Contacts of the helix formed by residues 895 - 907 (chain S) in PDB entry 1BKD
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 895 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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893S ILE 3.6 1.1 + - - -
894S PRO* 1.3 69.0 - - - +
896S ARG* 1.3 66.8 + - - +
898S LYS* 3.0 22.1 + - - +
899S LYS* 3.1 31.6 + - - +
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Residues in contact with ARG 896 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857S GLU* 4.6 5.9 + - - -
894S PRO* 3.9 20.4 - - + +
895S SER* 1.3 78.1 - - - +
897S GLN* 1.3 94.4 + - + +
899S LYS* 3.2 14.5 + - - +
900S ILE* 3.1 33.9 + - + +
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Residues in contact with GLN 897 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853S SER* 2.6 38.8 + - - -
856S ILE* 3.5 22.7 - - + +
857S GLU* 3.7 25.1 + - + +
893S ILE* 4.1 9.1 - - + +
894S PRO* 3.3 29.5 + - + +
895S SER 3.2 0.8 - - - -
896S ARG* 1.3 110.8 - - + +
898S LYS* 1.3 65.4 + - - +
900S ILE* 3.2 14.9 + - + +
901S LEU* 3.1 19.8 + - - +
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Residues in contact with LYS 898 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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856S ILE* 5.4 1.1 - - - -
890S PHE* 3.0 37.9 + - + +
891S GLU* 3.9 15.8 + - - +
893S ILE* 3.3 23.8 + - + +
894S PRO 3.2 12.8 + - - +
895S SER* 3.0 14.5 + - - +
897S GLN* 1.3 76.2 - - - +
899S LYS* 1.3 59.8 + - + +
901S LEU* 3.5 9.4 + - + +
902S GLU* 2.9 29.2 + - - +
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Residues in contact with LYS 899 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895S SER* 3.1 27.0 + - - +
896S ARG* 3.5 11.6 - - - +
897S GLN 3.2 0.4 - - - -
898S LYS* 1.3 78.9 - - + +
900S ILE* 1.3 55.3 + - - +
902S GLU* 3.8 10.8 - - - +
903S GLU* 2.8 36.6 + - - +
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Residues in contact with ILE 900 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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856S ILE* 4.2 11.7 - - + +
857S GLU* 6.3 0.7 - - - -
859S LEU* 3.9 17.7 - - + -
860S GLN* 3.7 40.2 - - + +
863S GLN* 4.8 6.2 + - + +
896S ARG* 3.1 25.2 + - + +
897S GLN* 3.4 21.8 - - + +
899S LYS* 1.3 76.4 - - + +
901S LEU* 1.3 58.7 + - - +
903S GLU* 3.6 13.2 - - - +
904S ALA* 3.0 25.6 + - - +
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Residues in contact with LEU 901 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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856S ILE* 4.3 20.0 - - + -
859S LEU* 4.1 17.9 - - + -
874S VAL* 5.3 1.8 - - + -
875S VAL* 5.0 10.5 - - + -
878S MET* 3.8 32.3 - - + -
890S PHE* 4.0 28.7 - - + -
897S GLN 3.1 13.5 + - - +
898S LYS* 3.7 8.1 - - + +
900S ILE* 1.3 78.7 - - - +
902S GLU* 1.3 60.7 + - - +
904S ALA* 3.1 6.1 + - + +
905S HIS* 2.8 31.5 + - + +
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Residues in contact with GLU 902 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898S LYS 2.9 17.9 + - - +
899S LYS* 3.8 10.8 - - - +
901S LEU* 1.3 76.2 - - - +
903S GLU* 1.3 64.5 + - - +
905S HIS* 3.1 9.6 + - + +
906S GLU* 3.0 51.6 + - + +
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Residues in contact with GLU 903 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863S GLN* 4.4 14.6 + - - +
899S LYS 2.8 21.2 + - - +
900S ILE* 3.6 11.9 - - - +
902S GLU* 1.3 76.7 + - - +
904S ALA* 1.3 62.0 + - - +
906S GLU* 3.5 23.0 + - - +
907S LEU* 3.8 10.2 + - - +
914S LYS* 6.0 0.2 - - - +
918S LYS* 4.5 9.7 + - - -
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Residues in contact with ALA 904 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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859S LEU* 3.6 27.1 - - + -
863S GLN* 4.2 14.8 - - - +
871S VAL* 4.4 2.4 - - + +
872S LEU* 5.1 0.5 - - - +
875S VAL* 3.9 20.3 - - + +
900S ILE 3.0 14.5 + - - +
901S LEU 3.1 8.7 + - - +
903S GLU* 1.3 76.4 - - - +
905S HIS* 1.3 64.5 + - - +
907S LEU* 3.1 26.1 + - - +
908S SER* 4.3 2.1 + - - -
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Residues in contact with HIS 905 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70R GLN* 5.2 7.2 - - + -
73R ARG* 6.1 3.8 - - + -
74R THR* 6.3 3.5 - - + +
875S VAL* 4.1 15.9 - - + +
879S ASN* 2.7 39.0 + - - -
901S LEU* 2.8 21.1 + - + +
902S GLU* 3.1 9.2 + - + +
904S ALA* 1.3 73.5 - - - +
906S GLU* 1.3 64.8 + - + +
907S LEU 3.1 1.1 + - - -
908S SER* 3.2 22.8 + - - -
909S GLU* 3.9 26.4 + - + +
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Residues in contact with GLU 906 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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902S GLU* 3.0 50.1 + - + +
903S GLU* 3.7 12.6 - - - +
904S ALA 3.1 0.6 - - - -
905S HIS* 1.3 76.8 - - + +
907S LEU* 1.3 63.9 + - - +
908S SER 3.2 0.4 + - - -
909S GLU* 3.5 42.5 + - - +
914S LYS* 3.1 43.2 + - + +
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Residues in contact with LEU 907 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863S GLN* 4.0 28.0 - - - +
868S PHE* 5.0 10.1 - - + -
871S VAL* 4.1 17.7 - - + -
872S LEU* 5.0 7.2 - - + -
903S GLU 3.8 8.4 + - - +
904S ALA* 3.1 18.6 + - - +
906S GLU* 1.3 78.9 - - - +
908S SER* 1.3 58.7 + - - +
909S GLU 4.1 0.5 - - - +
912S TYR* 3.2 23.2 - - - -
914S LYS* 3.9 14.7 + - + +
915S TYR* 3.4 45.9 + - + +
918S LYS* 4.2 20.2 - - + +
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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
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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