Contacts of the helix formed by residues 633 - 650 (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 PHE 633 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599B MET* 4.0 16.2 - - + -
622B ILE* 3.6 32.5 - - + -
625B LEU* 5.4 0.4 - - + -
626B ALA* 3.7 33.4 - - + +
629B LEU* 3.7 12.8 - - + +
630B GLY 3.2 12.6 + - - +
631B LYS 3.0 1.6 + - - -
632B GLY* 1.3 75.1 - - - +
634B GLU* 1.3 65.6 + - - +
635B LYS 3.2 2.7 - - - -
636B TYR* 2.9 46.2 + + + +
637B LEU* 3.3 13.4 + - + -
640B PHE* 4.1 12.3 - + - -
662B PHE* 3.8 24.7 - + - -
666B ILE* 4.5 10.1 - - + -
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Residues in contact with GLU 634 (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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630B GLY 4.5 0.8 + - - -
631B LYS* 3.1 18.2 + - - +
632B GLY 3.4 0.4 - - - -
633B PHE* 1.3 76.5 - - - +
635B LYS* 1.3 57.5 + - - +
636B TYR 3.0 5.7 + - - -
637B LEU* 3.0 23.3 + - - +
638B GLU* 4.2 2.4 + - - +
666B ILE* 6.0 0.8 - - - +
670B LEU* 3.9 26.0 - - + +
673B ASP* 4.5 18.4 - - - +
676B ARG* 4.2 13.5 + - - -
677B TYR* 2.9 37.5 + - + +
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Residues in contact with LYS 635 (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* 5.4 5.1 - - - +
629B LEU* 5.5 1.6 - - - +
631B LYS 5.0 0.2 + - - -
632B GLY* 3.5 25.5 + - - +
633B PHE 3.0 0.4 + - - -
634B GLU* 1.3 76.4 - - - +
636B TYR* 1.3 95.2 + - + +
638B GLU* 5.1 5.2 + - - +
639B THR* 5.0 6.4 - - - +
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Residues in contact with TYR 636 (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* 3.6 5.2 - - - +
596B ASP* 3.4 33.4 + - + +
599B MET* 3.8 26.7 - - + -
603B PHE* 4.0 24.5 - + + -
629B LEU* 4.0 17.0 - - + -
632B GLY 4.1 0.2 - - - -
633B PHE* 2.9 42.4 + + + +
635B LYS* 1.3 114.8 - - + +
637B LEU* 1.3 66.6 + - - +
638B GLU 3.1 3.4 - - - -
639B THR* 3.0 11.4 + - + +
640B PHE* 2.9 20.9 + - - +
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Residues in contact with LEU 637 (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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633B PHE* 3.3 20.3 + - + +
634B GLU* 3.0 18.4 + - - +
636B TYR* 1.3 77.8 - - - +
638B GLU* 1.3 64.2 + - - +
640B PHE* 4.3 2.9 - - + -
641B SER* 2.9 31.0 + - - +
644B LEU* 4.9 7.9 - - + -
662B PHE* 4.7 14.6 - - + -
666B ILE* 4.6 20.9 - - + -
670B LEU* 4.1 16.6 - - + -
674B PHE* 6.1 0.4 - - + -
677B TYR* 3.7 50.5 - - + -
681B MET* 5.8 3.4 - - + -
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Residues in contact with GLU 638 (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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634B GLU 4.2 3.9 + - - +
635B LYS 5.1 5.2 - - - +
636B TYR 4.5 1.1 - - - +
637B LEU* 1.3 80.7 - - - +
639B THR* 1.3 72.1 + - + +
641B SER* 3.2 17.8 - - - -
642B PRO* 3.7 3.5 - - - +
677B TYR* 4.7 15.8 - - + +
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Residues in contact with THR 639 (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 35.7 - - + -
635B LYS 5.0 5.6 - - - +
636B TYR* 3.0 10.2 + - + +
638B GLU* 1.3 84.4 - - + +
640B PHE* 1.3 56.7 + - - +
641B SER 3.3 0.2 - - - -
642B PRO* 3.3 16.3 - - - +
643B TYR* 3.5 16.5 - - - -
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Residues in contact with PHE 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B PHE* 3.8 15.7 - + + -
606B LEU* 5.1 0.9 - - + -
619B PHE* 3.5 35.9 - + - -
622B ILE* 3.6 42.8 - - + -
623B SER* 5.2 0.4 - - - -
633B PHE* 4.1 11.0 - + + -
636B TYR 2.9 18.5 + - - +
637B LEU* 3.9 6.7 - - + +
639B THR* 1.3 79.7 + - - +
641B SER* 1.3 63.2 + - - +
642B PRO 3.4 0.7 - - - -
643B TYR* 3.0 26.7 + + + -
644B LEU* 3.1 23.5 + - + -
662B PHE* 3.7 42.2 - + - -
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Residues in contact with SER 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B LEU* 2.9 20.9 + - - +
638B GLU* 3.2 17.3 - - - -
640B PHE* 1.3 75.6 - - - +
642B PRO* 1.4 65.8 - - - +
644B LEU* 3.1 9.8 + - - +
645B LEU* 3.1 36.0 + - - +
