Contacts of the helix formed by residues 656 - 677 (chain A) in PDB entry 3BK0
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 ARG 656 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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654A ARG 3.6 7.1 + - - +
655A LEU* 1.3 74.2 - - - +
657A VAL* 1.3 65.6 + - - +
658A LYS* 4.1 13.9 - - + +
659A THR* 3.0 29.2 + - - +
660A LEU* 3.0 13.8 + - - +
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Residues in contact with VAL 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A LEU 3.9 2.0 + - - +
656A ARG* 1.3 72.6 - - - +
658A LYS* 1.3 63.1 + - - +
660A LEU* 3.2 15.9 + - + +
661A LEU* 3.0 33.9 + - + +
754A PHE* 4.2 7.2 - - + -
784A LEU* 4.2 22.7 - - + +
786A PRO* 4.1 13.5 - - + -
821A HIS* 3.6 32.5 - - + +
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Residues in contact with LYS 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656A ARG* 3.2 11.5 - - + +
657A VAL* 1.3 77.6 - - - +
659A THR* 1.3 58.3 + - - +
661A LEU* 3.4 3.4 + - - +
662A GLN* 3.0 27.9 + - + +
818A ARG* 3.4 42.2 - - + +
821A HIS* 4.1 38.5 - - + +
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Residues in contact with THR 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A LEU* 4.4 16.6 - - + -
656A ARG* 3.0 30.4 + - - +
658A LYS* 1.3 75.9 - - - +
660A LEU* 1.3 68.0 + - + +
662A GLN* 3.2 7.5 + - + +
663A MET* 3.0 42.5 + - + +
695A ASN* 4.7 14.1 - - + +
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Residues in contact with LEU 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A PHE* 5.5 0.9 - - + -
648A LEU* 3.7 29.8 - - + -
655A LEU* 3.7 27.1 - - + +
656A ARG 3.0 20.1 + - - +
657A VAL* 3.2 14.1 + - + +
659A THR* 1.3 75.4 - - - +
661A LEU* 1.3 57.2 + - - +
663A MET* 3.2 10.5 + - - +
664A VAL* 2.9 34.4 + - - +
753A THR* 3.8 14.6 - - + +
754A PHE* 3.8 33.2 - - + +
756A LEU* 4.0 17.5 - - + -
784A LEU* 5.8 6.3 - - + -
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Residues in contact with LEU 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657A VAL* 3.0 34.4 + - + +
658A LYS 3.6 4.3 - - - +
660A LEU* 1.3 73.0 - - - +
662A GLN* 1.3 60.3 + - - +
664A VAL* 3.6 4.5 - - - +
665A GLY* 2.8 26.3 + - - -
754A PHE* 3.7 20.6 - - + -
786A PRO* 5.1 0.7 - - + -
789A VAL* 3.8 19.1 - - + -
814A LEU* 3.9 31.3 - - + +
817A ILE* 3.9 7.0 - - + -
818A ARG* 3.6 38.7 - - + +
821A HIS* 3.9 14.4 - - + +
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Residues in contact with GLN 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658A LYS* 3.0 15.2 + - + +
659A THR* 3.6 11.4 - - + +
661A LEU* 1.3 75.7 - - - +
663A MET* 1.3 61.3 + - + +
665A GLY* 3.3 2.3 + - - -
666A ASP* 2.9 43.4 + - - +
695A ASN 5.5 2.7 - - - +
818A ARG* 4.3 16.2 - - - +
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Residues in contact with MET 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A PHE* 3.6 33.7 - - + -
647A PHE* 3.6 31.2 - - + -
655A LEU* 5.5 0.2 - - - -
659A THR* 3.0 33.1 + - + +
660A LEU* 3.7 7.9 - - - +
662A GLN* 1.3 79.8 - - + +
664A VAL* 1.3 63.0 + - - +
666A ASP* 3.2 11.2 + - - +
667A ALA 3.1 16.6 + - - -
691A VAL* 3.6 28.7 - - + -
695A ASN* 3.5 24.9 - - - +
697A LEU* 3.6 18.0 - - + +
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Residues in contact with VAL 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A PHE* 4.6 6.1 - - + -
660A LEU 2.9 19.6 + - - +
661A LEU* 3.6 11.7 - - - +
663A MET* 1.3 74.4 - - - +
665A GLY* 1.3 62.2 + - - +
667A ALA* 3.3 7.9 + - - +
668A ALA* 2.9 24.4 + - - +
697A LEU* 5.1 0.2 - - - -
746A PHE* 3.5 10.8 - - + -
749A LEU* 4.8 11.2 - - + +
750A LEU* 3.7 30.5 - - + -
753A THR* 3.1 39.3 - - + +
754A PHE* 4.3 5.4 - - + -
814A LEU* 3.9 13.5 - - + -
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Residues in contact with GLY 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661A LEU 2.8 18.9 + - - -
662A GLN* 3.6 2.7 - - - -
664A VAL* 1.3 78.0 - - - +
666A ASP* 1.3 51.7 + - - +
668A ALA* 3.2 2.8 + - - -
669A ALA* 2.8 30.1 + - - +
811A TYR* 3.4 23.8 - - - -
814A LEU* 4.1 14.6 - - - +
815A GLN 6.1 0.4 - - - -
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Residues in contact with ASP 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618A ASN* 3.3 40.4 + - - +
662A GLN* 2.9 27.9 + - - +
663A MET* 3.2 12.2 - - - +
665A GLY* 1.3 75.1 - - - +
667A ALA* 1.3 57.0 + - - +
669A ALA* 3.2 2.4 + - - +
670A GLY 3.0 24.3 + - - -
695A ASN 4.1 1.9 - - - +
696A VAL* 3.5 12.9 - - - +
697A LEU* 3.0 30.9 + - + +
