Contacts of the helix formed by residues 865 - 882 (chain A) in PDB entry 5OQN
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 ASP 865 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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824A LYS* 4.5 1.4 + - - +
826A THR* 4.2 17.4 - - + +
863A GLU 3.5 2.9 + - - -
864A GLN* 1.3 82.8 - - - +
866A TYR* 1.3 60.1 + - - +
867A SER* 2.5 42.9 + - - -
868A THR* 2.8 21.9 + - - +
869A LEU* 3.1 23.6 - - - +
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Residues in contact with TYR 866 (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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864A GLN 4.4 0.7 - - - -
865A ASP* 1.3 80.3 + - - +
867A SER* 1.3 71.9 + - - +
868A THR 3.3 0.2 - - - -
869A LEU* 3.6 6.5 + - + +
870A LYS* 3.3 44.7 + - + +
904A ILE* 4.4 24.7 - - + +
907A ILE* 3.3 44.8 - - + +
908A ASN* 4.7 14.6 + - - -
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Residues in contact with SER 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865A ASP* 2.5 27.4 + - - -
866A TYR* 1.3 84.2 - - - +
868A THR* 1.3 58.2 + - - -
870A LYS* 3.2 10.6 + - - +
871A GLU* 2.9 28.6 + - - +
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Residues in contact with THR 868 (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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826A THR* 4.6 8.5 + - - +
829A LEU* 4.2 21.3 - - + -
830A THR* 4.4 15.0 - - + -
833A ILE* 3.7 19.5 - - + +
865A ASP* 2.8 24.8 + - - +
866A TYR 3.3 0.4 - - - -
867A SER* 1.3 77.1 + - - +
869A LEU* 1.3 65.5 + - - +
871A GLU* 3.3 9.7 + - - +
872A LEU* 2.9 28.3 + - - +
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Residues in contact with LEU 869 (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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829A LEU* 3.3 31.4 - - + -
860A LEU* 5.4 3.4 - - + -
861A SER 4.4 7.9 - - - +
864A GLN* 4.0 12.3 - - + +
865A ASP 3.1 22.2 - - - +
866A TYR* 3.6 7.4 + - - +
867A SER 3.4 0.4 - - - -
868A THR* 1.3 73.9 - - - +
870A LYS* 1.3 56.2 + - - +
872A LEU* 3.2 7.3 + - - +
873A LEU* 2.7 37.0 + - - +
900A LEU* 3.8 25.3 - - + +
903A LEU* 3.9 35.4 - - + -
904A ILE* 4.9 10.5 - - + -
907A ILE* 6.3 2.2 - - + -
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Residues in contact with LYS 870 (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 TYR* 3.3 38.2 + - + +
867A SER* 3.2 13.6 + - - +
869A LEU* 1.3 77.5 - - - +
871A GLU* 1.3 56.8 + - - +
873A LEU* 3.1 10.7 + - + +
874A GLU* 2.8 61.8 + - + +
904A ILE* 5.6 8.8 - - + +
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Residues in contact with GLU 871 (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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833A ILE* 3.2 32.1 - - + +
837A LYS* 5.3 2.3 + - - -
867A SER 2.9 13.1 + - - +
868A THR* 3.5 12.4 - - - +
870A LYS* 1.3 75.9 - - - +
872A LEU* 1.3 65.5 + - - +
874A GLU* 3.0 22.1 + - - +
875A TYR* 3.0 43.0 + - + -
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Residues in contact with LEU 872 (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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829A LEU* 3.8 33.0 - - + -
832A LEU* 4.1 27.6 - - + -
833A ILE* 3.8 20.8 - - + +
836A LEU* 3.3 27.4 - - + -
858A ILE* 5.8 0.2 - - + -
860A LEU* 5.4 2.2 - - + -
868A THR 2.9 16.4 + - - +
869A LEU* 3.6 6.5 - - - +
871A GLU* 1.3 76.7 - - - +
873A LEU* 1.3 58.1 + - - +
875A TYR* 3.4 2.3 + - - +
876A SER* 2.9 30.3 + - - -
896A LEU* 5.2 11.4 - - + -
900A LEU* 5.1 15.3 - - + -
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Residues in contact with LEU 873 (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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869A LEU 2.7 20.5 + - - +
870A LYS* 3.5 9.4 - - + +
872A LEU* 1.3 74.5 - - - +
874A GLU* 1.3 58.0 + - + +
876A SER* 2.7 25.8 + - - +
