Contacts of the helix formed by residues 594 - 608 (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 VAL 594 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547D MET* 3.6 35.9 - - + -
590D SER 4.0 4.3 - - - +
591D VAL* 3.0 19.3 - - - +
592D GLU 3.1 0.4 - - - -
593D PRO* 1.3 82.1 - - + +
595D ALA* 1.3 56.6 + - - +
596D ASP* 3.2 3.6 - - - +
597D MET* 2.7 60.6 + - + +
598D LEU* 3.2 5.0 + - - +
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Residues in contact with ALA 595 (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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591D VAL 2.8 11.2 + - - +
592D GLU* 3.0 22.1 + - - +
593D PRO 3.5 0.6 - - - -
594D VAL* 1.3 75.7 - - - +
596D ASP* 1.3 57.1 + - - +
598D LEU* 3.4 5.0 + - - +
599D MET* 3.0 32.6 + - - +
625D LEU* 4.7 6.0 - - + +
629D LEU* 4.3 20.2 - - + -
635D LYS* 5.5 3.8 - - - +
636D TYR* 3.5 16.6 - - + +
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Residues in contact with ASP 596 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594D VAL 3.2 0.9 - - - -
595D ALA* 1.3 76.0 - - - +
597D MET* 1.3 55.7 + - - +
599D MET* 4.6 3.5 - - - +
600D GLY* 2.7 30.9 + - - -
636D TYR* 3.5 17.5 + - + +
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Residues in contact with MET 597 (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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547D MET* 4.5 15.0 - - + -
594D VAL* 2.7 51.9 + - + +
596D ASP* 1.3 69.8 - - - +
598D LEU* 1.3 56.4 + - - +
600D GLY* 2.9 3.0 + - - -
601D LEU* 2.7 51.6 + - + +
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Residues in contact with LEU 598 (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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547D MET* 3.8 26.4 - - + -
580D LEU* 3.7 36.6 - - + -
584D ILE* 3.7 21.5 - - + -
591D VAL* 3.5 34.8 - - + +
594D VAL 3.2 5.6 + - - +
595D ALA 3.8 7.0 - - - +
597D MET* 1.3 76.2 - - - +
599D MET* 1.3 53.8 - - - +
601D LEU* 3.0 8.5 + - + +
602D PHE* 2.6 54.4 + - + -
625D LEU* 3.9 17.5 - - + -
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Residues in contact with MET 599 (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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595D ALA 3.0 18.2 + - - +
596D ASP* 4.2 1.3 - - - +
598D LEU* 1.3 78.3 - - - +
600D GLY* 1.3 54.5 + - - +
602D PHE* 4.2 3.4 - - + -
603D PHE* 2.6 84.3 + - + -
622D ILE* 3.8 36.6 - - + -
625D LEU* 3.7 24.9 - - + -
633D PHE* 4.0 17.5 - - + -
636D TYR* 3.7 37.2 - - + -
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Residues in contact with GLY 600 (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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596D ASP* 2.7 28.8 + - - -
597D MET 3.3 0.9 - - - -
599D MET* 1.3 73.5 - - - +
601D LEU* 1.3 57.9 + - - +
603D PHE* 3.9 5.6 - - - +
604D ARG* 3.0 34.6 + - - +
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Residues in contact with LEU 601 (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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547D MET* 3.4 39.9 - - + +
550D LEU* 4.0 19.1 - - + -
551D GLY* 3.9 16.4 - - - +
554D MET* 3.5 25.8 - - + +
597D MET* 2.7 31.6 + - + +
598D LEU* 3.5 7.9 - - + +
600D GLY* 1.3 71.2 - - - +
602D PHE* 1.3 56.5 + - + +
604D ARG* 3.2 12.5 + - - +
605D LEU* 2.7 36.7 + - - +
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Residues in contact with PHE 602 (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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550D LEU* 4.4 5.2 - - + -
