Contacts of the helix formed by residues 611 - 630 (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 SER 611 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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605B LEU 3.6 18.6 - - - -
606B LEU* 4.1 7.6 + - - -
608B LYS* 3.5 22.6 + - - +
609B LYS 4.3 0.7 - - - -
610B ASP* 1.3 75.7 + - - +
612B ALA* 1.3 65.5 + - - +
613B PHE* 2.9 6.8 + - - -
614B ILE* 2.9 26.2 + - - +
615B GLU* 2.9 39.9 + - - +
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Residues in contact with ALA 612 (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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35A PHE* 3.2 30.7 - - + +
37A LYS* 3.5 32.4 - - + +
152A LYS* 5.5 0.7 - - - -
610B ASP* 3.5 2.9 - - - +
611B SER* 1.3 78.5 + - - +
613B PHE* 1.3 61.5 + - - +
614B ILE 3.5 0.3 + - - -
615B GLU* 3.8 22.9 + - - +
616B ASP* 4.7 2.3 + - - +
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Residues in contact with PHE 613 (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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29A ARG* 3.6 28.3 - - - +
35A PHE* 3.6 24.6 - - + +
152A LYS* 3.4 31.5 - - - +
558B GLU* 5.1 2.0 - - - -
570B GLN* 3.4 47.6 - - + -
573B GLN* 3.5 22.9 - - + -
574B SER* 3.4 20.1 + - - -
608B LYS* 5.3 3.1 - - - -
610B ASP 3.6 24.7 - - - -
611B SER 2.9 2.2 + - - -
612B ALA* 1.3 79.8 - - - +
614B ILE* 1.3 88.4 + - + +
616B ASP 5.2 0.2 + - - -
617B ASP* 4.3 2.4 - - - +
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Residues in contact with ILE 614 (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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573B GLN* 4.5 8.3 - - + +
574B SER* 4.4 6.5 - - - +
577B LEU* 3.5 24.2 - - + -
605B LEU* 3.8 29.6 - - + +
606B LEU* 5.2 0.9 - - + +
608B LYS* 5.6 0.2 - - - -
611B SER* 2.9 43.4 + - - +
613B PHE* 1.3 109.0 - - + +
615B GLU* 1.3 74.5 + - + +
616B ASP 3.3 2.2 - - - -
617B ASP* 2.7 28.2 + - - +
618B VAL* 2.8 23.0 + - + -
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Residues in contact with GLU 615 (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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37A LYS* 2.7 39.9 + - - +
606B LEU* 3.8 28.6 - - + +
611B SER* 2.9 36.9 + - - +
612B ALA* 3.8 15.1 + - - +
613B PHE 3.7 0.6 - - - -
614B ILE* 1.3 75.1 - - - +
616B ASP* 1.3 58.8 + - - +
618B VAL* 3.2 3.0 + - - +
619B PHE* 2.8 30.9 + - - +
646B LYS* 3.0 23.5 + - - -
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Residues in contact with ASP 616 (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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37A LYS* 3.1 34.3 + - - +
152A LYS* 4.4 16.8 + - - +
612B ALA 4.7 2.1 + - - -
614B ILE 3.0 1.4 + - - -
615B GLU* 1.3 75.2 - - - +
617B ASP* 1.3 58.1 + - - +
619B PHE* 3.2 7.3 + - - +
620B TYR* 2.8 54.2 + - + -
650B GLN* 4.8 0.3 + - - -
653B SER* 4.0 9.9 + - - -
655B VAL* 3.8 27.2 - - + +
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Residues in contact with ASP 617 (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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152A LYS* 3.1 28.0 + - - +
574B SER* 5.1 9.2 + - - +
577B LEU* 4.0 25.3 - - + +
581B ALA* 5.4 2.6 - - - +
613B PHE 4.3 4.3 - - - +
614B ILE* 2.7 26.7 + - + +
616B ASP* 1.3 72.2 - - - +