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Residues in contact with ALA 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663A MET 3.1 7.0 + - - +
664A VAL* 3.5 10.5 - - - +
666A ASP* 1.3 77.4 - - - +
668A ALA* 1.3 57.3 + - - +
670A GLY* 3.2 2.4 + - - -
671A MET* 2.9 33.1 + - - +
684A LEU* 5.4 0.9 - - + -
689A CYS* 5.1 0.4 - - - -
697A LEU* 3.8 24.1 - - + +
699A ILE* 3.6 10.0 - - + +
746A PHE* 3.7 15.9 - - + -
749A LEU* 3.8 19.3 - - + -
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Residues in contact with ALA 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664A VAL 2.9 17.2 + - - +
665A GLY 3.6 4.9 - - - +
667A ALA* 1.3 75.0 - - - +
669A ALA* 1.3 56.7 + - - +
671A MET* 3.3 5.1 + - - +
672A GLU* 2.9 30.1 + - - +
746A PHE* 3.6 18.3 - - + -
807A PHE* 4.4 6.6 - - + +
810A ILE* 3.9 18.2 - - + -
811A TYR* 3.9 21.1 - - + +
814A LEU* 4.1 3.4 - - + -
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Residues in contact with ALA 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A HIS* 3.8 12.2 + - + +
618A ASN* 3.7 13.7 - - - +
665A GLY 2.8 13.5 + - - +
666A ASP* 3.2 9.4 + - - +
668A ALA* 1.3 76.6 - - - +
670A GLY* 1.3 61.3 + - - +
672A GLU* 3.3 10.6 + - - +
673A TYR* 3.0 24.1 + - - +
811A TYR* 3.8 20.5 - - + -
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Residues in contact with GLY 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A HIS* 3.8 11.5 - - - -
618A ASN* 4.1 3.4 - - - -
619A ILE* 3.7 19.3 - - - +
666A ASP 3.0 14.0 + - - -
667A ALA 3.2 3.6 + - - -
669A ALA* 1.3 73.9 - - - +
671A MET* 1.3 56.2 + - - +
673A TYR* 3.3 5.0 + - - +
674A LEU* 3.0 30.9 + - - +
699A ILE* 3.9 10.3 - - - -
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Residues in contact with MET 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667A ALA 2.9 21.2 + - - +
668A ALA 3.8 1.3 - - - +
670A GLY* 1.3 73.5 - - - +
672A GLU* 1.3 59.8 + - - +
674A LEU* 3.7 18.6 - - + +
675A GLU* 2.9 30.8 + - - +
679A CYS 5.8 0.2 - - - +
681A HIS* 4.2 11.4 - - + -
684A LEU* 4.1 25.8 - - + -
699A ILE* 3.5 21.1 - - + -
742A ASP* 3.5 40.4 - - + +
746A PHE* 4.4 1.6 - - + -
807A PHE* 3.5 40.3 - - + -
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Residues in contact with GLU 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668A ALA 2.9 16.9 + - - +
669A ALA* 3.3 10.3 + - - +
671A MET* 1.3 75.6 - - - +
673A TYR* 1.3 63.1 + - - +
675A GLU* 3.5 8.8 + - - +
676A SER* 3.1 22.9 + - - -
807A PHE* 3.8 14.9 - - + +
808A SER* 2.5 44.3 + - - +
811A TYR* 4.6 14.0 - - - +
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Residues in contact with TYR 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A GLN 4.2 1.0 + - - -
614A TYR* 3.4 33.3 - + + -
615A SER* 3.0 35.6 + - - -
616A HIS* 3.6 37.0 - + + -
619A ILE* 4.2 10.1 - - + -
669A ALA 3.0 12.9 + - - +
670A GLY 3.3 7.8 + - - +
672A GLU* 1.3 75.3 - - - +
674A LEU* 1.3 68.3 + - + +
676A SER* 2.5 29.1 + - - -
677A LYS* 3.1 38.6 + - + +
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Residues in contact with LEU 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A TYR* 3.4 38.4 - - + -
619A ILE* 3.9 15.0 - - + -
670A GLY 3.0 16.1 + - - +
671A MET* 3.3 36.8 + - + +
673A TYR* 1.3 78.3 - - + +
675A GLU* 1.3 62.7 + - - +
677A LYS* 3.0 11.1 + - - +
679A CYS* 2.9 39.0 + - + +
681A HIS* 4.3 12.3 - - + -
699A ILE* 4.6 1.3 - - + -
702A PHE* 3.7 30.1 - - + -
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Residues in contact with GLU 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671A MET 2.9 15.9 + - - +
672A GLU* 3.6 10.5 - - - +
674A LEU* 1.3 75.8 - - - +
676A SER* 1.3 56.6 + - - +
678A CYS* 3.0 21.5 + - - +
679A CYS 4.1 3.8 + - - +
739A SER* 3.4 35.6 - - - +
806A SER* 5.1 9.3 - - - -
807A PHE* 4.0 27.9 + - + +
808A SER* 4.8 4.3 + - - -
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Residues in contact with SER 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672A GLU* 3.1 12.3 + - - -
673A TYR* 2.5 29.1 + - - -
675A GLU* 1.3 76.1 - - - +
677A LYS* 1.3 66.6 + - - +
678A CYS* 3.4 5.4 + - - -
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Residues in contact with LYS 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A GLN* 4.3 10.5 + - - -
614A TYR* 3.7 32.6 + - + +
673A TYR* 3.3 51.2 + - + +
674A LEU 3.0 7.6 + - - +
676A SER* 1.3 87.3 - - - +
678A CYS* 1.3 70.7 + - - +
679A CYS 3.2 1.0 + - - -
707A GLU* 4.0 14.6 - - - +
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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
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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