677B TYR* 6.1 2.0 - - - -
680B ALA* 5.5 2.9 - - - +
681B MET* 4.3 10.4 - - - +
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Residues in contact with PRO 642 (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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638B GLU 3.7 5.2 - - - +
639B THR* 3.3 18.8 - - - +
640B PHE 3.4 0.9 - - - -
641B SER* 1.4 95.5 - - - +
643B TYR* 1.3 67.3 + - + +
645B LEU* 3.3 10.5 + - + +
646B LYS* 2.9 26.6 + - - +
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Residues in contact with TYR 643 (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* 4.1 17.4 + + - +
606B LEU* 3.6 50.7 - - + -
607B GLU* 3.8 28.2 + - - +
619B PHE* 4.1 7.0 - - + -
639B THR 3.5 24.7 - - - -
640B PHE* 3.0 24.6 + + + +
642B PRO* 1.3 83.3 - - + +
644B LEU* 1.3 60.1 + - - +
646B LYS* 3.3 13.8 - - + +
647B ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B PHE* 3.8 26.7 - - + -
637B LEU* 4.9 8.3 - - + -
640B PHE* 3.1 19.1 + - + +
641B SER* 3.1 9.6 + - - +
643B TYR* 1.3 76.0 - - - +
645B LEU* 1.3 59.2 + - - +
647B ALA* 3.2 2.6 + - - +
648B LEU* 2.9 32.5 + - + +
659B ALA* 4.1 14.6 - - + +
662B PHE* 3.5 42.6 - - + -
663B ILE* 4.3 2.5 - - + -
666B ILE* 5.9 0.2 - - + -
681B MET* 3.4 36.8 - - + -
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Residues in contact with LEU 645 (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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641B SER* 3.1 25.2 + - - +
642B PRO* 3.6 9.2 - - + +
644B LEU* 1.3 75.4 - - - +
646B LYS* 1.3 65.9 + - - +
648B LEU* 3.8 7.7 - - + +
649B ASN* 2.9 38.0 + - - +
680B ALA* 3.9 14.1 - - + +
681B MET* 3.5 27.4 - - + -
684B VAL* 3.6 30.5 - - + -
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Residues in contact with LYS 646 (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* 3.9 9.3 - - - +
615B GLU* 3.0 35.3 + - - -
642B PRO 2.9 13.9 + - - +
643B TYR* 3.3 20.4 - - + +
645B LEU* 1.3 77.4 - - - +
647B ALA* 1.3 60.4 + - - +
649B ASN* 3.6 8.4 + - - +
650B GLN* 3.1 30.9 + - + +
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Residues in contact with ALA 647 (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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619B PHE* 3.4 42.8 - - + -
643B TYR 2.9 9.6 + - - +
644B LEU 3.6 2.0 - - - +
645B LEU 3.2 0.2 - - - -
646B LYS* 1.3 75.1 - - - +
648B LEU* 1.3 67.0 + - - +
650B GLN* 3.2 22.3 + - - +
655B VAL* 4.1 13.5 - - + -
656B SER* 3.3 19.9 + - - -
659B ALA* 4.0 2.9 - - + -
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Residues in contact with LEU 648 (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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644B LEU* 2.9 25.2 + - + +
645B LEU* 3.4 18.8 + - + +
647B ALA* 1.3 76.9 - - - +
649B ASN* 1.3 62.0 + - - +
650B GLN 3.4 0.5 + - - -
651B VAL* 3.9 4.0 - - - +
656B SER* 3.7 6.7 - - - -
659B ALA* 4.0 20.1 - - + +
660B VAL* 4.0 7.4 - - + -
663B ILE* 3.6 27.4 - - + -
681B MET* 4.5 6.1 - - - +
684B VAL* 3.8 24.5 - - + -
685B LEU* 3.8 13.2 - - + -
688B MET* 3.4 47.9 - - + +
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Residues in contact with ASN 649 (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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645B LEU* 2.9 29.0 + - - +
646B LYS* 4.0 5.8 - - - +
647B ALA 3.2 0.4 - - - -
648B LEU* 1.3 72.9 - - - +
650B GLN* 1.3 56.9 + - - +
651B VAL* 2.8 24.2 + - - +
684B VAL* 3.8 18.6 - - - +
687B GLN* 3.3 32.5 + - - +
688B MET* 5.4 1.2 - - - +
691B ASN* 5.0 2.1 - - - +
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Residues in contact with GLN 650 (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 41.4 + - - +
38A LYS* 6.5 1.3 - - + -
616B ASP* 4.8 0.4 + - - -
646B LYS* 3.1 39.3 + - + +
647B ALA* 3.2 16.2 + - - +
649B ASN* 1.3 72.5 - - - +
651B VAL* 1.3 58.4 + - - +
652B ASP* 3.1 12.1 - - - +
653B SER* 2.8 29.8 + - - +
655B VAL* 3.8 18.2 - - + +
656B SER* 3.3 13.6 + - - -
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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