Contacts of the helix formed by residues 884 - 898 (chain A) in PDB entry 5L6O
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 LYS 884 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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818A ALA* 5.6 6.9 - - - +
821A VAL* 4.7 2.5 - - - -
879A ARG 5.3 4.8 + - - -
880A ASN* 4.9 12.4 + - - +
882A ARG 4.6 9.2 + - - +
883A PRO* 1.3 77.8 - - - +
885A PHE* 1.3 68.0 + - - +
886A SER* 3.9 17.3 - - - +
887A GLN* 2.9 23.2 + - - +
888A ILE* 3.1 20.5 + - - +
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Residues in contact with PHE 885 (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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743A ALA* 4.0 10.7 - - + +
746A MET* 3.4 56.3 - - + -
747A LYS* 3.5 24.9 - - + +
750A SER* 4.0 15.7 + - - +
817A SER* 3.8 13.7 - - - -
820A ASP* 3.7 20.6 - - + -
821A VAL* 3.6 24.2 - - + +
824A TYR* 3.7 25.8 - + + -
884A LYS* 1.3 72.8 - - - +
886A SER* 1.3 61.7 + - - +
888A ILE* 3.2 15.5 + - + +
889A VAL* 2.9 26.7 + - - +
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Residues in contact with SER 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A LYS* 3.7 37.3 - - - +
884A LYS* 3.9 13.2 - - - +
885A PHE* 1.3 77.3 - - - +
887A GLN* 1.4 62.4 + - - +
889A VAL* 3.5 2.8 + - - +
890A ASN* 3.0 39.0 + - - +
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Residues in contact with GLN 887 (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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870A LEU* 6.0 0.2 - - - -
882A ARG 4.6 1.0 - - - +
883A PRO* 3.4 17.4 - - + +
884A LYS* 2.9 43.7 + - + +
886A SER* 1.4 78.9 + - - +
888A ILE* 1.3 61.4 + - - +
890A ASN* 3.3 12.7 + - - +
891A THR* 2.9 35.3 + - - +
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Residues in contact with ILE 888 (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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743A ALA* 3.8 13.7 - - + -
821A VAL* 4.0 15.3 - - + -
824A TYR* 3.5 32.8 - - + +
870A LEU* 4.2 16.6 - - + -
874A CYS* 3.9 22.0 - - - -
883A PRO* 3.7 16.6 - - + -
884A LYS 3.1 19.6 + - - +
885A PHE* 3.2 27.1 + - + +
887A GLN* 1.3 72.6 - - - +
889A VAL* 1.4 59.4 + - - +
891A THR* 3.2 6.3 + - - -
892A LEU* 2.9 35.2 + - + +
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Residues in contact with VAL 889 (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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740A ARG* 3.6 38.1 - - - +
743A ALA* 3.6 36.1 - - + +
744A ALA* 3.7 9.9 - - + +
747A LYS* 4.2 15.3 - - + -
885A PHE 2.9 17.2 + - - +
886A SER* 3.6 9.6 - - - +
888A ILE* 1.4 75.1 - - - +
890A ASN* 1.4 60.9 + - - +
892A LEU* 3.3 5.4 + - - +
893A ASP* 2.9 32.6 + - - +
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Residues in contact with ASN 890 (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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886A SER* 3.0 29.5 + - - +
887A GLN* 3.6 12.0 - - - +
888A ILE 3.3 0.2 - - - -
889A VAL* 1.4 81.9 - - - +
891A THR* 1.3 56.5 + - - +
893A ASP* 3.4 9.2 + - - +
894A LYS* 3.0 27.9 + - - +
897A ARG* 4.9 2.6 + - - -
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Residues in contact with THR 891 (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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866A ALA 5.6 1.8 - - - +
870A LEU* 3.9 32.4 - - + +
887A GLN* 2.9 20.6 + - - +
888A ILE* 3.7 5.6 - - - -
890A ASN* 1.3 73.3 - - - +
892A LEU* 1.4 59.1 + - - +
894A LYS* 3.2 13.6 + - + +
895A LEU* 3.0 38.6 + - + +
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Residues in contact with LEU 892 (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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736A VAL* 4.1 14.2 - - + +
739A LEU* 3.8 6.1 - - + +
740A ARG* 3.7 36.3 - - + +
743A ALA* 4.3 2.5 - - + -
824A TYR* 3.3 25.8 - - - +
828A MET* 4.9 3.1 - - + -
867A LEU* 4.0 21.8 - - + -
870A LEU* 3.7 23.1 - - + -
888A ILE* 2.9 26.8 + - + +
889A VAL* 3.8 3.8 - - - +
891A THR* 1.4 74.6 - - - +
893A ASP* 1.4 57.4 + - - +
895A LEU* 3.2 9.0 + - + +
896A ILE* 3.0 33.4 + - - +
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Residues in contact with ASP 893 (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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740A ARG* 2.8 47.2 + - - +
889A VAL* 2.9 22.7 + - - +
890A ASN* 3.7 8.9 - - - +
891A THR 3.3 0.2 - - - -
892A LEU* 1.4 72.1 - - - +
894A LYS* 1.3 61.5 + - - +
896A ILE* 3.2 12.9 + - - +
897A ARG* 2.9 48.7 + - + +
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Residues in contact with LYS 894 (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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890A ASN 3.0 15.1 + - - +
891A THR* 3.2 16.1 + - + +
893A ASP* 1.3 74.6 - - - +
895A LEU* 1.4 60.7 + - + +
897A ARG* 3.4 25.4 + - - +
898A ASN* 2.9 46.3 + - - +
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Residues in contact with LEU 895 (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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736A VAL* 5.0 3.1 - - + -
866A ALA* 3.7 28.9 - - + +
867A LEU* 3.8 28.5 - - + -
870A LEU* 5.4 0.7 - - + -
891A THR* 3.0 31.9 + - + +
892A LEU* 3.2 15.2 + - + +
894A LYS* 1.4 79.2 - - + +
896A ILE* 1.4 62.8 + - - +
898A ASN* 3.0 22.7 - - + +
899A PRO* 3.4 5.9 - - - +
901A SER* 3.2 24.0 - - - +
902A LEU* 3.8 26.8 - - + +
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Residues in contact with ILE 896 (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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733A ILE* 4.6 24.6 - - + +
736A VAL* 3.7 26.7 - - + -
737A GLY* 4.8 5.6 - - - +
740A ARG* 4.4 15.5 - - + -
892A LEU 3.0 25.3 + - - +
893A ASP* 3.6 19.5 - - - +
895A LEU* 1.4 77.1 - - - +
897A ARG* 1.4 62.2 + - + +
898A ASN 3.5 0.3 + - - -
899A PRO* 3.5 13.7 - - - +
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Residues in contact with ARG 897 (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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890A ASN 4.9 2.4 + - - -
893A ASP* 2.9 37.2 + - - +
894A LYS* 3.7 39.8 - - - +
896A ILE* 1.4 75.9 - - + +
898A ASN* 1.3 68.4 + - - +
899A PRO* 3.5 7.9 - - - +
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Residues in contact with ASN 898 (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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894A LYS* 2.9 37.4 + - + +
895A LEU* 3.0 4.5 - - + +
897A ARG* 1.3 90.9 - - - +
899A PRO* 1.4 60.0 - - - +
900A ALA* 3.1 6.1 + - + -
901A SER* 2.7 37.5 + - - +
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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