Contacts of the helix formed by residues 495 - 508 (chain D) in PDB entry 2BKU
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 PHE 495 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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448D PRO 4.7 4.3 - - - -
452D LEU* 3.5 32.8 - - + -
453D PRO* 4.0 40.2 - - + -
456D VAL* 3.9 29.6 - - + -
491D PRO 3.5 15.9 - - - -
492D ILE* 2.7 18.4 + - + +
494D ASN* 1.3 83.8 - - + +
496D TYR* 1.3 57.1 + - - +
497D PRO* 3.4 3.4 - - - -
498D ALA* 3.3 11.1 + - + +
499D LEU* 2.9 34.9 + - + +
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Residues in contact with TYR 496 (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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481D VAL* 3.8 6.9 - - + +
492D ILE* 3.3 21.9 + - + -
493D TYR* 3.1 45.6 + + - +
495D PHE* 1.3 77.0 - - - +
497D PRO* 1.4 62.2 - - + +
499D LEU* 4.8 0.4 - - + -
500D VAL* 2.7 49.1 + - + +
527D MET* 2.5 66.1 + - + -
530D TYR* 3.3 21.1 + - - +
531D ALA* 4.5 5.2 - - + -
535D VAL* 3.7 30.3 - - + -
538D THR* 4.2 5.8 - - + -
539D SER* 5.9 2.2 - - - -
542D ILE* 5.9 1.3 - - + -
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Residues in contact with PRO 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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493D TYR 3.8 7.0 - - - +
494D ASN 4.0 7.4 - - - +
495D PHE 3.4 4.0 - - - -
496D TYR* 1.4 94.6 - - + +
498D ALA* 1.3 55.9 + - - +
500D VAL* 4.3 0.2 - - - +
501D ASP* 2.9 35.3 + - - +
535D VAL* 4.8 3.6 - - + -
538D THR* 4.4 22.2 - - + +
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Residues in contact with ALA 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456D VAL* 4.8 7.6 - - + -
460D LEU* 3.5 31.8 - - + +
495D PHE* 3.3 16.2 + - + +
497D PRO* 1.3 79.9 - - - +
499D LEU* 1.3 61.8 + - - +
501D ASP* 3.7 5.2 - - - +
502D GLY 3.2 15.8 + - - -
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Residues in contact with LEU 499 (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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456D VAL* 3.8 32.1 - - + +
459D CYS* 4.9 1.1 - - + -
460D LEU* 4.2 10.7 - - + +
477D ILE* 4.0 38.1 - - + -
480D LEU* 5.6 2.7 - - + -
481D VAL* 5.1 0.4 - - + -
492D ILE* 3.5 34.5 - - + -
495D PHE* 2.9 24.5 + - + +
496D TYR* 4.7 0.4 - - - +
498D ALA* 1.3 74.1 - - - +
500D VAL* 1.3 61.2 + - - +
501D ASP 3.1 1.8 - - - -
502D GLY* 3.0 2.9 + - - -
503D LEU* 2.9 34.2 + - + +
527D MET* 3.5 21.5 - - + -
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Residues in contact with VAL 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496D TYR* 2.7 27.7 + - + +
497D PRO 4.3 1.6 - - - +
499D LEU* 1.3 71.1 - - - +
501D ASP* 1.3 58.2 + - - +
503D LEU* 4.0 6.7 - - - +
504D ILE* 3.1 37.0 + - + +
524D LEU* 4.5 1.6 - - + -
527D MET* 3.3 23.3 - - + +
538D THR* 3.2 30.1 - - - +
541D SER* 5.0 3.4 - - - -
542D ILE* 3.5 39.3 - - + -
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Residues in contact with ASP 501 (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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497D PRO 2.9 21.7 + - - +
498D ALA* 3.7 6.1 - - - +
500D VAL* 1.3 80.3 - - - +
502D GLY* 1.3 61.7 + - - +
504D ILE* 3.5 7.5 + - - +
505D GLY* 3.4 16.1 + - - -