577D LEU* 3.8 14.8 - - + -
580D LEU* 3.7 24.2 - - + -
584D ILE* 4.2 11.2 - - + -
598D LEU* 2.6 54.9 + - + +
599D MET* 3.7 8.7 - - + +
601D LEU* 1.3 73.4 - - - +
603D PHE* 1.3 58.4 + - - +
605D LEU* 3.2 9.2 + - + +
606D LEU* 2.8 35.7 + - - +
618D VAL* 3.6 26.7 - - + -
621D ALA* 3.9 24.7 - - + -
622D ILE* 3.6 28.3 - - + -
625D LEU* 4.8 3.6 - - + -
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Residues in contact with PHE 603 (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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599D MET* 2.6 69.0 + - + +
600D GLY* 4.0 5.4 - - - +
602D PHE* 1.3 73.9 - - - +
604D ARG* 1.3 57.2 + - - +
606D LEU* 3.5 5.8 + - + +
607D GLU* 2.9 42.1 + - + +
622D ILE* 5.0 1.3 - - + -
636D TYR* 4.1 17.7 - + + -
639D THR* 3.1 38.4 - - + -
640D PHE* 3.8 25.8 - + + -
643D TYR* 3.9 21.6 + + - +
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Residues in contact with ARG 604 (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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551D GLY* 4.7 4.6 + - - -
554D MET* 3.1 57.1 + - - +
555D SER* 4.5 7.9 + - - +
600D GLY 3.0 25.7 + - - +
601D LEU* 3.4 12.9 - - - +
603D PHE* 1.3 73.4 - - - +
605D LEU* 1.3 63.6 + - - +
607D GLU* 3.2 23.9 + - - +
608D LYS* 3.3 16.0 + - - +
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Residues in contact with LEU 605 (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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550D LEU* 4.0 22.0 - - + -
554D MET* 3.9 12.0 - - + -
573D GLN* 4.0 16.6 - - + +
577D LEU* 3.6 31.6 - - + -
601D LEU 2.7 16.7 + - - +
602D PHE* 3.2 12.5 + - + +
604D ARG* 1.3 74.9 - - - +
606D LEU* 1.3 60.5 + - - +
607D GLU 3.4 0.2 + - - -
608D LYS* 3.4 43.1 - - - +
611D SER* 3.7 12.0 - - - -
614D ILE* 3.8 24.9 - - + -
618D VAL* 3.8 14.4 - - + -
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Residues in contact with LEU 606 (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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602D PHE 2.8 20.6 + - - +
603D PHE* 4.0 4.3 - - + +
605D LEU* 1.3 71.0 - - - +
607D GLU* 1.3 64.6 + - - +
608D LYS 3.9 4.4 - - - +
611D SER* 4.1 9.9 + - - -
614D ILE* 5.2 0.9 - - + -
615D GLU* 3.9 41.6 - - + +
618D VAL* 3.6 31.2 - - + -
619D PHE* 5.5 1.3 - - + +
622D ILE* 4.0 15.5 - - + -
640D PHE* 5.6 0.2 - - + -
643D TYR* 3.4 56.8 + - + +
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Residues in contact with GLU 607 (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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603D PHE* 2.9 32.2 + - + +
604D ARG* 3.2 15.7 + - - +
606D LEU* 1.3 77.8 - - - +
608D LYS* 1.3 67.2 + - - +
609D LYS* 3.8 0.9 + - - +
643D TYR* 4.1 10.1 - - - +
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Residues in contact with LYS 608 (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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553D THR 5.1 0.6 + - - -
554D MET* 3.9 21.7 + - + +
556D VAL 5.9 2.0 + - - -
569D LEU* 5.9 2.0 - - - +
573D GLN* 3.0 34.0 + - - +
604D ARG 3.3 9.2 + - - +
605D LEU* 3.4 29.4 - - - +
606D LEU 3.9 0.5 - - - +
607D GLU* 1.3 84.6 - - - +
609D LYS* 1.3 73.5 + - - +
610D ASP 5.3 4.5 - - - -
611D SER* 3.6 18.3 + - - -
613D PHE* 5.6 4.0 - - - -
614D ILE* 5.6 1.1 - - - -
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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