Contacts of the helix formed by residues 605 - 612 (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 LEU 605 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465A ILE* 5.3 0.7 - - + -
466A PRO* 3.7 26.2 - - + -
469A GLU* 3.7 40.2 - - + +
601A LYS 4.8 0.2 + - - -
602A ALA 4.8 1.8 + - - -
603A LYS 3.3 0.8 - - - -
604A PHE* 1.3 80.7 - - + +
606A GLN* 1.3 64.1 + - - +
607A GLU 3.3 0.7 - - - -
608A ALA* 3.1 7.1 + - + +
609A ARG* 3.0 23.8 + - - +
625A VAL* 3.7 27.8 - - + -
627A THR* 4.0 13.0 - - + -
632A ILE* 4.0 18.6 - - + -
634A ILE* 4.1 14.4 - - + -
823A EDO 4.1 13.0 - - - +
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Residues in contact with GLN 606 (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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603A LYS* 3.0 21.3 + - + +
604A PHE 3.2 0.2 - - - -
605A LEU* 1.3 75.8 - - - +
607A GLU* 1.3 64.7 + - - +
609A ARG* 3.0 40.8 + - - +
610A ILE* 3.0 43.5 + - + +
702A PHE 4.4 1.8 - - - +
703A GLY 3.9 9.6 - - - +
705A SER 2.9 29.3 + - - +
706A ARG* 3.7 25.4 - - - +
707A GLU 4.8 0.8 - - - +
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Residues in contact with GLU 607 (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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590A LYS* 2.6 41.1 + - + +
604A PHE 4.0 2.4 + - - -
605A LEU 3.3 0.8 - - - -
606A GLN* 1.3 77.7 - - - +
608A ALA* 1.3 58.5 + - - +
610A ILE* 3.6 1.3 + - - +
611A LEU* 3.0 46.9 + - + +
620A VAL* 6.1 0.2 - - - +
634A ILE* 4.3 11.9 - - + -
636A MET* 4.0 13.4 - - - +
700A SER* 4.7 0.9 + - - -
701A ASP* 3.7 8.0 + - - -
702A PHE* 2.8 51.0 + - + +
703A GLY* 3.7 2.3 + - - -
826A STU 3.3 19.6 - - - -
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Residues in contact with ALA 608 (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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605A LEU* 3.1 10.8 + - + +
607A GLU* 1.3 76.9 - - - +
609A ARG* 1.3 65.1 + - - +
612A LYS* 2.9 32.5 + - - +
622A LEU* 3.8 11.4 - - + +
625A VAL* 3.6 32.8 - - + -
634A ILE* 4.2 19.0 - - + +
823A EDO 4.0 8.5 - - - +
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Residues in contact with ARG 609 (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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469A GLU* 3.1 32.5 + - - +
472A GLU* 4.5 19.6 - - - +
602A ALA 4.8 7.1 + - - -
603A LYS* 5.6 0.6 - - - +
605A LEU 3.0 7.4 + - - +
606A GLN* 3.0 48.5 + - - +
608A ALA* 1.3 76.0 - - - +
610A ILE* 1.3 63.3 + - + +
612A LYS* 3.9 7.7 - - - +
613A GLN* 3.4 20.3 + - - +
823A EDO 3.6 34.1 + - - +
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Residues in contact with ILE 610 (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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606A GLN* 3.0 40.9 + - - +
607A GLU* 3.8 4.0 - - - +
609A ARG* 1.3 79.0 - - + +
611A LEU* 1.3 64.7 + - + +
613A GLN* 3.2 26.9 + - - +
614A TYR* 3.3 37.0 - - + +
679A CYS* 4.3 3.6 - - - -
702A PHE* 3.9 13.2 - - + -
705A SER* 3.5 26.2 - - - +
706A ARG 4.5 2.2 - - - -
707A GLU* 4.0 35.4 - - + +
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Residues in contact with LEU 611 (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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554A TRP* 5.4 1.2 - - - -
607A GLU* 3.0 46.5 + - + +
608A ALA 4.4 0.2 - - - +
610A ILE* 1.3 70.6 - - - +
612A LYS* 1.3 65.2 + - - +
613A GLN 3.0 3.7 + - - -
614A TYR* 3.1 33.0 + - + +
619A ILE* 3.8 29.2 - - + -
620A VAL* 3.8 17.7 - - + +
622A LEU* 4.0 28.0 + - + +
636A MET* 4.3 14.8 - - + -
702A PHE* 3.8 24.5 - - + -
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Residues in contact with LYS 612 (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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552A ASP* 2.8 28.3 + - - +
554A TRP* 3.5 53.9 + - + +
555A VAL* 6.2 0.2 - - - +
608A ALA 2.9 24.3 + - - +
609A ARG* 3.9 8.5 - - - +
610A ILE 3.3 0.2 - - - -
611A LEU* 1.3 76.0 - - - +
613A GLN* 1.3 62.0 + - + +
614A TYR 3.6 1.9 + - - +
622A LEU* 3.4 18.0 - - + +
625A VAL* 4.3 6.5 - - - -
823A EDO 2.8 46.1 + - - +
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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