Contacts of the helix formed by residues 594 - 608 (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 VAL 594 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547B MET* 3.7 33.0 - - + -
590B SER 4.0 4.5 - - - +
591B VAL* 3.1 22.7 - - - +
592B GLU 3.1 0.2 - - - -
593B PRO* 1.3 83.3 - - + +
595B ALA* 1.3 56.8 + - - +
596B ASP* 3.1 4.5 - - - -
597B MET* 2.6 59.8 + - + +
598B LEU 3.3 2.8 + - - -
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Residues in contact with ALA 595 (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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591B VAL 2.8 12.0 + - - +
592B GLU* 3.1 17.7 + - - +
593B PRO 3.5 0.8 - - - -
594B VAL* 1.3 75.6 - - - +
596B ASP* 1.3 58.7 + - - +
598B LEU* 3.3 5.9 + - - +
599B MET* 3.0 31.2 + - - +
625B LEU* 4.6 6.0 - - + +
629B LEU* 4.3 22.4 - - + -
635B LYS* 5.4 4.7 - - - +
636B TYR* 3.6 16.4 - - + +
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Residues in contact with ASP 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B VAL* 3.1 1.3 - - - -
595B ALA* 1.3 76.1 - - - +
597B MET* 1.3 57.8 + - - +
599B MET* 4.5 2.2 - - - -
600B GLY* 2.5 38.1 + - - +
636B TYR* 3.4 19.4 + - + +
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Residues in contact with MET 597 (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* 4.1 19.1 - - + -
594B VAL* 2.6 51.4 + - + +
596B ASP* 1.3 74.8 + - - +
598B LEU* 1.3 54.5 + - - +
600B GLY* 3.3 0.3 - - - -
601B LEU* 2.7 54.8 + - + +
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Residues in contact with LEU 598 (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* 3.7 27.4 - - + -
580B LEU* 3.6 35.7 - - + -
584B ILE* 3.6 26.2 - - + -
591B VAL* 3.5 33.2 - - + +
594B VAL 3.3 4.2 + - - +
595B ALA 3.7 6.3 - - - +
597B MET* 1.3 78.2 - - - +
599B MET* 1.3 53.9 + - - +
601B LEU* 3.1 6.5 + - + +
602B PHE* 2.6 51.9 + - + -
625B LEU* 3.9 14.4 - - + -
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Residues in contact with MET 599 (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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595B ALA 3.0 18.4 + - - +
596B ASP 4.2 0.7 - - - +
598B LEU* 1.3 72.2 - - - +
600B GLY* 1.3 60.0 + - - +
602B PHE* 4.2 3.4 - - - -
603B PHE* 2.7 78.2 + - + -
622B ILE* 3.7 35.4 - - + -
625B LEU* 3.5 26.7 - - + -
633B PHE* 4.0 22.2 - - + -
636B TYR* 3.8 32.8 - - + -
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Residues in contact with GLY 600 (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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596B ASP* 2.5 32.0 + - - -
597B MET* 3.3 1.1 - - - -
599B MET* 1.3 73.3 - - - +
601B LEU* 1.3 58.4 + - - +
603B PHE* 3.9 6.3 - - - +
604B ARG* 3.1 34.4 + - - +
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Residues in contact with LEU 601 (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* 3.5 35.0 - - + +
550B LEU* 4.1 18.8 - - + -
551B GLY* 4.0 15.7 - - - +
554B MET* 3.6 24.4 - - + +
597B MET* 2.7 37.2 + - + +
598B LEU* 3.5 5.8 - - + +
600B GLY* 1.3 71.7 - - - +
602B PHE* 1.3 62.0 + - + +
604B ARG* 3.3 12.7 + - - +
605B LEU* 2.9 30.3 + - - +
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Residues in contact with PHE 602 (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* 4.5 5.4 - - + -
