Contacts of the helix formed by residues 876 - 895 (chain B) in PDB entry 3KZ1
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 ILE 876 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836B GLN* 3.8 17.5 - - - +
840B LEU* 5.8 4.5 - - + -
872B ARG 3.3 21.7 + - - +
873B ASP* 3.8 14.6 - - - +
874B LEU 3.3 1.4 - - - -
875B ILE* 1.3 79.3 - - + +
877B SER* 1.3 56.3 + - - +
878B GLU 3.4 0.9 - - - -
879B MET* 3.3 23.4 + - + -
880B GLN* 3.0 47.0 + - + +
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Residues in contact with SER 877 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749B HIS* 3.3 17.3 + - - -
752B THR* 3.3 22.9 - - - +
753B LEU* 5.1 6.1 - - - -
756B LEU* 5.5 0.2 - - - -
873B ASP 3.9 3.8 + - - -
874B LEU* 2.5 26.0 + - - -
875B ILE 3.1 1.6 - - - -
876B ILE* 1.3 74.3 - - - +
878B GLU* 1.3 62.4 + - - +
880B GLN* 3.4 16.5 + - - +
881B ARG* 2.8 30.3 + - - +
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Residues in contact with GLU 878 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749B HIS* 3.2 23.0 + - - -
753B LEU* 3.8 4.7 - - + +
785B LEU* 3.5 37.1 - - + +
789B HIS* 2.8 27.0 + - - -
825B LEU* 4.7 3.5 - - - +
829B ALA* 4.5 5.6 - - + -
832B PHE* 4.3 15.5 - - + -
833B CYS* 4.3 18.4 - - - -
875B ILE 4.2 2.3 + - - +
876B ILE 3.4 0.6 - - - -
877B SER* 1.3 76.0 - - - +
879B MET* 1.3 61.0 + - - +
881B ARG* 3.0 3.5 + - - +
882B LEU* 2.8 58.2 + - + +
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Residues in contact with MET 879 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833B CYS* 4.1 19.8 - - + -
836B GLN* 5.4 2.0 - - - +
875B ILE 5.3 0.2 + - - -
876B ILE* 3.3 31.4 + - + +
878B GLU* 1.3 75.9 - - - +
880B GLN* 1.3 65.1 + - + +
882B LEU* 3.1 19.3 + - - +
883B THR* 3.0 25.2 + - + +
917B LEU* 6.1 3.8 - - - -
920B VAL* 4.7 13.5 - - + -
921B ASN* 3.1 29.6 - - - +
924B VAL* 4.5 22.2 - - + -
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Residues in contact with GLN 880 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1064A SER* 5.2 5.9 + - - -
1065A SER* 4.3 20.1 + - - -
873B ASP 4.4 5.3 + - - -
876B ILE* 3.0 32.6 + - + +
877B SER* 3.6 26.8 + - - +
878B GLU 3.3 0.2 - - - -
879B MET* 1.3 79.3 - - + +
881B ARG* 1.3 56.6 + - - +
883B THR* 3.3 12.3 - - - +
884B LYS* 3.1 30.8 + - - +
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Residues in contact with ARG 881 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742B LEU* 3.5 13.1 + - - +
745B THR* 3.1 42.8 + - - -
746B GLU* 3.2 36.2 + - - +
749B HIS* 3.4 34.6 - - + +
789B HIS* 4.6 0.9 - - + -
877B SER 2.8 17.8 + - - +
878B GLU* 3.3 6.5 - - - +
880B GLN* 1.3 75.2 - - - +
882B LEU* 1.3 66.1 + - - +
883B THR 3.1 0.2 - - - -
884B LYS* 3.0 24.4 + - - +
885B TYR* 3.1 48.8 + - + +
888B LEU* 4.0 11.3 - - - +
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Residues in contact with LEU 882 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817B PHE* 5.5 0.4 - - + -
825B LEU* 4.6 13.0 - - + -
829B ALA* 4.4 14.1 - - + -
878B GLU* 2.8 57.1 + - + +
879B MET* 3.1 12.5 + - - +
881B ARG* 1.3 77.5 - - + +
883B THR* 1.3 58.4 + - - +
885B TYR* 3.8 22.6 + - + +
886B PRO* 3.2 22.0 - - - +
913B CYS* 5.1 4.2 - - + +
916B ILE* 3.9 28.9 - - + -
917B LEU* 4.1 16.3 - - + +
920B VAL* 5.0 10.3 - - + -
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Residues in contact with THR 883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879B MET* 3.0 24.5 + - - +
880B GLN* 3.3 17.9 - - - +
882B LEU* 1.3 78.7 - - - +
884B LYS* 1.3 58.6 + - - +
886B PRO* 3.4 9.2 - - - +
887B LEU* 3.6 18.2 - - - +
917B LEU* 3.7 24.6 - - - +
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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
----------------------------------------------------------
741B GLU* 5.4 3.8 + - - +
880B GLN* 3.1 17.3 + - - +
881B ARG* 3.0 21.1 + - - +
883B THR* 1.3 77.9 - - - +
885B TYR* 1.3 65.2 + - - +
887B LEU* 3.0 19.8 + - + +
888B LEU* 2.9 51.0 + - + +
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Residues in contact with TYR 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742B LEU* 4.4 12.3 - - + -
746B GLU* 2.7 24.5 + - - -
789B HIS* 3.1 26.5 + + - -
792B TRP* 4.0 12.9 - + - -
817B PHE* 3.4 35.0 - + + -
825B LEU* 5.2 2.2 - - + -
