Contacts of the helix formed by residues 515 - 530 (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 ASN 515 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A TYR* 3.3 39.6 + - + +
156A ASN* 2.7 34.0 + - - +
159A LYS* 3.9 8.9 - - - +
471B THR* 3.4 5.6 - - + +
512B ASN* 3.2 28.9 + - - -
513B GLU 3.2 2.4 - - - -
514B PHE* 1.3 76.8 - - - +
516B ALA* 1.3 53.7 + - - +
517B ARG 3.3 2.9 - - - -
518B ALA* 4.1 2.1 - - + +
519B SER* 2.5 44.4 + - - +
571B GLU* 4.0 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 516 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B PRO* 3.6 41.7 - - + +
470B ALA* 4.4 6.5 - - + +
471B THR* 3.3 8.9 + - - +
474B SER* 4.8 1.6 + - - -
506B ALA* 4.3 6.8 - - - +
509B ARG* 4.0 21.3 - - - +
512B ASN* 3.6 0.4 + - - -
513B GLU 3.4 4.9 + - - +
514B PHE 3.1 2.6 + - - -
515B ASN* 1.3 78.5 - - - +
517B ARG* 1.3 58.9 + - - +
519B SER* 3.9 3.5 - - - -
520B ALA* 3.5 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 517 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B ALA 4.1 9.2 - - - +
507B ALA 3.5 25.1 - - - +
509B ARG* 3.3 29.3 + - + +
510B ILE 3.4 16.4 + - - -
511B ASP* 3.5 20.9 + - - +
512B ASN* 3.2 28.4 + - - +
516B ALA* 1.3 77.5 - - - +
518B ALA* 1.3 65.5 + - - +
520B ALA* 3.2 11.8 + - - +
521B PHE* 3.2 27.8 + - + -
549B LYS* 5.7 2.7 - - - +
568B SER* 4.0 27.1 + - - -
569B LEU* 5.7 0.4 - - - +
571B GLU* 5.5 0.6 + - - -
572B LEU* 3.8 36.3 - - + +
575B ASN* 5.4 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 518 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A TYR* 4.6 12.8 - - + -
475B TRP* 5.7 0.4 - - - -
512B ASN* 2.9 23.2 + - - +
515B ASN* 3.4 12.3 + - - +
517B ARG* 1.3 76.0 - - - +
519B SER* 1.3 61.8 + - - +
521B PHE* 3.4 3.9 + - - +
522B SER* 3.1 25.6 + - - -
571B GLU* 4.3 4.7 - - - +
575B ASN* 3.6 31.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 519 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A TYR* 5.9 0.4 - - - -
471B THR* 3.2 30.3 - - - +
474B SER* 3.6 23.6 - - - -
475B TRP* 3.5 21.1 + - - -
478B ILE* 4.6 1.6 - - - +
515B ASN* 2.5 27.9 + - - +
516B ALA 3.9 4.7 - - - -
518B ALA* 1.3 76.5 - - - +
520B ALA* 1.3 57.3 + - - +
522B SER* 3.1 5.2 + - - -
523B ALA* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 520 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B SER* 3.7 10.7 + - - +
503B LEU* 3.6 26.4 - - + +
506B ALA* 3.8 8.5 - - + -
507B ALA* 3.7 14.1 - - - +
516B ALA 3.5 11.3 + - - +
517B ARG 3.2 10.3 + - - +
519B SER* 1.3 78.9 - - - +
521B PHE* 1.3 58.5 + - - +
523B ALA* 3.2 6.8 + - - +
524B LEU* 2.8 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 521 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B ALA* 3.7 34.1 - - + -
517B ARG* 3.2 28.2 + - + -
518B ALA 3.8 6.3 - - - +
520B ALA* 1.3 77.0 - - - +
522B SER* 1.3 57.7 + - - +
524B LEU* 3.3 7.5 + - + -
525B THR* 2.9 32.0 + - - -
545B PHE* 4.2 11.4 - + - -
546B VAL* 4.1 16.6 - - + -
549B LYS* 4.6 5.8 - - + -
572B LEU* 3.7 27.4 - - + -
575B ASN* 3.8 40.2 - - + +
576B ILE* 3.7 19.7 - - + -
578B THR* 6.2 0.2 - - - -
579B VAL* 3.3 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 522 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B TRP* 4.2 24.4 - - - -
478B ILE* 3.9 6.5 - - - +
