Contacts of the helix formed by residues 495 - 508 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B PRO 4.7 4.0 - - - -
452B LEU* 3.6 33.0 - - + -
453B PRO* 4.0 38.6 - - + -
456B VAL* 4.0 31.4 - - + -
491B PRO* 3.5 17.0 - - + -
492B ILE* 2.7 17.6 + - + +
494B ASN* 1.3 82.9 - - + +
496B TYR* 1.3 63.0 + - - -
497B PRO* 3.3 3.6 - - - -
498B ALA* 3.1 12.4 + - + +
499B LEU* 3.0 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 496 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B VAL* 4.0 4.3 - - + +
492B ILE* 3.3 22.1 + - + -
493B TYR* 3.0 44.2 + + - +
495B PHE* 1.3 75.6 - - - +
497B PRO* 1.3 63.2 - - + +
499B LEU* 3.1 1.8 + - + -
500B VAL* 2.7 52.4 + - + +
527B MET* 2.7 60.2 + - + -
530B TYR* 3.2 22.9 + - - +
531B ALA* 4.3 5.2 - - + -
535B VAL* 3.7 32.8 - - + -
538B THR* 4.3 6.7 - - + -
539B SER* 5.8 2.5 - - - -
542B ILE* 6.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 497 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B TYR 3.9 6.7 - - - +
494B ASN 4.3 6.5 - - - +
495B PHE 3.4 4.0 - - - -
496B TYR* 1.3 95.6 - - + +
498B ALA* 1.3 55.8 + - - +
500B VAL* 4.4 0.6 - - + +
501B ASP* 3.0 32.1 + - - +
535B VAL* 5.0 2.0 - - + -
538B THR* 4.2 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 498 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B VAL* 4.7 8.3 - - + -
460B LEU* 3.5 31.1 - - + +
495B PHE* 3.1 16.0 + - + +
497B PRO* 1.3 80.4 - - - +
499B LEU* 1.3 61.5 + - - +
501B ASP* 3.8 4.5 - - - +
502B GLY 3.3 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 499 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B VAL* 4.0 30.5 - - + -
459B CYS* 4.9 1.6 - - + -
460B LEU* 4.0 14.6 - - + +
463B LEU* 4.9 0.2 - - - +
477B ILE* 4.0 35.7 - - + -
480B LEU* 5.7 3.1 - - + -
481B VAL* 5.0 0.2 - - + -
492B ILE* 3.9 30.5 - - + -
495B PHE* 3.0 23.8 + - + +
496B TYR* 4.9 0.4 - - - -
498B ALA* 1.3 73.0 - - - +
500B VAL* 1.3 61.5 + - - +
501B ASP 3.1 1.7 + - - -
502B GLY* 3.2 2.1 + - - -
503B LEU* 2.9 34.5 + - + +
527B MET* 3.4 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 500 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B TYR* 2.7 30.1 + - + +
497B PRO* 4.4 1.6 - - + +
499B LEU* 1.3 73.4 - - - +
501B ASP* 1.3 60.8 - - - +
503B LEU* 3.9 5.2 - - - +
504B ILE* 3.2 35.0 + - + +
524B LEU* 4.5 2.5 - - + -
527B MET* 3.5 23.8 - - + -
538B THR* 3.4 26.0 - - - +
541B SER* 5.1 3.6 - - - -
542B ILE* 3.5 40.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 501 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B PRO 3.0 21.8 + - - +
498B ALA* 3.8 6.3 - - - +
499B LEU 3.1 0.2 - - - -
500B VAL* 1.3 79.9 - - - +
502B GLY* 1.3 61.3 + - - +
504B ILE* 3.5 6.9 + - - +
505B GLY* 3.3 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 502 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B LEU* 4.4 6.1 - - - -
463B LEU* 3.7 23.4 - - - +
498B ALA 3.3 9.2 + - - -
499B LEU 3.2 5.8 + - - -
501B ASP* 1.3 78.8 + - - +
503B LEU* 1.3 63.5 + - - +
505B GLY* 3.4 4.0 + - - -
506B ALA* 3.2 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 503 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B LEU* 3.9 8.5 - - + +
474B SER* 3.8 17.3 - - - +
477B ILE* 4.1 23.6 - - + -
499B LEU 2.9 21.1 + - - +
500B VAL 3.9 0.2 - - - +
502B GLY* 1.3 73.9 - - - +
504B ILE* 1.3 59.8 + - - +
506B ALA* 3.2 6.0 + - - +
507B ALA* 2.8 27.5 + - - +
520B ALA* 3.6 10.3 - - - +
523B ALA* 3.5 33.7 - - + -
524B LEU* 3.5 22.6 - - + +
527B MET* 3.7 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 504 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B VAL* 3.2 31.7 + - + +
501B ASP* 3.8 7.0 - - - +
502B GLY 3.3 0.4 - - - -
503B LEU* 1.3 72.2 - - - +
505B GLY* 1.3 56.7 + - - +
507B ALA* 2.9 7.7 + - - -
508B ASN* 2.8 51.8 + - - +
524B LEU* 4.1 11.9 - - + -
541B SER* 4.3 14.6 - - - +
542B ILE* 4.7 2.9 - - - -
545B PHE* 3.8 43.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 505 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B ASP 3.3 10.6 + - - -
502B GLY* 3.4 5.8 + - - -
503B LEU 3.3 0.6 - - - -
504B ILE* 1.3 80.3 - - - +
506B ALA* 1.3 58.6 + - - +
508B ASN* 3.3 19.1 + - - +
509B ARG* 3.7 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 506 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B LEU* 4.2 26.4 + - + +
470B ALA* 5.3 2.0 - - + -
474B SER* 5.4 0.2 - - - +
502B GLY 3.2 10.4 + - - +
503B LEU 3.2 8.4 + - - +
504B ILE 3.1 0.4 - - - -
505B GLY* 1.3 73.4 - - - +
507B ALA* 1.3 63.8 + - - +
508B ASN 3.1 0.4 - - - -
509B ARG* 3.1 43.6 + - - +
516B ALA 4.4 3.4 - - - +
517B ARG* 4.1 7.8 - - - -
520B ALA* 3.8 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 507 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B LEU 2.8 13.6 + - - +
504B ILE* 2.9 9.6 + - - +
506B ALA* 1.3 75.2 - - - +
508B ASN* 1.3 57.4 + - - +
509B ARG 3.2 3.8 + - - -
517B ARG* 3.5 20.1 - - - +
520B ALA* 3.7 11.3 - - + +
521B PHE* 3.7 30.4 - - + -
524B LEU* 4.3 7.2 - - + -
545B PHE* 3.8 20.2 - - + -
549B LYS* 3.9 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 508 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B ILE* 2.8 24.9 + - - +
505B GLY* 3.3 12.2 + - - +
506B ALA 3.1 0.6 - - - -
507B ALA* 1.3 73.8 - - - +
509B ARG* 1.3 65.4 + - - +
510B ILE* 3.6 2.3 + - - +
545B PHE* 3.2 29.9 - - - -
549B LYS* 2.7 32.1 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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