Contacts of the helix formed by residues 837 - 858 (chain B) in PDB entry 1ZUC
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 837 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741B ASN 4.4 0.7 + - - -
742B LEU* 3.7 12.6 - - - -
743B HIS* 2.8 32.0 + - - +
746B ASP* 2.7 18.6 + - - -
835B LEU* 4.5 2.5 - - - -
836B ARG* 1.3 71.8 - - - +
838B GLN* 1.3 58.6 + - - +
839B THR 3.3 2.9 - - - -
840B GLN* 3.2 31.0 + - - +
841B PHE* 2.9 26.2 + - - +
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Residues in contact with GLN 838 (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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830B ILE* 3.5 25.3 - - - +
834B GLY* 3.5 8.7 - - - -
835B LEU* 2.8 43.5 + - - +
836B ARG 3.3 4.6 + - - -
837B SER* 1.3 76.2 - - - +
839B THR* 1.3 57.1 + - - +
841B PHE* 3.4 17.3 + - - +
842B GLU* 2.9 54.9 + - + +
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Residues in contact with THR 839 (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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837B SER 3.3 0.4 - - - -
838B GLN* 1.3 77.8 - - - +
840B GLN* 1.3 71.8 + - + +
842B GLU* 3.3 8.4 + - - +
843B GLU* 3.1 38.7 + - + +
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Residues in contact with GLN 840 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741B ASN* 4.4 19.2 + - + +
742B LEU* 3.7 19.2 - - + +
837B SER* 3.2 32.1 + - - +
839B THR* 1.3 82.3 + - + +
841B PHE* 1.3 65.1 + - - +
843B GLU* 3.3 12.0 + - - +
844B MET* 2.9 24.3 + - - +
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Residues in contact with PHE 841 (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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742B LEU* 3.5 14.7 - - + +
750B LEU* 4.1 8.5 - - + -
827B LEU* 3.3 56.1 - - + -
830B ILE* 3.5 26.9 - - + -
835B LEU* 3.5 26.5 - - + -
837B SER 2.9 17.3 + - - +
838B GLN* 3.6 21.8 - - - +
840B GLN* 1.3 76.9 - - - +
842B GLU* 1.3 67.5 + - - +
844B MET* 3.2 3.8 + - - +
845B ARG* 2.8 52.4 + - + +
928B LEU* 3.8 6.3 - - + -
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Residues in contact with GLU 842 (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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838B GLN* 2.9 43.5 + - + +
839B THR* 3.3 8.9 + - + +
841B PHE* 1.3 86.5 - - - +
843B GLU* 1.3 56.9 + - + +
845B ARG* 4.0 14.3 + - - +
846B SER* 2.9 40.3 + - - +
928B LEU* 5.8 0.5 - - - +
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Residues in contact with GLU 843 (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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839B THR* 3.1 32.5 + - + +
840B GLN* 3.6 13.2 - - - +
842B GLU* 1.3 75.0 - - + +
844B MET* 1.3 57.0 + - - +
846B SER* 3.9 4.8 - - - -
847B SER* 3.0 29.3 + - - -
850B ARG* 4.6 2.9 + - - -
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Residues in contact with MET 844 (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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736B LEU* 3.9 15.0 - - + -
737B PRO 3.4 22.4 - - - +
738B GLY* 3.7 23.6 - - - +
739B PHE* 3.6 30.7 - - + +
742B LEU* 4.3 9.0 - - + -
827B LEU* 4.1 23.8 - - + -
840B GLN 2.9 17.2 + - - +
841B PHE* 3.7 4.7 - - - +
843B GLU* 1.3 74.9 - - - +
845B ARG* 1.3 67.1 + - - +
847B SER* 3.1 6.0 + - - -
848B TYR* 3.1 49.3 + - + -
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Residues in contact with ARG 845 (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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824B LEU* 3.9 11.8 + - + +
827B LEU* 3.7 27.3 + - + +
828B ASN* 4.1 4.6 + - - -
841B PHE* 2.8 48.7 + - + +
842B GLU* 4.0 13.4 + - - +
844B MET* 1.3 72.6 - - - +
846B SER* 1.3 63.6 + - - +
848B TYR* 3.2 2.8 + - - -
849B ILE* 3.0 45.8 + - + +
928B LEU* 3.5 36.5 - - - +
929B LEU 4.5 8.1 + - - -
930B PHE* 3.7 30.3 - - - -
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Residues in contact with SER 846 (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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842B GLU* 2.9 27.1 + - - +
843B GLU* 3.9 4.7 - - - -
845B ARG* 1.3 76.7 + - - +
847B SER* 1.3 57.6 + - - +
849B ILE* 3.3 13.8 + - - +
850B ARG* 2.9 50.1 + - - +
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Residues in contact with SER 847 (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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687B LEU* 4.3 14.9 - - - +
843B GLU 3.0 19.4 + - - -
844B MET* 3.1 7.4 + - - -
846B SER* 1.3 78.1 - - - +
848B TYR* 1.3 60.6 + - - +
850B ARG* 3.4 26.0 + - - +
851B GLU* 2.9 27.9 + - - +
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Residues in contact with TYR 848 (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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687B LEU* 3.6 31.5 - - + +
691B LEU* 4.0 19.1 - - + -
736B LEU* 3.4 17.1 - - + +
737B PRO* 2.7 43.5 + - + +
820B CYS* 4.4 6.6 - - - +
823B VAL* 3.5 28.9 - - + -
824B LEU* 3.7 24.8 - - + +
827B LEU* 4.3 1.8 - - + -
