Contacts of the helix formed by residues 483 - 502 (chain A) in PDB entry 2BS3
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 ASP 483 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481A PHE 5.3 1.0 - - - +
482A ARG* 1.3 79.9 - - - +
484A GLY* 1.3 64.9 + - - +
485A PRO* 3.1 16.3 - - + +
486A HIS* 2.6 57.5 + - - +
487A LEU* 3.0 23.9 + - - +
549A ARG* 3.8 3.8 - - - +
550A GLU* 4.3 17.2 - - + +
551A ASP* 3.5 15.5 - - + +
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Residues in contact with GLY 484 (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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483A ASP* 1.3 70.5 - - - +
485A PRO* 1.3 66.3 - - - +
487A LEU* 3.2 0.9 + - - -
488A GLU* 2.9 35.4 + - - +
538A LEU* 3.6 12.5 - - - +
549A ARG* 3.2 21.2 - - - +
551A ASP* 2.8 15.5 + - - -
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Residues in contact with PRO 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ASP* 3.1 17.0 - - + +
484A GLY* 1.3 90.8 - - - +
486A HIS* 1.3 67.5 + - + +
488A GLU* 3.5 10.1 + - + +
489A LYS* 3.3 18.2 + - - +
551A ASP* 4.3 4.9 - - + +
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Residues in contact with HIS 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A ASP 5.5 3.1 - - - +
477A ASN* 3.5 34.5 - - + +
483A ASP* 2.6 48.2 + - - +
485A PRO* 1.3 75.8 - - + +
487A LEU* 1.3 60.5 + - - +
489A LYS* 3.2 21.1 + - + +
490A ALA* 2.9 27.9 + - - +
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Residues in contact with LEU 487 (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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477A ASN 3.3 24.0 - - - +
478A VAL* 4.1 15.7 - - + -
482A ARG* 3.9 11.2 - - + -
483A ASP 3.0 20.0 + - - +
484A GLY 3.7 3.8 - - - +
486A HIS* 1.3 73.2 - - - +
488A GLU* 1.3 60.4 + - - +
490A ALA* 3.2 4.2 + - + +
491A VAL* 2.9 33.5 + - - +
534A ALA* 4.2 5.6 - - - +
537A ALA* 3.5 45.3 - - + +
538A LEU* 3.6 17.9 - - + +
549A ARG* 3.9 21.1 - - - +
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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
----------------------------------------------------------
484A GLY* 2.9 24.1 + - - +
485A PRO* 3.7 8.3 - - + +
487A LEU* 1.3 77.0 - - - +
489A LYS* 1.3 63.2 + - - +
491A VAL* 3.5 1.7 + - - +
492A LYS* 3.2 31.7 + - + +
538A LEU* 3.6 29.0 - - + +
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Residues in contact with LYS 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A ARG* 6.3 0.4 - - - +
476A ASP* 5.7 2.0 - - - +
477A ASN* 3.0 40.2 + - - +
485A PRO 3.3 9.9 + - - +
486A HIS* 3.2 22.2 + - - +
488A GLU* 1.3 81.0 - - - +
490A ALA* 1.3 60.7 + - - +
492A LYS* 3.4 6.8 + - - +
493A GLU* 3.0 33.8 + - + +
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Residues in contact with ALA 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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473A VAL* 3.8 19.2 - - + +
477A ASN* 3.7 23.3 - - + +
478A VAL* 4.5 11.0 - - + -
486A HIS 2.9 13.1 + - - +
487A LEU* 3.2 11.0 + - - +
489A LYS* 1.3 75.7 - - - +
491A VAL* 1.3 59.7 + - - +
493A GLU* 3.2 2.9 + - - +
494A LEU* 2.8 36.8 + - + +
534A ALA* 4.8 5.4 - - + -
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Residues in contact with VAL 491 (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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487A LEU 2.9 21.6 + - - +
488A GLU* 3.8 6.3 - - - +
490A ALA* 1.3 75.9 - - - +
492A LYS* 1.3 64.0 - - + +
494A LEU* 3.3 7.3 + - - +
495A GLU* 3.0 28.2 + - - +
531A LEU* 3.8 7.1 - - + +
534A ALA* 4.0 9.4 - - + -
535A LYS* 3.8 44.6 - - + +
538A LEU* 4.1 13.2 - - + -
575A LEU* 3.8 27.1 - - + -
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Residues in contact with LYS 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A GLU* 3.2 19.8 + - + +
489A LYS* 3.7 6.7 - - - +
491A VAL* 1.3 82.5 - - + +
493A GLU* 1.3 63.0 + - - +
495A GLU* 3.0 32.0 + - - +
496A GLU* 3.1 23.2 + - - +
575A LEU* 5.6 4.8 - - - +
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Residues in contact with GLU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A ARG* 2.6 49.2 + - - +
473A VAL* 3.7 18.6 - - + +
477A ASN* 5.7 0.5 + - - -
489A LYS* 3.0 28.9 + - + +
490A ALA* 3.8 3.3 - - - +
492A LYS* 1.3 74.3 - - - +
494A LEU* 1.3 61.0 + - - +
496A GLU* 3.2 12.0 + - + +
