Contacts of the helix formed by residues 483 - 502 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481D PHE 5.3 0.7 - - - +
482D ARG* 1.3 78.8 - - - +
484D GLY* 1.3 67.8 + - - +
485D PRO* 3.1 15.9 - - + +
486D HIS* 2.6 56.6 + - - +
487D LEU* 3.0 23.5 + - - +
549D ARG* 3.8 3.8 - - - +
550D GLU* 4.3 18.5 - - + +
551D ASP* 3.5 14.8 - - + +
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Residues in contact with GLY 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483D ASP* 1.3 70.5 - - - +
485D PRO* 1.3 67.2 - - - +
487D LEU* 3.2 1.0 + - - -
488D GLU* 2.9 35.2 + - - +
538D LEU* 3.6 11.6 - - - +
549D ARG* 3.2 21.0 - - - +
551D ASP* 2.8 16.2 + - - -
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Residues in contact with PRO 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483D ASP* 3.1 16.6 - - + +
484D GLY* 1.3 90.4 - - - +
486D HIS* 1.3 66.4 + - + +
488D GLU* 3.5 9.4 + - + +
489D LYS* 3.3 18.2 + - - +
551D ASP* 4.3 5.2 - - + +
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Residues in contact with HIS 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476D ASP 5.5 3.1 - - - -
477D ASN* 3.5 33.5 - - + +
483D ASP* 2.6 48.6 + - - +
485D PRO* 1.3 75.2 - - + +
487D LEU* 1.3 61.4 + - - +
489D LYS* 3.2 19.7 + - - +
490D ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477D ASN 3.3 24.5 - - - +
478D VAL* 4.1 16.6 - - + -
482D ARG* 3.9 9.2 - - + -
483D ASP 3.0 20.9 + - - +
484D GLY 3.7 3.6 - - - +
486D HIS* 1.3 74.8 - - - +
488D GLU* 1.3 60.6 + - - +
490D ALA* 3.3 3.8 + - + +
491D VAL* 3.0 34.3 + - - +
534D ALA* 4.2 6.1 - - - +
537D ALA* 3.5 46.9 - - + +
538D LEU* 3.6 17.0 - - + +
549D ARG* 3.9 20.9 - - - +
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Residues in contact with GLU 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484D GLY* 2.9 24.5 + - - +
485D PRO* 3.7 8.5 - - - +
487D LEU* 1.3 76.2 - - - +
489D LYS* 1.3 62.9 + - - +
491D VAL* 3.5 2.2 + - - +
492D LYS* 3.2 31.5 + - + +
538D LEU* 3.6 28.6 - - + +
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Residues in contact with LYS 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469D ARG* 6.3 0.7 - - - +
476D ASP* 5.7 1.6 - - - +
477D ASN* 2.9 41.1 + - - +
485D PRO 3.3 9.4 + - - +
486D HIS* 3.2 23.8 + - - +
488D GLU* 1.3 80.2 - - - +
490D ALA* 1.3 60.4 + - - +
492D LYS* 3.4 5.8 + - - +
493D GLU* 3.0 33.2 + - + +
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Residues in contact with ALA 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473D VAL* 3.8 19.5 - - + +
477D ASN* 3.7 23.8 - - + +
478D VAL* 4.5 11.2 - - + -
486D HIS 2.9 13.4 + - - +
487D LEU* 3.5 11.2 - - - +
489D LYS* 1.3 77.6 - - - +
491D VAL* 1.3 57.0 + - - +
493D GLU* 3.2 2.4 + - - +
494D LEU* 2.8 36.1 + - + +
534D ALA* 4.8 5.4 - - + -
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Residues in contact with VAL 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487D LEU 3.0 22.0 + - - +
488D GLU* 3.8 5.6 - - - +
489D LYS 3.4 0.2 - - - -
490D ALA* 1.3 75.4 - - - +
492D LYS* 1.3 64.6 + - + +
494D LEU* 3.4 7.4 + - - +
495D GLU* 3.0 28.1 + - - +
531D LEU* 3.8 7.1 - - + +
534D ALA* 4.0 9.2 - - + +
535D LYS* 3.9 44.0 - - + +
538D LEU* 4.1 13.5 - - + -
575D LEU* 3.8 27.4 - - + -
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Residues in contact with LYS 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488D GLU* 3.2 20.3 + - + +
489D LYS* 3.7 6.1 - - - +
491D VAL* 1.3 81.6 - - + +
493D GLU* 1.3 64.1 + - - +
495D GLU* 3.0 32.1 + - - +
496D GLU* 3.1 24.2 + - - +
575D LEU* 5.6 3.7 - - - +
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Residues in contact with GLU 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469D ARG* 2.6 49.9 + - - +
473D VAL* 3.7 17.3 - - + +
477D ASN* 5.7 0.7 + - - -
489D LYS* 3.0 29.4 + - + +
