Contacts of the helix formed by residues 871 - 887 (chain B) in PDB entry 5J67
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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798B MET* 3.4 37.0 - - - -
800B TYR 3.8 8.5 - - - -
802B MET* 3.8 7.3 - - - +
869B PHE* 3.3 9.2 - - - +
870B PRO* 1.3 82.8 - - - +
872B LYS* 1.3 64.0 + - - +
873B LYS* 3.4 6.2 + - - +
874B VAL* 2.9 32.4 + - - +
875B GLN* 3.3 16.8 + - - +
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Residues in contact with LYS 872 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781B PRO* 6.6 0.4 - - + -
798B MET 4.5 4.0 + - - +
800B TYR 3.9 3.6 + - - +
802B MET* 3.6 37.5 - - + +
871B SER* 1.3 72.9 - - - +
873B LYS* 1.3 62.5 + - - +
875B GLN* 3.7 4.4 + - - +
876B GLN* 3.3 50.0 + - + +
1026B GLU* 5.9 4.5 - - - +
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Residues in contact with LYS 873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798B MET* 5.0 4.2 + - - +
871B SER* 3.2 7.9 + - - +
872B LYS* 1.3 77.0 - - - +
874B VAL* 1.3 67.3 + - + +
876B GLN* 3.1 12.5 + - - +
877B GLN* 3.0 53.5 + - + +
1282B TYR 5.2 7.3 + - - -
1283B GLY* 5.7 3.6 - - - -
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Residues in contact with VAL 874 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798B MET* 4.8 10.8 - - + -
869B PHE* 4.7 0.9 - - + -
870B PRO* 3.7 31.9 - - + -
871B SER* 2.9 26.1 + - - +
873B LYS* 1.3 77.2 - - + +
875B GLN* 1.3 63.0 + - - +
877B GLN* 3.7 3.5 + - - +
878B LEU* 3.1 34.0 + - + +
918B LEU* 3.4 40.0 - - + +
922B VAL* 4.4 3.1 - - + -
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Residues in contact with GLN 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781B PRO* 2.9 36.5 - - - +
802B MET* 4.5 5.4 - - + +
804B GLN* 2.7 36.4 + - - +
869B PHE* 3.7 40.2 - - + -
871B SER 3.3 8.4 + - - +
872B LYS* 3.9 8.7 - - - +
873B LYS 3.2 0.8 - - - -
874B VAL* 1.3 76.2 - - - +
876B GLN* 1.3 65.2 + - + +
878B LEU* 2.8 5.1 + - - +
879B TRP* 2.7 44.8 + - + +
900B PHE* 4.6 5.0 - - + -
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Residues in contact with GLN 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872B LYS* 3.3 47.0 + - + +
873B LYS* 3.1 9.5 + - - +
875B GLN* 1.3 84.0 - - + +
877B GLN* 1.3 58.0 + - + +
879B TRP* 3.8 5.9 - - - +
880B LEU* 3.0 44.5 + - + +
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Residues in contact with GLN 877 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873B LYS* 3.0 51.7 + - + +
874B VAL* 4.6 1.2 - - - +
876B GLN* 1.3 77.1 - - + +
878B LEU* 1.3 51.4 + - - +
880B LEU* 3.7 5.9 - - - +
881B GLN* 2.7 36.0 + - - +
918B LEU* 3.5 41.1 - - + +
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Residues in contact with LEU 878 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869B PHE* 4.2 7.4 - - + -
874B VAL* 3.1 22.6 + - + +
875B GLN* 2.8 13.0 + - - +
877B GLN* 1.3 72.8 - - - +
879B TRP* 1.3 57.9 + - - +
881B GLN* 3.7 12.6 - - - +
882B TYR* 2.8 30.7 + - - +
900B PHE* 3.9 7.1 - - + -
903B TYR* 4.1 4.1 - - + -
904B LEU* 3.8 23.8 - - + -
918B LEU* 3.5 23.8 - - + -
919B ILE* 3.3 33.0 - - + -
922B VAL* 3.8 29.2 - - + -
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Residues in contact with TRP 879 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778B LEU* 3.6 30.1 - - + -
804B GLN* 5.2 4.0 - - - -
875B GLN* 2.7 28.1 + - + +
876B GLN* 3.8 7.9 - - - +
878B LEU* 1.3 72.1 - - - +
880B LEU* 1.3 75.8 + - + +
882B TYR* 3.5 18.0 + + - +
883B GLN* 2.9 59.0 + - - +
900B PHE* 3.7 38.3 - + + -
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Residues in contact with LEU 880 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876B GLN* 3.0 32.3 + - + +
877B GLN* 3.9 5.8 - - - +
879B TRP* 1.3 90.9 - - + +
881B GLN* 1.3 58.9 + - - +
883B GLN* 3.3 12.5 + - + +
884B LYS* 3.0 29.8 + - - +
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Residues in contact with GLN 881 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877B GLN 2.7 21.7 + - - +
878B LEU* 3.7 14.8 - - - +
880B LEU* 1.3 74.2 - - - +
882B TYR* 1.3 61.2 + - - +
884B LYS* 3.6 5.0 + - - +
885B GLU* 3.2 41.1 + - - +
903B TYR* 2.9 21.5 + - - +
907B LEU* 4.0 13.1 - - - +
917B GLN* 5.4 8.0 + - - +
918B LEU* 3.5 24.8 - - - +
919B ILE* 4.8 2.0 - - - +
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Residues in contact with TYR 882 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878B LEU 2.8 22.0 + - - +
879B TRP* 3.5 34.3 - + - +
881B GLN* 1.3 74.2 - - - +
883B GLN* 1.3 63.1 + - + +
885B GLU* 3.5 1.2 + - - +
886B THR* 3.0 49.7 + - + +
898B MET* 2.6 31.9 + - + -
899B PRO* 3.6 4.0 - - - +
900B PHE* 3.3 36.9 + + + -
903B TYR* 3.6 42.7 - + + -
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Residues in contact with GLN 883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879B TRP* 2.9 56.7 + - - +
880B LEU* 3.3 14.6 + - + +
882B TYR* 1.3 78.8 - - + +
884B LYS* 1.3 63.5 + - - +
886B THR* 3.8 9.0 - - + -
887B THR* 2.9 34.0 + - - +
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Residues in contact with LYS 884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880B LEU 3.0 17.5 + - - +
881B GLN* 3.8 6.7 - - - +
883B GLN* 1.3 76.1 - - - +
885B GLU* 1.3 65.7 + - + +
886B THR 3.3 0.9 + - - -
887B THR 3.4 22.2 - - - +
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Residues in contact with GLU 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881B GLN* 3.2 38.3 + - - +
882B TYR 3.8 1.8 - - - +
884B LYS* 1.3 79.9 - - + +
886B THR* 1.3 58.4 + - - +
903B TYR* 3.5 26.8 + - + -
907B LEU* 6.1 0.5 - - - +
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Residues in contact with THR 886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882B TYR* 3.0 40.6 + - + +
883B GLN* 3.6 16.2 - - + +
885B GLU* 1.3 79.4 - - - +
887B THR* 1.3 74.9 - - + +
897B SER* 3.8 33.8 + - - -
898B MET* 4.2 11.1 + - - +
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Residues in contact with THR 887 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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883B GLN* 2.9 24.1 + - - +
884B LYS* 3.4 16.4 - - - +
886B THR* 1.3 92.3 - - + +
897B SER 6.2 1.3 - - - +
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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