Contacts of the helix formed by residues 536 - 555 (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 ALA 536 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532B THR 4.6 1.1 - - - +
533B ASP* 3.2 17.7 + - - +
534B THR 3.6 2.2 + - - -
535B VAL* 1.3 73.7 - - - +
537B GLU* 1.3 58.9 + - - +
538B THR 3.2 1.6 - - - -
539B SER* 3.5 4.7 - - - -
540B ALA* 2.7 38.4 + - - +
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Residues in contact with GLU 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B VAL* 4.7 0.2 - - - +
536B ALA* 1.3 77.7 - - - +
538B THR* 1.3 57.8 + - + +
540B ALA* 3.5 7.4 - - - +
541B SER* 3.0 30.4 + - - +
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Residues in contact with THR 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B TYR* 4.2 11.6 + - + -
497B PRO* 4.2 19.1 - - + +
500B VAL* 3.4 31.2 - - - +
535B VAL* 3.5 37.9 - - + -
537B GLU* 1.3 76.8 - - + +
539B SER* 1.3 66.2 + - - +
540B ALA 3.1 1.6 - - - -
541B SER* 3.1 19.6 + - - -
542B ILE* 3.2 15.4 + - - +
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Residues in contact with SER 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B TYR* 5.8 2.6 - - - -
500B VAL* 6.1 0.2 - - - -
528B VAL* 4.7 12.3 - - - +
531B ALA* 4.3 18.8 - - - +
535B VAL 3.3 19.9 + - - -
536B ALA* 3.2 6.4 + - - -
538B THR* 1.3 81.0 - - - +
540B ALA* 1.3 60.0 + - - +
542B ILE* 3.5 25.5 - - - +
543B SER* 3.5 8.3 + - - -
583B VAL* 4.9 5.4 - - - +
587B SER* 3.8 18.3 + - - -
590B SER* 4.6 2.3 + - - -
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Residues in contact with ALA 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B ALA 2.7 21.6 + - - +
537B GLU* 3.5 9.2 - - - +
538B THR 3.1 0.2 - - - -
539B SER* 1.3 70.7 - - - +
541B SER* 1.3 62.3 + - - +
542B ILE 3.1 1.8 - - - -
543B SER* 3.0 20.6 + - - -
544B THR* 3.1 19.6 + - - +
590B SER* 4.1 18.8 - - - -
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Residues in contact with SER 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B VAL* 5.1 7.0 - - - -
504B ILE* 4.3 8.6 - - - +
537B GLU* 3.0 19.0 + - - +
538B THR* 3.1 13.6 + - - -
540B ALA* 1.3 75.1 - - - +
542B ILE* 1.3 57.7 - - - +
544B THR* 3.8 6.8 - - - +
545B PHE* 3.1 27.9 + - - +
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Residues in contact with ILE 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496B TYR* 6.1 1.1 - - + -
500B VAL* 3.5 40.4 - - + -
504B ILE* 4.7 3.4 - - + -
524B LEU* 4.2 24.0 - - + +
527B MET* 4.3 7.2 - - + -
528B VAL* 3.6 26.5 - - + +
538B THR 3.2 7.1 + - - +
539B SER* 3.5 13.5 - - - +
540B ALA 3.1 0.4 - - - -
541B SER* 1.3 73.8 - - - +
543B SER* 1.3 61.2 + - - +
545B PHE* 3.1 7.2 + - - +
546B VAL* 3.0 30.2 + - + +
579B VAL* 3.5 29.6 - - + -
583B VAL* 4.4 2.5 - - + -
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Residues in contact with SER 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B SER 3.5 5.4 + - - -
540B ALA* 3.0 16.1 + - - -
542B ILE* 1.3 78.4 - - - +
544B THR* 1.3 56.1 + - - +
546B VAL* 3.5 10.6 - - - +
547B MET* 3.0 49.0 + - - +
580B LEU* 5.0 1.8 - - - -
583B VAL* 3.8 29.4 - - - -
590B SER* 3.5 19.2 + - - -
591B VAL* 4.0 5.4 - - - -
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Residues in contact with THR 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B ALA* 3.1 20.1 + - - +
541B SER* 3.8 7.4 - - - +
543B SER* 1.3 77.5 + - - +
545B PHE* 1.3 62.6 + - - +
547B MET* 3.9 9.8 - - - +
548B ASP* 3.3 23.4 + - + +
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Residues in contact with PHE 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B ILE* 3.8 32.5 - - + -
507B ALA* 3.8 26.2 - - + -
508B ASN* 3.2 41.5 - - - -
521B PHE* 4.2 13.5 - + - -
524B LEU* 4.3 5.4 - - + -
541B SER 3.1 19.6 + - - +
542B ILE 3.1 3.1 + - - +
544B THR* 1.3 78.7 - - - +
546B VAL* 1.3 69.3 + - + +
548B ASP* 3.4 7.9 + - + +
549B LYS* 2.9 45.2 + - + +
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Residues in contact with VAL 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521B PHE* 4.1 15.9 - - + -
524B LEU* 4.9 1.8 - - + -
