.0 - - + -
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Residues in contact with VAL 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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476A PHE* 2.9 47.2 + - + +
477A TRP* 3.2 17.2 + - + +
479A MET* 1.3 75.7 - - + +
481A TRP* 1.3 63.8 + - - +
484A ASP* 3.1 17.5 + - - -
485A SER* 3.2 28.5 + - - +
488A ILE* 4.3 7.6 - - + -
535A LEU* 3.5 20.4 - - + -
542A GLN* 4.3 0.7 + - - -
544A VAL* 3.8 22.2 - - + -
585A VAL* 4.4 11.2 - - + -
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Residues in contact with TRP 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A TRP 2.9 17.8 + - - +
478A GLN* 3.8 7.9 - - - +
480A VAL* 1.3 76.0 - - - +
482A GLN* 1.3 68.1 + - + +
484A ASP* 3.0 10.6 + - - +
515A VAL* 3.7 16.8 - - + -
535A LEU* 3.5 44.6 - - + +
536A LYS 4.0 1.8 - - - -
537A GLN* 3.4 49.9 + - + +
540A HIS* 3.5 38.8 - + + -
542A GLN* 3.0 59.7 + - + +
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Residues in contact with GLN 482 (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* 4.2 4.6 - - - +
433A CYS 2.9 25.7 + - - -
434A LEU* 3.3 5.5 - - - +
435A ARG* 2.7 69.5 + - - +
451A TYR* 4.6 0.2 + - - -
478A GLN* 2.9 43.6 + - - +
479A MET* 3.5 11.2 - - - +
481A TRP* 1.3 80.8 - - + +
483A GLU* 1.3 84.0 + - - +
484A ASP* 3.7 1.0 + - - +
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Residues in contact with GLU 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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432A VAL* 3.7 2.4 - - - +
435A ARG* 4.6 3.8 + - - -
451A TYR* 2.6 43.7 + - - -
460A LYS* 4.7 5.4 + - - +
463A ILE* 3.8 15.7 - - + -
479A MET* 3.0 23.8 + - + +
482A GLN* 1.3 101.8 + - + +
484A ASP* 1.3 69.3 + - - +
485A SER* 3.8 13.9 - - - +
582A GLY* 3.1 16.3 - - - -
583A PRO* 3.8 11.2 - - + +
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Residues in contact with ASP 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A VAL 3.1 2.3 + - - -
481A TRP 3.0 15.5 + - - +
482A GLN 3.4 1.5 - - - +
483A GLU* 1.3 80.2 - - - +
485A SER* 1.3 64.3 + - - +
542A GLN* 3.5 24.6 - - - +
580A GLY 4.6 1.9 - - - +
581A ARG* 3.0 51.2 + - - +
582A GLY 2.8 17.8 + - - +
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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