881B ARG* 3.1 54.1 + - + +
882B LEU* 4.0 24.2 - - + +
884B LYS* 1.3 75.0 - - - +
886B PRO* 1.4 71.3 - - + +
888B LEU* 2.9 6.9 + - + +
889B LEU* 2.9 28.6 + - + +
913B CYS* 4.0 16.6 - - - -
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Residues in contact with PRO 886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882B LEU 3.2 18.8 - - - +
883B THR 3.4 13.0 - - - +
885B TYR* 1.4 91.6 - - + +
887B LEU* 1.3 66.2 + - + +
889B LEU* 4.0 5.4 - - + +
890B GLU* 3.1 28.0 + - - +
910B ARG* 4.4 8.1 - - + +
913B CYS* 4.0 20.2 - - + -
914B ARG* 4.3 30.1 - - + +
917B LEU* 4.3 13.9 - - + -
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Residues in contact with LEU 887 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883B THR* 3.6 20.2 - - - +
884B LYS* 3.0 22.1 + - + +
886B PRO* 1.3 85.1 - - + +
888B LEU* 1.3 66.7 + - + +
890B GLU* 3.5 6.9 + - - +
891B SER* 3.3 21.0 + - - -
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Residues in contact with LEU 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738B VAL* 3.8 9.0 - - + +
741B GLU* 4.1 22.0 - - - +
742B LEU* 3.9 40.8 - - + +
745B THR* 4.1 7.9 - - - +
881B ARG* 4.0 15.5 - - - +
884B LYS* 2.9 43.2 + - + +
885B TYR* 2.9 12.0 + - + +
887B LEU* 1.3 77.4 - - + +
889B LEU* 1.3 65.8 + - + +
891B SER* 3.2 8.9 + - - -
892B ILE* 3.2 26.0 + - - +
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Residues in contact with LEU 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742B LEU* 5.2 1.6 - - + -
813B MET* 3.7 34.8 - - + -
817B PHE* 4.4 8.5 - - + -
885B TYR* 2.9 15.5 + - + +
886B PRO 4.1 3.1 - - - +
888B LEU* 1.3 75.6 - - + +
890B GLU* 1.3 66.4 + - - +
892B ILE* 2.9 15.7 + - + +
893B ILE* 2.9 28.6 + - + +
906B LEU* 3.9 17.3 - - + +
909B ALA* 3.7 12.8 - - + +
910B ARG* 3.5 42.2 - - + +
913B CYS* 3.8 16.8 - - + -
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Residues in contact with GLU 890 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886B PRO 3.1 17.9 + - - +
887B LEU* 3.5 9.1 - - - +
888B LEU 3.3 0.2 - - - -
889B LEU* 1.3 75.4 - - - +
891B SER* 1.3 57.6 + - - +
893B ILE* 3.3 12.1 + - + +
894B LYS* 2.9 28.6 + - - +
910B ARG* 2.7 34.9 + - - +
914B ARG* 2.8 26.2 + - - -
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Residues in contact with SER 891 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738B VAL* 3.7 25.8 - - - +
887B LEU 3.3 8.8 + - - -
888B LEU* 3.2 12.3 + - - -
889B LEU 3.1 0.4 - - - -
890B GLU* 1.3 81.7 - - - +
892B ILE* 1.3 60.5 + - - +
894B LYS* 3.2 21.4 + - - +
895B HIS* 3.3 22.9 + - - -
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Residues in contact with ILE 892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735B ARG* 4.7 9.4 - - + +
738B VAL* 3.5 21.1 - - + -
739B ILE* 4.2 30.7 - - + -
742B LEU* 3.8 29.6 - - + -
809B ILE* 4.5 13.0 - - + -
813B MET* 5.4 0.2 - - - -
888B LEU 3.2 14.6 + - - +
889B LEU* 2.9 20.7 + - + +
891B SER* 1.3 74.6 - - - +
893B ILE* 1.3 55.7 - - - +
895B HIS* 3.2 12.2 + - - +
896B THR* 2.4 28.2 + - - +
902B GLU* 5.7 0.2 - - - +
906B LEU* 3.9 20.0 - - + -
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Residues in contact with ILE 893 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889B LEU* 2.9 27.2 + - + +
890B GLU* 3.5 10.1 - - + +
892B ILE* 1.3 72.7 - - - +
894B LYS* 1.3 66.7 + - - +
895B HIS 3.0 2.2 - - - -
896B THR* 2.9 26.7 + - - +
903B HIS* 3.9 24.5 + - + +
906B LEU* 3.9 33.2 - - + +
907B CYS* 4.2 10.8 - - - +
910B ARG* 4.0 40.6 - - + +
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Residues in contact with LYS 894 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731B ARG* 3.2 14.2 + - - -
890B GLU 2.9 13.6 + - - +
891B SER* 3.2 16.8 + - - +
893B ILE* 1.3 77.9 - - - +
895B HIS* 1.3 72.9 + - + +
896B THR 3.5 0.4 - - - +
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Residues in contact with HIS 895 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731B ARG* 3.4 42.8 - - + +
734B ASP* 3.6 45.5 + - + +
735B ARG* 3.4 27.5 - - + -
738B VAL* 4.3 11.7 - - + +
891B SER* 3.3 22.9 + - - -
892B ILE* 3.2 6.0 + - - +
893B ILE 3.0 1.0 - - - -
894B LYS* 1.3 94.0 - - + +
896B THR* 1.3 58.4 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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