Contacts of the helix formed by residues 654 - 670 (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 PRO 654 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616B ASP* 5.9 0.2 - - - +
620B TYR* 3.9 13.2 - - - +
652B ASP 4.4 0.9 - - - +
653B SER* 1.3 88.7 - - - +
655B VAL* 1.3 57.7 + - - +
656B SER 3.1 0.2 - - - -
657B ILE* 2.9 27.4 + - + +
658B THR* 3.4 13.6 + - + +
695B ARG* 3.4 36.3 - - - +
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Residues in contact with VAL 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616B ASP* 3.8 27.6 - - + +
619B PHE* 3.7 32.4 - - + -
620B TYR* 3.6 13.6 + - + +
647B ALA* 3.8 19.5 - - + +
650B GLN* 3.8 24.5 - - + +
653B SER* 3.1 21.6 + - - +
654B PRO* 1.3 77.9 - - - +
656B SER* 1.3 59.2 + - - +
658B THR* 3.4 6.0 + - - -
659B ALA* 3.0 26.7 + - - +
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Residues in contact with SER 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647B ALA 3.3 16.8 - - - -
648B LEU* 3.7 15.6 - - - +
650B GLN 3.3 18.0 + - - -
651B VAL* 3.8 7.3 + - - -
653B SER 2.7 20.5 + - - -
655B VAL* 1.3 81.2 - - - +
657B ILE* 1.3 58.9 + - - +
659B ALA* 3.3 5.3 + - - +
660B VAL* 2.9 30.8 + - - +
688B MET* 4.3 0.7 - - - -
695B ARG* 5.5 0.2 - - - +
698B LEU* 3.7 18.0 - - - +
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Residues in contact with ILE 657 (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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653B SER 4.8 0.4 - - - +
654B PRO* 2.9 14.1 + - + +
656B SER* 1.3 80.3 + - - +
658B THR* 1.3 59.5 + - + +
660B VAL* 3.3 6.6 + - - +
661B GLY* 3.0 22.0 + - - -
695B ARG* 3.9 17.5 - - + +
697B GLU* 3.4 43.5 - - + +
698B LEU* 4.0 26.7 - - + +
701B ALA* 4.3 15.4 - - + +
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Residues in contact with THR 658 (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* 3.5 13.9 - - - -
620B TYR* 3.4 39.9 - - + +
623B SER* 4.3 8.5 + - - -
654B PRO* 3.4 8.3 + - + +
655B VAL 3.4 6.2 + - - -
656B SER 3.4 0.2 - - - -
657B ILE* 1.3 76.3 - - + +
659B ALA* 1.3 56.5 + - - +
661B GLY* 3.5 3.0 - - - +
662B PHE* 2.7 33.1 + - - +
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Residues in contact with ALA 659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B PHE* 3.5 25.1 - - + -
644B LEU* 4.1 3.7 - - + +
647B ALA* 4.0 0.7 - - + -
648B LEU* 4.0 28.7 - - + +
655B VAL 3.0 14.8 + - - +
656B SER* 3.3 14.4 - - - +
658B THR* 1.3 75.3 + - - +
660B VAL* 1.3 64.9 + - - +
662B PHE* 3.2 4.7 + - - +
663B ILE* 3.1 26.2 + - - +
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Residues in contact with VAL 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B LEU* 4.0 9.6 - - + -
656B SER 2.9 19.9 + - - +
657B ILE 3.3 8.0 + - - +
659B ALA* 1.3 73.1 - - - +
661B GLY* 1.3 62.9 + - - +
663B ILE* 3.1 10.3 + - - +
664B ALA* 3.0 18.6 + - + +
685B LEU* 4.4 2.5 - - + -
688B MET* 4.0 11.7 - - + -
698B LEU* 4.0 6.7 - - + -
701B ALA* 3.3 37.0 - - + +
702B VAL* 3.9 23.8 - - + +
705B VAL* 3.6 19.2 - - + +
838D GLN* 5.4 1.6 - - - +
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Residues in contact with GLY 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657B ILE 3.0 14.3 + - - -
658B THR* 3.5 6.1 - - - -
659B ALA 3.2 0.2 - - - -
660B VAL* 1.3 74.6 - - - +
662B PHE* 1.3 63.5 + - - +
664B ALA* 3.1 11.1 + - - +
665B ASP* 3.1 28.8 + - - +
837D GLY* 5.4 6.0 - - - -
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Residues in contact with PHE 662 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B PHE* 4.8 0.4 - - + -
622B ILE* 5.0 0.2 - - + -
623B SER* 3.9 26.0 - - - +
626B ALA* 3.6 31.4 - - + -
633B PHE* 3.8 17.9 - + - -
637B LEU* 4.7 8.1 - - + -
640B PHE* 3.7 24.0 - + - -
644B LEU* 3.5 38.4 - - + -
658B THR 2.7 16.9 + - - +
659B ALA* 3.2 10.5 + - - +
661B GLY* 1.3 72.5 - - - +
663B ILE* 1.3 66.4 + - - +