877A ASP* 2.9 34.8 + - + +
897A ARG* 4.4 29.6 - - + +
900A LEU* 4.2 21.7 - - + +
901A ASN* 3.8 24.7 - - - +
904A ILE* 4.4 14.1 - - + -
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Residues in contact with GLU 874 (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 LYS* 2.8 60.0 + - + +
871A GLU* 3.4 11.8 + - - +
873A LEU* 1.3 76.7 - - + +
875A TYR* 1.3 61.3 + - + +
877A ASP* 2.6 27.0 - - - +
878A ASP* 3.2 12.8 - - - +
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Residues in contact with TYR 875 (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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833A ILE* 4.5 7.9 - - + -
836A LEU* 3.8 29.6 - - + -
837A LYS* 3.4 48.4 + - + +
871A GLU* 3.0 55.3 + - + -
872A LEU* 3.9 3.1 - - - +
874A GLU* 1.3 80.5 - - + +
876A SER* 1.3 65.2 + - - +
878A ASP* 3.5 5.2 + - + +
879A ILE* 3.1 30.6 + - + +
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Residues in contact with SER 876 (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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836A LEU* 4.2 12.3 - - - +
872A LEU* 2.9 18.2 + - - -
873A LEU* 2.7 34.1 + - - +
875A TYR* 1.3 76.4 - - - +
877A ASP* 1.3 62.2 + - - +
879A ILE* 3.2 8.4 + - - +
880A ALA* 2.9 22.7 + - - +
893A LEU* 4.3 21.5 - - - +
896A LEU* 5.1 11.4 - - - -
897A ARG* 4.1 10.1 - - - +
900A LEU* 5.2 1.8 - - - +
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Residues in contact with ASP 877 (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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873A LEU* 2.9 23.6 + - + +
874A GLU* 2.6 23.5 - - - +
876A SER* 1.3 80.9 + - - +
878A ASP* 1.3 88.3 + - - +
880A ALA 3.0 8.3 + - - -
881A GLU* 2.5 36.8 + - - +
897A ARG* 3.3 28.1 + - - +
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Residues in contact with ASP 878 (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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874A GLU 3.2 17.9 - - - +
875A TYR* 3.5 7.9 - - - +
876A SER 3.2 0.4 - - - -
877A ASP* 1.3 89.6 + - - +
879A ILE* 1.3 68.7 + - - +
881A GLU* 5.7 0.2 - - - -
882A ASN* 3.2 41.5 + - - +
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Residues in contact with ILE 879 (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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836A LEU* 3.9 41.1 - - + +
839A TYR* 3.4 43.5 - - + -
852A ILE* 5.4 1.3 - - + -
875A TYR* 3.1 18.5 + - + +
876A SER* 3.2 6.5 + - - +
878A ASP* 1.3 84.0 - - - +
880A ALA* 1.3 63.8 + - - +
881A GLU 3.4 0.2 + - - -
882A ASN* 5.5 0.7 - - - -
883A ASP* 3.5 27.4 + - + +
885A LEU* 3.7 7.2 - - + +
893A LEU* 4.5 13.9 - - + -
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Residues in contact with ALA 880 (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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876A SER 2.9 16.2 + - - +
877A ASP 3.0 2.2 + - - +
879A ILE* 1.3 78.1 - - - +
881A GLU* 1.3 79.5 + - - +
883A ASP 3.8 2.9 - - - +
885A LEU* 3.5 20.8 - - + +
890A LYS* 6.0 1.4 - - - +
893A LEU* 4.1 19.1 - - + -
894A ASP* 4.6 7.2 - - - +
897A ARG* 3.7 15.7 - - - -
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Residues in contact with GLU 881 (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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877A ASP* 2.5 42.7 + - - +
880A ALA* 1.3 90.9 - - - +
882A ASN* 1.3 71.3 + - - +
883A ASP 3.6 2.7 - - - -
894A ASP* 4.9 2.3 - - - +
897A ARG* 2.9 31.4 + - - -
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Residues in contact with ASN 882 (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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878A ASP* 3.2 35.9 + - - +
879A ILE* 4.3 0.9 - - - -
881A GLU* 1.3 95.9 - - - +
883A ASP* 1.3 61.7 + - - +
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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