518B ALA 3.1 15.4 + - - -
519B SER 3.4 8.3 - - - -
521B PHE* 1.3 73.1 - - - +
523B ALA* 1.3 65.2 + - - +
525B THR* 3.3 10.3 - - - -
526B THR* 3.1 24.4 + - - -
578B THR* 5.7 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 523 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B SER* 4.0 10.1 - - - +
477B ILE* 4.9 4.0 - - + +
478B ILE* 3.6 23.2 - - + +
503B LEU* 3.5 28.9 - - + -
519B SER 2.9 12.0 + - - +
520B ALA 3.2 8.0 + - - +
522B SER* 1.3 74.2 - - - +
524B LEU* 1.3 61.0 + - - +
526B THR* 2.9 5.7 + - - -
527B MET* 2.8 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 524 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B VAL* 4.2 13.5 - - + +
503B LEU* 3.5 30.1 - - + -
504B ILE* 4.1 20.2 - - + -
507B ALA* 4.3 18.6 - - + -
520B ALA 2.8 19.7 + - - +
521B PHE* 3.3 15.7 + - + +
523B ALA* 1.3 71.5 - - - +
525B THR* 1.3 63.6 + - - +
527B MET* 3.2 6.1 + - + +
528B VAL* 3.0 27.9 + - - +
542B ILE* 4.2 22.4 - - + +
545B PHE* 4.3 12.6 - - + -
546B VAL* 4.9 5.6 - - + -
579B VAL* 4.0 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 525 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B PHE 2.9 17.8 + - - -
522B SER* 3.3 11.0 - - - -
524B LEU* 1.3 75.4 - - - +
526B THR* 1.3 58.2 + - - +
528B VAL* 3.1 8.5 + - - +
529B GLU* 2.8 48.8 + - + +
578B THR* 3.3 33.9 - - + +
579B VAL* 3.3 14.1 - - - +
582B ALA* 3.9 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 526 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B ILE* 3.6 41.5 - - + +
481B VAL* 4.3 13.5 - - + -
482B GLU* 4.5 3.5 + - + +
522B SER 3.1 10.6 + - - -
523B ALA 2.9 8.5 + - - -
525B THR* 1.3 74.6 - - - +
527B MET* 1.3 68.2 + - - +
529B GLU* 2.9 20.0 + - - +
530B TYR* 3.0 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B ILE* 4.0 14.1 - - - -
481B VAL* 3.8 25.4 - - - -
496B TYR* 2.7 54.0 + - + +
499B LEU* 3.4 37.5 - - + -
500B VAL* 3.5 29.2 - - + +
503B LEU* 3.7 14.4 - - + -
523B ALA 2.8 22.5 + - - +
524B LEU* 3.2 9.2 + - - +
526B THR* 1.3 72.5 - - - +
528B VAL* 1.3 61.9 + - - +
531B ALA* 3.3 6.6 + - - +
542B ILE* 4.3 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B LEU 3.0 15.9 + - - +
525B THR* 3.4 7.9 - - - +
527B MET* 1.3 73.4 - - - +
529B GLU* 1.3 67.2 + - - +
530B TYR 3.1 1.8 - - - -
531B ALA* 3.1 20.7 + - + +
539B SER* 4.7 11.4 - - - +
542B ILE* 3.6 34.5 - - + -
579B VAL* 4.7 2.9 - - + -
582B ALA* 3.5 38.6 - - + +
583B VAL* 3.5 18.6 - - + +
586B LYS* 3.7 12.9 - - + +
587B SER* 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 529 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LYS* 4.3 20.9 + - - +
525B THR* 2.8 45.9 + - + +
526B THR* 2.9 10.9 + - + +
528B VAL* 1.3 73.8 - - - +
530B TYR* 1.3 73.4 + - + +
582B ALA* 4.2 16.9 - - - +
585B ARG* 5.6 1.9 - - - +
586B LYS* 3.0 27.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B VAL* 3.7 28.3 - - + -
482B GLU* 3.6 33.4 + - + +
485B ALA* 3.8 23.8 - - + -
486B GLU* 5.6 2.2 - - + -
493B TYR* 3.0 23.6 + - - -
496B TYR* 3.2 10.5 + - - +
526B THR* 3.0 36.8 + - + +
529B GLU* 1.3 88.4 - - + +
531B ALA* 1.3 61.8 + - - +
532B THR* 5.2 0.2 - - - -
586B LYS* 4.8 0.2 - - - +
----------------------------------------------------------
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