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Residues in contact with GLY 502 (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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460D LEU* 4.3 6.5 - - - -
463D LEU* 3.5 26.9 - - - +
498D ALA 3.2 8.8 + - - -
499D LEU 3.0 5.8 + - - -
501D ASP* 1.3 77.5 - - - +
503D LEU* 1.3 63.5 + - - +
504D ILE 3.4 0.2 - - - -
505D GLY* 3.6 2.8 + - - -
506D ALA* 3.3 16.5 + - - +
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Residues in contact with LEU 503 (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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463D LEU* 3.8 10.3 - - + -
474D SER* 4.0 13.5 - - - +
477D ILE* 3.8 28.7 - - + -
499D LEU 2.9 19.2 + - - +
500D VAL 4.0 0.4 - - - +
501D ASP 3.3 0.2 - - - -
502D GLY* 1.3 75.6 - - - +
504D ILE* 1.3 60.5 + - - +
506D ALA* 3.2 5.6 + - - +
507D ALA* 2.8 27.4 + - - +
520D ALA* 3.5 8.6 - - - +
523D ALA* 3.6 35.2 - - + -
524D LEU* 3.4 21.5 - - + +
527D MET* 3.6 34.8 - - + -
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Residues in contact with ILE 504 (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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500D VAL* 3.1 34.6 + - + +
501D ASP* 3.8 8.5 - - - +
503D LEU* 1.3 75.0 - - - +
505D GLY* 1.3 57.4 + - - +
507D ALA* 3.0 8.1 + - - +
508D ASN* 2.8 45.8 + - - +
524D LEU* 4.2 12.6 - - + -
541D SER* 4.3 24.2 - - - +
542D ILE* 4.7 2.2 - - + -
545D PHE* 3.7 36.8 - - + -
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Residues in contact with GLY 505 (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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463D LEU 5.8 0.4 - - - -
501D ASP 3.4 10.6 + - - -
502D GLY* 3.6 5.1 + - - -
503D LEU 3.3 0.6 - - - -
504D ILE* 1.3 80.6 - - - +
506D ALA* 1.3 59.6 + - - +
508D ASN* 3.4 16.5 + - - +
509D ARG* 3.6 8.3 + - - -
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Residues in contact with ALA 506 (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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463D LEU* 4.1 28.9 + - + +
470D ALA* 5.2 1.3 - - + -
474D SER* 5.2 0.2 - - - +
502D GLY 3.3 12.0 + - - +
503D LEU 3.2 8.6 + - - +
504D ILE 3.2 0.2 - - - -
505D GLY* 1.3 73.2 - - - +
507D ALA* 1.3 64.6 + - - +
508D ASN 3.2 0.2 - - - -
509D ARG* 3.1 40.5 + - - +
516D ALA 4.4 3.4 - - - +
517D ARG* 4.1 7.3 - - - -
520D ALA* 3.8 14.6 - - + -
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Residues in contact with ALA 507 (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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503D LEU 2.8 13.4 + - - +
504D ILE* 3.0 10.5 + - - +
506D ALA* 1.3 75.9 - - - +
508D ASN* 1.3 56.0 + - - +
509D ARG 3.2 3.6 + - - -
517D ARG* 3.6 22.0 - - - +
520D ALA* 3.7 9.3 - - + +
521D PHE* 3.7 29.3 - - + -
524D LEU* 4.3 7.0 - - + -
545D PHE* 3.6 24.2 - - + -
549D LYS* 4.1 6.6 - - - -
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Residues in contact with ASN 508 (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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504D ILE* 2.8 23.2 + - - +
505D GLY* 3.7 10.8 - - - +
506D ALA 3.2 0.6 - - - -
507D ALA* 1.3 73.1 - - - +
509D ARG* 1.3 68.4 + - - +
510D ILE* 3.5 2.1 + - - +
545D PHE* 3.0 32.7 - - - -
549D LYS* 3.0 26.6 + - - +
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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