577B LEU* 4.3 14.8 - - + -
580B LEU* 3.8 31.0 - - + -
584B ILE* 4.1 12.1 - - + -
598B LEU* 2.6 47.2 + - + +
599B MET* 3.8 11.2 - - + +
601B LEU* 1.3 73.5 - - + +
603B PHE* 1.3 58.0 + - - +
605B LEU* 3.3 12.4 + - + +
606B LEU* 2.9 33.7 + - - +
618B VAL* 3.6 24.4 - - + +
621B ALA* 3.9 25.4 - - + -
622B ILE* 3.6 29.4 - - + -
625B LEU* 4.9 1.6 - - + -
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Residues in contact with PHE 603 (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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599B MET* 2.7 64.6 + - + +
600B GLY* 3.9 6.3 - - - +
602B PHE* 1.3 69.7 - - - +
604B ARG* 1.3 60.5 + - - +
606B LEU* 3.4 6.5 + - + +
607B GLU* 2.9 42.7 + - + +
622B ILE* 4.9 0.9 - - + -
636B TYR* 4.0 22.9 - + + -
639B THR* 2.9 30.7 - - + -
640B PHE* 3.8 31.6 - + + -
643B TYR* 4.1 17.1 + + - +
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Residues in contact with ARG 604 (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* 4.6 5.7 + - - -
554B MET* 3.2 55.2 + - - +
555B SER* 4.9 3.4 + - - +
600B GLY 3.1 22.3 + - - +
601B LEU* 3.5 12.9 - - - +
603B PHE* 1.3 76.5 - - - +
605B LEU* 1.3 64.4 + - - +
607B GLU* 3.0 27.4 + - - +
608B LYS* 3.1 16.3 + - - +
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Residues in contact with LEU 605 (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* 4.0 22.9 - - + -
554B MET* 3.8 19.9 - - + -
573B GLN* 4.5 11.2 - - + +
577B LEU* 3.8 28.0 - - + -
601B LEU 2.9 11.1 + - - +
602B PHE* 3.4 13.9 - - + +
604B ARG* 1.3 77.3 - - - +
606B LEU* 1.3 61.0 + - - +
607B GLU 3.4 0.2 + - - -
608B LYS* 3.5 41.2 - - - +
611B SER* 3.6 12.3 - - - -
614B ILE* 3.8 27.8 - - + -
618B VAL* 3.8 12.3 - - + -
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Residues in contact with LEU 606 (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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602B PHE 2.9 21.6 + - - +
603B PHE* 4.0 4.0 - - + +
605B LEU* 1.3 73.5 - - - +
607B GLU* 1.3 64.9 + - - +
608B LYS 4.0 3.7 - - - +
611B SER* 4.1 8.2 + - - -
614B ILE* 5.3 1.1 - - + -
615B GLU* 3.8 45.0 - - + +
618B VAL* 3.7 23.3 - - + -
619B PHE* 5.3 3.1 - - + +
622B ILE* 4.1 15.7 - - + -
640B PHE* 5.1 1.3 - - + -
643B TYR* 3.6 57.7 - - + -
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Residues in contact with GLU 607 (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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603B PHE* 2.9 30.8 + - - +
604B ARG* 3.0 20.8 + - - +
606B LEU* 1.3 78.4 - - - +
608B LYS* 1.3 67.3 + - - +
609B LYS* 5.5 0.5 - - - +
643B TYR* 3.8 13.9 - - - +
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Residues in contact with LYS 608 (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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553B THR 5.0 0.6 + - - -
554B MET* 4.3 13.4 - - + +
556B VAL 5.7 0.4 + - - -
557B ASP* 4.8 15.4 - - + +
558B GLU* 3.4 32.7 + - - +
569B LEU* 5.6 2.6 - - - +
573B GLN* 3.3 36.6 + - - +
604B ARG 3.1 9.3 + - - +
605B LEU* 3.5 29.4 - - - +
606B LEU 4.0 0.3 - - - +
607B GLU* 1.3 84.9 - - - +
609B LYS* 1.3 68.5 + - - +
610B ASP 5.0 3.6 - - - -
611B SER* 3.5 20.8 + - - -
613B PHE* 5.3 3.8 - - - -
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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