542B ILE* 3.0 24.1 + - + +
543B SER* 3.5 8.1 - - - +
545B PHE* 1.3 87.2 - - + +
547B MET* 1.3 57.9 + - - +
549B LYS* 3.5 6.5 - - - +
550B LEU* 2.7 36.0 + - - +
576B ILE* 3.5 15.2 - - + +
579B VAL* 3.7 33.0 - - + -
580B LEU* 3.3 28.7 - - + -
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Residues in contact with MET 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B SER* 3.0 39.6 + - - +
544B THR* 3.9 10.5 - - - +
546B VAL* 1.3 73.9 - - - +
548B ASP* 1.3 66.4 + - - +
550B LEU* 3.5 2.0 + - - -
551B GLY* 3.1 19.4 + - - -
580B LEU* 4.0 7.9 - - + -
590B SER 4.3 3.4 - - - +
591B VAL* 3.6 20.9 - - + -
594B VAL* 3.7 28.3 - - + -
597B MET* 4.1 21.5 - - + +
598B LEU* 3.7 32.5 - - + -
601B LEU* 3.5 22.0 - - + +
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Residues in contact with ASP 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B THR* 3.3 17.6 + - + +
545B PHE* 3.4 8.2 - - + +
547B MET* 1.3 79.2 - - - +
549B LYS* 1.3 57.4 + - - +
551B GLY* 3.3 1.9 + - - -
552B GLN* 3.0 39.8 + - - +
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Residues in contact with LYS 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B ALA 3.9 13.4 + - - -
508B ASN* 2.7 41.6 + - - +
509B ARG 5.3 2.0 + - - -
517B ARG* 5.7 2.4 - - - +
521B PHE* 4.6 2.7 - - + -
545B PHE* 2.9 31.2 + - + +
546B VAL* 3.5 9.2 - - - +
548B ASP* 1.3 74.8 - - - +
550B LEU* 1.3 65.4 + - - +
552B GLN* 3.2 21.7 + - + +
553B THR* 3.0 28.3 + - + +
572B LEU* 4.6 18.2 - - + -
576B ILE* 3.6 20.9 - - + -
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Residues in contact with LEU 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B VAL 2.7 20.5 + - - +
547B MET* 3.8 4.9 - - - +
549B LYS* 1.3 71.6 - - - +
551B GLY* 1.3 63.8 + - - +
553B THR* 2.5 31.5 + - - +
554B MET* 3.2 21.3 + - + +
573B GLN* 4.4 17.7 - - + +
576B ILE* 3.7 18.8 - - + +
577B LEU* 5.0 3.8 - - + -
580B LEU* 3.6 27.6 - - + -
601B LEU* 4.1 19.3 - - + -
602B PHE* 4.5 3.6 - - + -
605B LEU* 4.0 31.6 - - + -
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Residues in contact with GLY 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547B MET 3.1 13.0 + - - -
548B ASP 3.7 3.6 - - - -
550B LEU* 1.3 77.4 - - - +
552B GLN* 1.3 62.4 + - - +
554B MET* 3.2 27.2 + - - +
555B SER* 3.4 13.2 + - - -
601B LEU* 4.0 10.0 - - - +
604B ARG* 4.6 5.1 + - - -
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Residues in contact with GLN 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548B ASP* 3.0 28.0 + - - +
549B LYS* 3.3 28.8 + - + +
550B LEU 3.1 0.2 - - - -
551B GLY* 1.3 76.9 - - - +
553B THR* 1.3 62.2 + - + +
555B SER* 3.1 25.4 + - - +
556B VAL* 4.6 1.7 + - - +
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Residues in contact with THR 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549B LYS* 3.0 14.4 + - + +
550B LEU* 2.5 24.6 + - - +
552B GLN* 1.3 75.8 - - + +
554B MET* 1.3 59.0 + - - +
555B SER 3.3 0.6 + - - -
556B VAL* 3.7 16.2 + - - +
569B LEU* 4.0 20.1 - - + +
572B LEU* 3.4 36.8 - - + -
573B GLN* 3.0 36.0 + - + +
576B ILE* 4.1 7.6 - - + -
608B LYS* 5.0 0.5 + - - -
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Residues in contact with MET 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550B LEU* 3.4 31.9 - - + +
551B GLY* 3.2 19.9 + - - +
552B GLN 3.1 1.0 - - - -
553B THR* 1.3 77.7 + - - +
555B SER* 1.3 64.3 + - - +
556B VAL* 3.3 6.8 + - - -
557B ASP* 4.3 4.2 + - - +
573B GLN* 3.8 15.0 - - - +
601B LEU* 3.6 43.3 - - + +
604B ARG* 3.2 39.2 + - + +
605B LEU* 3.8 23.8 - - + -
608B LYS* 4.3 15.8 + - + +
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Residues in contact with SER 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551B GLY 3.4 9.3 + - - -
552B GLN* 3.1 19.9 + - - +
554B MET* 1.3 78.1 - - - +
556B VAL* 1.3 63.1 + - - +
557B ASP 4.0 1.6 + - - -
604B ARG* 4.9 5.7 + - - +
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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
------------------------------------------------------------
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