497A LEU* 2.8 38.3 + - + +
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Residues in contact with LEU 494 (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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470A MET* 4.1 25.8 - - + +
473A VAL* 4.1 19.3 - - + -
474A MET* 3.9 12.1 - - - -
490A ALA* 2.8 21.2 + - + +
491A VAL 3.7 0.2 - - - +
493A GLU* 1.3 76.5 - - - +
495A GLU* 1.3 58.7 + - - +
497A LEU* 3.1 12.0 + - + +
498A TYR* 2.8 29.5 + - - +
527A LEU* 4.1 12.5 - - + +
530A ALA* 3.8 22.2 - - + +
531A LEU* 3.6 19.8 - - + +
534A ALA* 3.7 30.5 - - + -
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Residues in contact with GLU 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A VAL 3.0 16.8 + - - +
492A LYS* 3.0 36.8 + - - +
493A GLU 3.2 0.2 - - - -
494A LEU* 1.3 76.3 - - - +
496A GLU* 1.3 63.0 + - - +
498A TYR* 3.3 8.8 + - - +
499A LYS* 3.1 32.4 + - + +
531A LEU* 3.9 6.2 - - - +
574A THR* 2.5 38.1 + - - +
575A LEU* 3.6 28.4 - - + +
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Residues in contact with GLU 496 (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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492A LYS 3.1 14.5 + - - +
493A GLU* 3.5 14.1 - - - +
495A GLU* 1.3 73.6 - - - +
497A LEU* 1.3 67.0 + - + +
499A LYS* 3.3 14.8 + - + +
500A LYS* 3.0 48.3 + - + +
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Residues in contact with LEU 497 (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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466A ILE* 4.1 24.0 - - + +
469A ARG* 3.8 25.8 - - + +
470A MET* 3.8 34.3 - - + +
473A VAL* 4.6 0.7 - - + -
493A GLU* 2.8 27.8 + - + +
494A LEU* 3.3 16.6 - - + +
496A GLU* 1.3 79.1 - - + +
498A TYR* 1.3 62.8 + - - +
500A LYS* 3.2 22.2 + - + +
501A SER* 2.9 23.2 + - - -
527A LEU* 3.7 13.1 - - + +
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Residues in contact with TYR 498 (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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494A LEU 2.8 12.9 + - - +
495A GLU* 3.4 11.7 - - - +
496A GLU 3.2 0.2 - - - -
497A LEU* 1.3 77.4 - - - +
499A LYS* 1.3 64.3 + - + +
501A SER* 2.5 27.5 + - - -
502A LYS* 3.6 26.3 + - + +
524A PRO* 3.9 24.9 - - + -
527A LEU* 3.6 16.4 - - + +
528A LYS* 3.7 42.8 + - + +
531A LEU* 4.5 9.4 - - + -
568A TRP* 4.6 10.2 - + - -
571A PRO 5.0 6.6 + - - -
573A GLN 4.8 2.6 + - - -
574A THR* 4.4 33.2 - - + -
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Residues in contact with LYS 499 (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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495A GLU* 3.1 29.3 + - + +
496A GLU* 3.7 13.3 - - + +
497A LEU 3.3 0.2 - - - -
498A TYR* 1.3 78.7 - - + +
500A LYS* 1.3 63.2 + - + +
502A LYS* 3.3 26.5 + - + +
503A ASN* 3.7 10.8 + - - -
574A THR* 4.6 18.8 - - + +
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Residues in contact with LYS 500 (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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461A GLU* 3.1 52.8 + - - +
466A ILE* 3.7 11.8 - - + +
496A GLU* 3.0 41.3 + - + +
497A LEU* 3.7 19.3 - - + +
499A LYS* 1.3 72.6 - - + +
501A SER* 1.3 57.1 + - - +
502A LYS 3.0 5.8 - - - -
503A ASN* 2.9 26.7 + - - +
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Residues in contact with SER 501 (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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454A LEU* 6.0 2.3 - - - +
466A ILE* 3.7 16.4 - - - +
497A LEU 2.9 12.9 + - - -
498A TYR* 2.5 25.1 + - - -
500A LYS* 1.3 76.7 - - - +
502A LYS* 1.3 60.2 + - - +
503A ASN 3.2 0.7 - - - -
504A VAL* 3.2 22.5 - - - +
520A ALA 5.1 1.7 - - - +
523A VAL* 4.6 4.9 - - - -
524A PRO* 3.7 35.0 - - - +
527A LEU* 3.8 14.4 - - - -
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Residues in contact with LYS 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A SER* 4.9 4.5 + - - -
498A TYR* 3.7 36.2 + - + +
499A LYS* 3.4 15.7 - - + +
500A LYS 3.0 0.8 - - - -
501A SER* 1.3 80.9 - - - +
503A ASN* 1.3 63.5 + - - +
504A VAL 3.4 2.8 + - - +
524A PRO* 6.0 2.2 - - + -
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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
------------------------------------------------------------
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