665B ASP* 3.3 10.3 + - + +
666B ILE* 3.0 48.2 + - + +
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Residues in contact with ILE 663 (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* 4.3 1.8 - - + -
648B LEU* 3.6 35.0 - - + -
659B ALA 3.1 14.3 + - - +
660B VAL* 3.1 7.6 + - - +
662B PHE* 1.3 81.5 - - + +
664B ALA* 1.3 67.7 + - - +
666B ILE* 3.7 7.4 - - + -
667B SER* 2.8 26.5 + - - -
674B PHE* 3.9 14.8 - - + -
681B MET* 3.8 21.5 - - - -
685B LEU* 4.0 17.9 - - + -
705B VAL* 3.9 8.7 - - + -
709B ILE* 3.9 28.9 - - + -
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Residues in contact with ALA 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660B VAL* 3.0 12.2 + - + +
661B GLY* 3.3 14.4 - - - +
663B ILE* 1.3 76.0 - - - +
665B ASP* 1.3 62.2 + - - +
667B SER* 2.7 20.4 + - - -
668B ASN* 2.9 19.9 + - - +
705B VAL* 3.8 6.4 - - + +
708B ASP* 3.7 25.6 - - - +
837D GLY 4.2 17.9 - - - +
845D LYS* 4.3 0.2 - - - +
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Residues in contact with ASP 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623B SER 5.3 1.9 - - - +
626B ALA* 6.0 1.1 - - + -
627B ALA* 4.3 27.1 - - - +
661B GLY 3.1 14.6 + - - +
662B PHE* 3.7 9.1 - - + +
663B ILE 3.2 0.2 - - - -
664B ALA* 1.3 74.6 - - - +
666B ILE* 1.3 63.1 + - + +
668B ASN* 3.1 6.6 + - - +
669B SER* 2.7 31.0 + - - -
835D ARG 5.3 1.6 - - - -
836D SER* 3.8 9.8 - - - -
837D GLY* 2.9 33.4 + - - -
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Residues in contact with ILE 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626B ALA* 5.0 5.8 - - + +
630B GLY 4.9 2.2 - - - +
633B PHE* 4.5 20.4 - - + -
634B GLU* 6.0 0.7 - - - +
637B LEU* 4.6 12.1 - - + -
662B PHE* 3.0 49.6 + - + +
663B ILE* 3.4 17.9 - - + +
665B ASP* 1.3 74.6 - - + +
667B SER* 1.3 82.2 + - - +
669B SER* 3.4 11.0 - - - +
670B LEU* 3.0 39.0 + - + +
674B PHE* 3.3 32.1 - - + -
681B MET* 5.9 0.9 - - - -
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Residues in contact with SER 667 (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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663B ILE* 2.8 17.1 + - - +
664B ALA* 2.7 24.6 + - - -
666B ILE* 1.3 77.6 - - - +
668B ASN* 1.3 52.0 + - - +
670B LEU 2.4 22.5 - - - +
671B GLU* 3.6 0.5 - - - +
674B PHE* 3.7 35.4 - - - -
708B ASP* 3.7 10.0 - - - +
709B ILE* 4.6 9.4 - - - -
712B ASN* 2.9 31.1 + - - +
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Residues in contact with ASN 668 (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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664B ALA* 2.9 21.0 + - - +
665B ASP 3.1 4.1 + - - +
667B SER* 1.3 77.8 + - - +
669B SER* 1.3 58.1 + - - +
670B LEU 3.0 11.8 - - - +
671B GLU* 3.8 4.2 - - - +
708B ASP* 2.9 25.0 + - - +
711B SER* 4.7 3.3 + - - -
712B ASN* 3.0 15.8 + - - +
835D ARG* 3.0 73.9 + - + +
842D GLN* 5.0 2.3 + - - -
845D LYS* 3.8 10.6 - - - +
849D ARG* 4.8 2.4 + - - -
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Residues in contact with SER 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626B ALA 5.5 0.2 + - - -
630B GLY* 3.5 38.7 + - - -
631B LYS* 3.1 28.6 + - - +
665B ASP 2.7 22.2 + - - -
666B ILE* 3.4 13.0 - - - +
668B ASN* 1.3 71.6 - - - +
670B LEU* 1.3 69.3 + - - +
671B GLU* 4.6 1.4 - - - +
832D LYS* 6.0 2.2 - - - -
849D ARG* 5.5 1.4 + - - -
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Residues in contact with LEU 670 (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 4.8 1.8 - - - +
631B LYS* 3.9 36.8 - - + +
634B GLU* 3.9 31.6 - - + +
637B LEU* 4.1 26.2 - - + -
666B ILE* 3.0 20.5 + - + +
667B SER 2.4 24.9 - - - +
668B ASN 3.0 6.6 - - - +
669B SER* 1.3 84.1 + - - +
671B GLU* 1.3 57.1 + - - +
673B ASP* 4.4 6.7 - - + +
674B PHE* 4.1 21.3 - - + +
677B TYR* 4.1 16.2 - - + -
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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