844B MET* 3.1 47.2 + - + +
845B ARG* 3.2 0.6 + - - -
847B SER* 1.3 76.6 - - - +
849B ILE* 1.3 60.7 + - - +
851B GLU* 3.2 6.0 + - + +
852B LEU* 2.9 28.2 + - - +
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Residues in contact with ILE 849 (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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824B LEU* 3.8 20.4 - - + -
845B ARG* 3.0 50.3 + - + +
846B SER* 3.6 12.8 - - - +
848B TYR* 1.3 72.7 - - - +
850B ARG* 1.3 67.6 + - + +
852B LEU* 3.2 5.2 + - + +
853B ILE* 3.0 29.6 + - + +
870B PHE* 3.9 28.0 - - + -
930B PHE* 4.1 20.0 - - + -
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Residues in contact with ARG 850 (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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843B GLU 4.6 2.6 + - - -
846B SER* 2.9 36.6 + - - +
847B SER* 3.6 32.3 + - - +
849B ILE* 1.3 77.1 - - + +
851B GLU* 1.3 63.8 + - - +
853B ILE* 3.3 17.6 + - + +
854B LYS* 3.1 30.6 + - - +
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Residues in contact with GLU 851 (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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685B PRO* 3.2 29.0 - - - +
687B LEU* 3.5 40.6 + - + +
688B ILE* 3.7 19.0 - - + +
820B CYS* 3.7 10.0 - - - -
847B SER* 2.9 17.1 + - - +
848B TYR* 3.6 12.1 - - + +
849B ILE 3.1 0.6 - - - -
850B ARG* 1.3 75.5 - - - +
852B LEU* 1.3 59.8 + - - +
854B LYS* 2.8 33.2 + - - +
855B ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 852 (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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817B GLU* 3.9 22.0 - - + +
820B CYS* 3.7 15.3 - - + -
821B MET* 3.9 27.8 - - + -
824B LEU* 3.9 21.5 - - + -
848B TYR 2.9 15.9 + - - +
849B ILE* 3.4 10.1 - - - +
851B GLU* 1.3 72.3 - - - +
853B ILE* 1.3 58.2 + - - +
855B ALA* 3.2 1.4 + - - +
856B ILE* 2.9 33.4 + - + +
870B PHE* 4.5 8.3 - - + -
873B LEU* 4.3 18.4 - - + -
874B THR* 4.0 26.0 - - + -
877B LEU* 5.2 1.1 - - + -
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Residues in contact with ILE 853 (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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849B ILE* 3.0 26.8 + - + +
850B ARG* 3.4 18.2 - - + +
851B GLU 3.2 0.2 - - - -
852B LEU* 1.3 77.2 - - - +
854B LYS* 1.3 58.2 + - + +
856B ILE* 3.4 9.9 + - + +
857B GLY* 3.0 23.6 + - - -
870B PHE* 3.6 33.4 - - + -
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Residues in contact with LYS 854 (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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685B PRO* 4.0 23.8 - - + +
686B PRO* 6.1 1.4 - - - +
688B ILE* 4.7 0.7 - - - -
850B ARG* 3.1 21.3 + - - +
851B GLU* 2.8 42.1 + - - +
853B ILE* 1.3 74.6 - - + +
855B ALA* 1.3 65.1 + - - +
857B GLY* 3.1 11.7 + - - -
858B LEU* 3.3 17.8 + - - +
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Residues in contact with ALA 855 (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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688B ILE* 3.6 22.3 - - + +
814B SER* 4.9 2.1 + - - -
816B GLU* 3.7 28.4 - - + +
817B GLU* 3.9 13.7 - - - +
820B CYS* 4.2 0.2 - - - -
851B GLU 2.9 12.1 + - - +
852B LEU* 3.4 12.1 - - - +
854B LYS* 1.3 71.0 - - - +
856B ILE* 1.3 65.8 + - - +
858B LEU* 3.2 25.4 + - - +
859B ARG* 4.3 2.3 + - - +
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Residues in contact with ILE 856 (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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817B GLU* 3.8 20.2 - - + +
852B LEU* 2.9 22.5 + - + +
853B ILE* 3.5 9.2 - - - +
855B ALA* 1.3 75.8 - - - +
857B GLY* 1.3 57.7 + - - +
858B LEU 3.0 1.4 + - - -
859B ARG* 3.2 2.8 + - - +
860B GLN* 3.0 38.4 + - + +
866B SER* 3.8 15.5 - - - +
869B ARG* 3.6 26.0 - - + -
870B PHE* 3.5 46.9 - - + +
873B LEU* 3.9 13.5 - - + -
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Residues in contact with GLY 857 (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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853B ILE 3.0 14.2 + - - -
854B LYS* 3.1 7.9 + - - -
856B ILE* 1.3 75.8 - - - +
858B LEU* 1.3 61.0 + - - +
859B ARG* 3.2 1.7 + - - -
860B GLN 3.9 16.3 + - - +
861B LYS* 4.8 5.9 - - - +
866B SER* 5.2 3.4 - - - -
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Residues in contact with LEU 858 (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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683B LEU* 3.6 33.7 - - + +
684B ILE* 3.9 15.7 - - + -
685B PRO* 4.0 15.7 - - + -
688B ILE* 4.6 0.4 - - + -
816B GLU* 3.6 36.3 - - + +
854B LYS 3.3 10.7 + - - +
855B ALA* 3.3 20.9 - - - +
856B ILE 3.0 0.8 + - - -
857B GLY* 1.3 77.8 - - - +
859B ARG* 1.3 69.5 + - + +
861B LYS* 5.3 3.7 - - - +
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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
------------------------------------------------------------
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