Contacts of the helix formed by residues 871 - 887 (chain A) in PDB entry 5J69
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 871 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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797A ALA 3.2 24.3 + - - -
798A MET* 3.5 10.6 - - - +
799A GLY* 3.3 16.2 + - - -
800A TYR 3.3 7.1 - - - +
802A MET* 3.5 10.9 - - - +
869A PHE* 4.1 0.5 - - - +
870A PRO* 1.3 82.6 - - - +
872A LYS* 1.3 61.7 + - - +
873A LYS* 3.5 5.4 - - - -
874A VAL* 3.2 25.6 - - - +
875A GLN* 2.9 14.4 - - - +
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Residues in contact with LYS 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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797A ALA 5.2 0.2 + - - -
798A MET 5.3 0.2 - - - -
799A GLY* 4.3 2.4 - - - -
800A TYR* 3.4 33.2 + - + -
802A MET* 3.5 26.2 - - + -
871A SER* 1.3 72.0 - - - +
873A LYS* 1.3 61.4 + - + +
875A GLN* 2.7 34.3 + - - +
876A GLN* 3.3 29.3 - - - +
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Residues in contact with LYS 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A GLU* 4.4 19.5 + - - +
797A ALA* 5.2 12.8 - - - +
871A SER* 3.5 4.1 - - - -
872A LYS* 1.3 81.5 - - + +
874A VAL* 1.3 61.7 + - + +
875A GLN 3.5 0.2 - - - -
876A GLN* 3.4 11.5 + - - +
877A GLN* 2.9 48.2 + - + +
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Residues in contact with VAL 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869A PHE* 4.1 7.0 - - + -
870A PRO* 3.7 25.6 - - + -
871A SER* 3.2 45.5 - - - +
873A LYS* 1.3 80.7 - - + +
875A GLN* 1.3 60.9 + - - +
877A GLN* 3.4 11.3 + - - +
878A LEU* 2.9 37.5 + - + +
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Residues in contact with GLN 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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781A PRO* 4.3 24.5 - - + +
802A MET* 3.2 26.5 - - + +
804A GLN* 5.0 4.2 + - - +
869A PHE* 3.6 38.8 - - + -
871A SER 2.9 22.3 - - - +
872A LYS* 2.7 34.0 + - - +
874A VAL* 1.3 77.1 - - - +
876A GLN* 1.3 77.2 + - + +
878A LEU* 3.9 3.0 - - - +
879A TRP* 2.9 29.0 + - + +
900A PHE* 5.4 1.6 - - - -
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Residues in contact with GLN 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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781A PRO* 6.5 0.4 - - + -
872A LYS* 3.3 47.2 + - - +
873A LYS* 3.4 13.0 + - - +
874A VAL 3.2 0.4 - - - -
875A GLN* 1.3 86.9 - - + +
877A GLN* 1.3 61.3 - - + +
879A TRP* 3.2 7.8 + - - +
880A LEU* 2.9 30.5 + - - +
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Residues in contact with GLN 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A LYS* 2.9 36.5 + - + +
874A VAL* 3.7 10.9 - - - +
876A GLN* 1.3 77.4 - - + +
878A LEU* 1.3 57.8 + - + +
880A LEU* 4.0 3.0 - - - +
881A GLN* 2.9 39.3 + - - +
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Residues in contact with LEU 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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869A PHE* 3.7 30.1 - - + -
874A VAL* 2.9 24.1 + - + +
875A GLN* 4.0 4.3 - - - +
877A GLN* 1.3 76.4 - - + +
879A TRP* 1.3 62.5 + - - +
881A GLN* 3.3 25.8 - - - +
882A TYR* 2.9 45.4 + - + +
900A PHE* 4.4 7.9 - - + -
904A LEU* 4.7 13.7 - - + -
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Residues in contact with TRP 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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778A LEU* 3.7 31.6 - - + -
780A GLU* 5.1 6.7 - - - -
781A PRO* 4.4 15.3 - - + -
804A GLN* 3.9 17.5 - - - -
875A GLN* 2.9 24.6 + - + +
876A GLN* 3.2 9.8 + - - +
878A LEU* 1.3 77.2 - - - +
880A LEU* 1.3 62.9 + - + +
882A TYR* 3.9 1.6 - - - +
883A GLN* 2.9 46.9 + - + +
900A PHE* 3.9 26.3 - + - -
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Residues in contact with LEU 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 GLN 2.9 16.3 + - - +
877A GLN* 4.1 3.4 - - - +
879A TRP* 1.3 77.6 - - + +
881A GLN* 1.3 62.8 + - - +
883A GLN* 3.0 20.6 + - - +
884A LYS* 2.9 59.8 + - + +
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Residues in contact with GLN 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 GLN* 2.9 28.5 + - - +
878A LEU* 3.3 32.3 - - - +
880A LEU* 1.3 76.7 - - - +
882A TYR* 1.3 73.6 + - + +
884A LYS* 3.1 10.0 + - - +
885A GLU* 2.9 36.1 + - + +
907A LEU* 5.0 7.5 - - - +
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Residues in contact with TYR 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 LEU* 2.9 41.9 + - + +
881A GLN* 1.3 96.2 - - + +
883A GLN* 1.3 61.1 + - - +
885A GLU* 3.8 6.4 - - + +
886A THR* 2.9 37.8 + - - +
899A PRO 5.3 0.4 - - - -
900A PHE* 3.5 38.4 - + + -
903A TYR* 3.2 28.9 + + + -
904A LEU* 3.2 44.8 + - + +
907A LEU* 3.2 38.3 - - + +
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Residues in contact with GLN 883 (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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879A TRP* 2.9 33.0 + - + +
880A LEU* 3.3 25.3 - - - +
882A TYR* 1.3 75.6 - - - +
884A LYS* 1.3 65.5 + - - +
886A THR* 4.9 2.9 - - - -
887A THR* 2.4 48.9 + - + +
900A PHE* 5.2 0.6 - - - -
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Residues in contact with LYS 884 (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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880A LEU* 2.9 49.8 + - + +
881A GLN* 3.1 10.5 + - - +
882A TYR 3.1 0.4 - - - -
883A GLN* 1.3 91.5 - - - +
885A GLU* 1.3 66.7 + - + +
887A THR* 3.5 20.5 - - - +
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Residues in contact with GLU 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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881A GLN* 2.9 27.0 + - + +
882A TYR* 3.2 8.5 + - + +
884A LYS* 1.3 79.8 - - - +
886A THR* 1.3 65.1 + - - +
887A THR 4.7 1.7 - - - +
903A TYR* 3.8 38.6 + - + -
907A LEU* 5.8 2.9 - - + -
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Residues in contact with THR 886 (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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882A TYR* 2.9 20.1 + - - +
883A GLN* 4.4 4.3 - - - -
885A GLU* 1.3 80.6 - - - +
887A THR* 1.3 68.3 + - + +
897A SER 3.7 22.8 + - - +
898A MET 3.3 28.4 + - - +
899A PRO* 4.0 10.0 + - + -
900A PHE* 5.3 1.7 - - - -
903A TYR* 5.4 4.7 - - - -
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Residues in contact with THR 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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883A GLN* 2.4 38.0 + - + +
884A LYS* 3.5 23.4 - - - +
885A GLU 4.7 1.2 - - - +
886A THR* 1.3 92.9 - - + +
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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