618B VAL* 1.3 56.6 + - - +
620B TYR* 3.4 13.6 + - - +
621B ALA* 3.0 28.6 + - - +
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Residues in contact with VAL 618 (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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577B LEU* 3.7 26.7 - - + -
602B PHE* 3.6 34.8 - - + +
605B LEU* 3.8 16.8 - - + -
606B LEU* 3.7 27.6 - - + -
614B ILE* 2.8 24.6 + - + +
615B GLU 3.6 5.4 - - - +
617B ASP* 1.3 72.5 - - - +
619B PHE* 1.3 60.9 + - - +
621B ALA* 3.5 5.8 - - - +
622B ILE* 2.8 30.2 + - + +
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Residues in contact with PHE 619 (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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606B LEU* 5.3 4.0 - - + +
615B GLU 2.8 18.6 + - - +
616B ASP* 3.2 5.6 + - - +
618B VAL* 1.3 78.1 - - - +
620B TYR* 1.3 63.5 + - - +
622B ILE* 3.4 6.4 + - - +
623B SER* 3.0 40.9 + - - -
640B PHE* 3.5 29.1 - + - -
643B TYR* 4.3 6.5 - - + -
644B LEU* 3.8 18.6 - - + -
647B ALA* 3.4 20.2 - - + -
655B VAL* 3.7 20.6 - - + -
658B THR* 3.5 23.8 - - - -
659B ALA* 3.5 33.9 - - + -
662B PHE* 4.8 0.9 - - + -
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Residues in contact with TYR 620 (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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152A LYS* 5.4 3.1 - - - -
581B ALA* 6.2 1.6 - - + -
585B ARG* 3.5 29.0 + - - +
616B ASP* 2.8 48.7 + - + +
617B ASP* 3.6 13.2 - - - +
619B PHE* 1.3 74.9 - + - +
621B ALA* 1.3 61.0 + - - +
623B SER* 3.5 5.5 + - - -
624B ALA* 3.2 18.2 + - - +
654B PRO* 3.9 12.8 - - - +
655B VAL* 3.6 28.7 + - + +
658B THR* 3.4 41.3 - - + -
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Residues in contact with ALA 621 (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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577B LEU* 4.3 8.3 - - + -
581B ALA* 4.6 15.2 - - + +
584B ILE* 4.0 12.0 - - + +
585B ARG* 5.3 1.1 - - - +
602B PHE* 3.9 26.9 - - + -
617B ASP 3.0 17.7 + - - +
618B VAL* 3.5 6.7 - - - +
620B TYR* 1.3 74.5 - - - +
622B ILE* 1.3 64.6 + - - +
624B ALA* 3.4 6.8 + - - +
625B LEU* 3.0 22.9 + - - +
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Residues in contact with ILE 622 (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* 3.7 17.9 - - + -
602B PHE* 3.6 23.6 - - + -
603B PHE* 4.9 1.8 - - + -
606B LEU* 4.1 11.2 - - + -
618B VAL* 2.8 37.9 + - + +
619B PHE 3.8 3.1 - - - +
621B ALA* 1.3 71.6 - - - +
623B SER* 1.3 54.7 + - - +
625B LEU* 3.1 8.1 + - - +
626B ALA* 2.7 33.3 + - + +
633B PHE* 3.6 31.9 - - + -
640B PHE* 3.6 37.7 - - + -
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Residues in contact with SER 623 (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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585B ARG* 5.9 0.2 - - - -
619B PHE* 3.0 34.2 + - - -
620B TYR* 3.6 11.9 - - - -
621B ALA 3.3 0.2 - - - -
622B ILE* 1.3 75.9 - - - +
624B ALA* 1.3 57.1 + - - +
626B ALA* 3.1 4.7 + - - +
627B ALA* 2.9 27.8 + - - +
640B PHE* 5.2 0.7 - - - -
658B THR* 4.3 9.1 + - - -
662B PHE* 3.9 29.9 - - - +
665B ASP* 5.3 1.9 - - - +
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Residues in contact with ALA 624 (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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584B ILE* 3.7 12.6 - - + +