490D ALA* 3.8 3.5 - - - +
492D LYS* 1.3 73.8 - - - +
494D LEU* 1.3 61.1 + - - +
496D GLU* 3.2 12.3 + - + +
497D LEU* 2.8 37.0 + - + +
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Residues in contact with LEU 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470D MET* 4.1 27.1 - - + +
473D VAL* 4.1 19.7 - - + -
474D MET* 3.9 12.6 - - - -
490D ALA* 2.8 21.2 + - + +
491D VAL 3.7 0.2 - - - +
493D GLU* 1.3 76.6 - - - +
495D GLU* 1.3 57.2 + - - +
497D LEU* 3.1 12.3 + - + +
498D TYR* 2.8 29.3 + - - +
527D LEU* 4.1 12.3 - - + +
530D ALA* 3.8 21.5 - - + +
531D LEU* 3.6 20.2 - - + +
534D ALA* 3.7 30.3 - - + -
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Residues in contact with GLU 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491D VAL 3.0 16.6 + - - +
492D LYS* 3.0 37.6 + - - +
494D LEU* 1.3 76.4 - - - +
496D GLU* 1.3 61.8 + - - +
498D TYR* 3.3 8.2 + - - +
499D LYS* 3.1 32.7 + - + +
531D LEU* 3.9 6.7 - - - +
574D THR* 2.6 37.9 + - - +
575D LEU* 3.6 29.0 - - + +
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Residues in contact with GLU 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492D LYS 3.1 14.6 + - - +
493D GLU* 3.2 14.6 + - - +
495D GLU* 1.3 74.6 - - - +
497D LEU* 1.3 67.4 + - + +
499D LYS* 3.3 14.1 + - + +
500D LYS* 3.0 47.3 + - + +
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Residues in contact with LEU 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466D ILE* 4.1 25.1 - - + +
469D ARG* 3.9 25.4 - - + +
470D MET* 3.8 34.1 - - + +
473D VAL* 4.6 0.7 - - + -
493D GLU* 2.8 27.0 + - + +
494D LEU* 3.3 18.2 - - + +
496D GLU* 1.3 78.0 - - + +
498D TYR* 1.3 63.9 + - - +
500D LYS* 3.2 21.4 + - + +
501D SER* 2.9 23.7 + - - -
527D LEU* 3.7 12.0 - - + +
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Residues in contact with TYR 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494D LEU 2.8 13.3 + - - +
495D GLU* 3.4 11.9 - - - +
496D GLU 3.2 0.2 - - - -
497D LEU* 1.3 78.0 - - - +
499D LYS* 1.3 64.6 + - - +
501D SER* 2.5 27.6 + - - -
502D LYS* 3.6 24.0 + - + +
524D PRO* 3.9 25.1 - - + -
527D LEU* 3.6 17.4 - - + +
528D LYS* 3.7 41.9 + - + +
531D LEU* 4.5 9.0 - - + -
568D TRP* 4.6 10.2 + + - -
571D PRO 5.0 6.1 + - - -
573D GLN 4.8 2.6 + - - -
574D THR* 4.5 31.6 - - + -
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Residues in contact with LYS 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495D GLU* 3.1 29.9 + - + +
496D GLU* 3.7 13.5 - - + +
497D LEU 3.3 0.2 - - - -
498D TYR* 1.3 79.7 - - + +
500D LYS* 1.3 63.4 + - + +
502D LYS* 3.3 25.2 + - + +
503D ASN* 3.7 10.7 + - - -
574D THR* 4.6 19.1 - - + -
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Residues in contact with LYS 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461D GLU* 3.1 53.5 + - - +
466D ILE* 3.7 12.2 - - + +
496D GLU* 3.0 42.3 + - + +
497D LEU* 3.2 20.2 + - + +
499D LYS* 1.3 73.9 - - + +
501D SER* 1.3 56.7 + - - +
502D LYS 3.0 6.3 - - - -
503D ASN* 2.9 26.8 + - - +
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Residues in contact with SER 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454D LEU* 6.0 2.4 - - - +
466D ILE* 3.7 16.8 - - - +
497D LEU 2.9 12.5 + - - -
498D TYR* 2.5 26.2 + - - -
500D LYS* 1.3 76.5 - - - +
502D LYS* 1.3 60.0 + - - +
503D ASN 3.2 0.7 - - - -
504D VAL* 3.2 22.7 - - - +
520D ALA 5.1 1.7 - - - +
523D VAL* 4.6 4.0 - - - -
524D PRO* 3.7 35.1 - - - +
527D LEU* 3.8 14.1 - - - -
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Residues in contact with LYS 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457D SER* 5.0 3.5 + - - -
498D TYR* 3.9 33.4 - - + +
499D LYS* 3.3 16.8 + - + +
500D LYS 3.0 0.6 - - - -
501D SER* 1.3 82.1 + - - +
503D ASN* 1.3 64.0 + - - +
504D VAL 3.4 2.7 + - - +
524D PRO* 6.1 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