585B ARG* 3.9 37.2 - - + +
620B TYR 3.2 10.0 + - - +
621B ALA* 3.7 7.4 - - - +
622B ILE 3.3 0.2 - - - -
623B SER* 1.3 78.8 - - - +
625B LEU* 1.3 62.8 + - - +
627B ALA* 3.3 15.8 + - - +
628B SER* 3.4 15.1 + - - -
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Residues in contact with LEU 625 (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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584B ILE* 3.3 21.2 - - + +
588B PRO* 4.9 8.1 - - + -
591B VAL* 4.2 15.9 - - + +
592B GLU* 5.3 2.7 - - + +
595B ALA* 4.6 6.1 - - - +
598B LEU* 3.9 31.0 - - + -
599B MET* 3.5 36.6 - - + -
602B PHE* 4.9 2.2 - - + -
621B ALA 3.0 15.2 + - - +
622B ILE* 3.4 9.2 - - - +
624B ALA* 1.3 75.2 - - - +
626B ALA* 1.3 63.6 + - - +
628B SER* 3.1 7.2 + - - -
629B LEU* 3.1 38.0 + - + +
633B PHE* 5.4 1.1 - - + -
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Residues in contact with ALA 626 (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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622B ILE 2.7 16.3 + - - +
623B SER 3.3 8.7 - - - +
625B LEU* 1.3 68.9 - - - +
627B ALA* 1.3 67.2 + - - +
629B LEU 3.5 0.2 + - - -
630B GLY* 3.1 25.1 + - - +
633B PHE* 3.7 30.1 - - + +
662B PHE* 3.6 29.6 - - + -
665B ASP* 6.0 2.0 - - + -
666B ILE* 5.0 5.9 - - + +
669B SER* 5.5 0.2 + - - -
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Residues in contact with ALA 627 (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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623B SER 2.9 12.0 + - - +
624B ALA* 3.5 13.5 - - - +
625B LEU 3.2 0.2 - - - -
626B ALA* 1.3 77.0 - - - +
628B SER* 1.3 62.8 + - - +
630B GLY* 3.8 6.8 + - - -
665B ASP* 4.3 24.6 - - - +
832D LYS* 5.5 2.4 + - - -
836D SER* 6.4 1.6 - - - -
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Residues in contact with SER 628 (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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584B ILE 4.5 3.1 + - - -
588B PRO* 3.2 27.3 - - - +
592B GLU* 3.7 24.8 - - - +
624B ALA 3.4 9.4 + - - -
625B LEU* 3.1 10.8 + - - -
627B ALA* 1.3 78.9 - - - +
629B LEU* 1.3 67.6 + - - +
630B GLY* 3.1 1.6 + - - -
832D LYS* 4.9 7.4 + - - -
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Residues in contact with LEU 629 (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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592B GLU* 3.7 36.8 - - + +
595B ALA* 4.3 14.8 - - + -
625B LEU* 3.1 27.2 + - + +
626B ALA 3.5 0.6 + - - +
628B SER* 1.3 79.4 - - - +
630B GLY* 1.3 53.7 + - - +
631B LYS 3.2 0.7 + - - -
632B GLY* 2.7 44.2 + - - +
633B PHE* 3.7 24.5 - - + +
635B LYS* 5.3 2.5 - - - +
636B TYR* 4.0 20.6 - - + -
832D LYS* 5.8 0.2 - - - -
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Residues in contact with GLY 630 (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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626B ALA 3.1 14.3 + - - +
627B ALA 3.8 5.1 + - - -
628B SER 3.1 5.1 + - - -
629B LEU* 1.3 73.4 - - - +
631B LYS* 1.3 63.7 + - - -
632B GLY 3.1 0.7 + - - -
633B PHE* 3.2 16.8 + - - +
634B GLU 4.5 0.9 + - - -
666B ILE* 4.9 2.6 - - - +
669B SER* 3.5 28.3 + - - -
670B LEU* 4.8 1.4 - - - +
832D LYS* 4.9 11.4 - - - -
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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