Contacts of the helix formed by residues 814 - 827 (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 814 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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765B TRP* 3.6 2.2 - - - -
812B GLN 3.4 3.2 + - - -
813B VAL* 1.3 75.7 - - - +
815B GLN* 1.3 59.6 + - - +
816B GLU* 3.5 17.0 + - - +
817B GLU* 3.0 38.8 + - - +
818B PHE* 2.9 30.3 + - - +
855B ALA 4.9 2.8 + - - -
859B ARG* 3.7 33.2 + - - +
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Residues in contact with GLN 815 (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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692B MET* 3.0 41.2 - - + +
765B TRP* 3.5 31.2 + - + +
814B SER* 1.3 74.3 - - - +
816B GLU* 1.3 71.0 + - - +
818B PHE* 3.4 2.3 + - + +
819B LEU* 3.0 41.3 + - + +
859B ARG* 5.2 1.2 - - - +
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Residues in contact with GLU 816 (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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684B ILE* 4.1 17.7 - - + +
688B ILE* 3.7 26.3 - - + +
814B SER* 3.5 9.6 - - - +
815B GLN* 1.3 90.6 + - + +
817B GLU* 1.3 65.7 + - - +
819B LEU* 3.6 3.1 + - + +
820B CYS* 3.3 28.2 + - - -
855B ALA* 3.8 10.8 - - + +
858B LEU* 3.6 33.0 - - + +
859B ARG* 3.4 26.9 + - - -
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Residues in contact with GLU 817 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813B VAL* 3.6 5.7 - - + -
814B SER* 3.0 33.8 + - - +
816B GLU* 1.3 74.9 - - - +
818B PHE* 1.3 59.0 + - - +
820B CYS* 3.3 2.9 + - - +
821B MET* 2.9 35.4 + - - +
852B LEU* 3.9 4.4 - - + +
855B ALA* 4.0 7.1 - - + +
856B ILE* 3.8 32.4 - - + +
859B ARG* 5.8 3.5 - - - +
860B GLN* 4.6 4.3 - - - +
869B ARG* 2.7 44.9 + - - +
873B LEU* 3.5 24.9 - - + +
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Residues in contact with PHE 818 (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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695B GLU* 4.0 12.3 - - - -
761B PHE* 3.5 39.7 - + - -
762B GLY* 4.3 7.4 - - - -
765B TRP* 3.3 68.4 - + + -
808B PHE* 4.4 4.3 - + - -
813B VAL* 3.9 7.3 - - + +
814B SER 2.9 18.1 + - - +
815B GLN* 3.5 7.2 - - + +
817B GLU* 1.3 74.6 - - - +
819B LEU* 1.3 67.0 + - + +
821B MET* 3.2 6.8 + - - +
822B LYS* 2.8 62.6 + - + +
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Residues in contact with LEU 819 (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* 4.2 15.0 - - + +
691B LEU* 3.9 22.2 - - + +
692B MET* 3.7 41.3 - - + +
695B GLU* 3.5 42.6 - - + +
815B GLN* 3.0 27.8 + - + +
816B GLU* 3.9 5.4 - - + +
817B GLU 3.4 0.2 - - - -
818B PHE* 1.3 86.5 - - + +
820B CYS* 1.3 60.4 + - - +
822B LYS* 3.5 7.1 + - - +
823B VAL* 3.3 24.9 + - - +
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Residues in contact with CYS 820 (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* 3.8 12.6 - - - -
691B LEU* 4.3 11.4 - - - -
816B GLU 3.3 13.2 + - - +
817B GLU 3.3 7.9 + - - +
819B LEU* 1.3 75.4 - - - +
821B MET* 1.3 66.6 + - - +
823B VAL* 3.2 7.4 + - - +
824B LEU* 3.1 27.1 + - - +
848B TYR* 4.4 6.1 - - - +
851B GLU* 3.7 42.6 - - - -
852B LEU* 3.7 23.1 - - + +
855B ALA* 4.2 0.4 - - - -
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Residues in contact with MET 821 (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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761B PHE* 3.6 29.8 - - + -
808B PHE* 5.3 1.1 - - + -
813B VAL* 4.4 8.3 - - + -
817B GLU* 2.9 28.7 + - - +
818B PHE 3.7 0.9 - - - +
820B CYS* 1.3 75.4 - - - +
822B LYS* 1.3 63.6 + - - +
824B LEU* 3.1 6.7 + - - +
825B LEU* 3.1 24.8 + - - +
852B LEU* 3.9 17.7 - - + -
873B LEU* 3.4 51.1 - - + +
876B LEU* 4.2 17.7 - - + -
877B LEU* 3.9 25.0 - - + +
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Residues in contact with LYS 822 (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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695B GLU* 2.8 31.6 + - - -
696B PRO* 5.3 3.3 - - - +
732B TRP* 3.7 27.1 - - + -
758B LEU* 3.4 35.2 - - + +
761B PHE* 3.6 17.9 - - + -
762B GLY* 5.0 3.6 - - - +
818B PHE* 2.8 48.5 + - + +
819B LEU* 3.8 6.9 + - - +
820B CYS 3.3 0.2 - - - -
821B MET* 1.3 77.4 - - - +
823B VAL* 1.3 61.6 + - - +
825B LEU* 3.3 10.4 + - - -
826B LEU* 3.4 10.0 + - - +
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Residues in contact with VAL 823 (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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691B LEU* 3.8 18.8 - - + -
732B TRP* 3.9 13.9 - - + -
736B LEU* 3.5 36.1 - - + -
819B LEU 3.3 13.4 + - - +
820B CYS 3.2 7.8 + - - +
822B LYS* 1.3 76.3 - - - +
824B LEU* 1.3 64.3 + - - +
826B LEU* 3.2 13.7 + - - +
827B LEU* 3.3 20.4 + - + +
848B TYR* 3.5 40.2 - - + -
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Residues in contact with LEU 824 (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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820B CYS 3.1 15.8 + - - +
821B MET* 3.1 7.1 + - - +
823B VAL* 1.3 77.2 - - - +
825B LEU* 1.3 61.3 + - - +
827B LEU* 3.1 8.2 + - + +
828B ASN* 3.1 26.4 + - - +
845B ARG* 3.9 18.0 + - + +
848B TYR* 3.7 27.6 - - + +
849B ILE* 3.8 30.7 - - + -
852B LEU* 3.9 28.0 - - + -
877B LEU* 4.2 13.2 - - + -
930B PHE* 4.0 23.1 - - + -
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Residues in contact with LEU 825 (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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754B SER* 3.5 13.4 - - - -
757B SER* 3.7 26.5 + - - +
758B LEU* 3.8 9.9 - - + -
761B PHE* 3.5 42.8 - - + -
821B MET 3.1 13.2 + - - +
822B LYS 3.6 7.9 - - - +
823B VAL 3.2 0.2 - - - -
824B LEU* 1.3 73.4 - - - +
826B LEU* 1.3 65.7 + - - +
828B ASN* 3.1 34.8 + - + +
829B THR 4.9 0.2 + - - -
877B LEU* 3.8 14.8 - - + +
880B LEU* 3.6 31.2 - - + -
881B HIS* 6.5 0.2 - - + -
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Residues in contact with LEU 826 (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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729B VAL* 5.1 0.9 - - + -
732B TRP* 3.9 15.9 - - + -
733B SER* 4.9 1.3 - - - -
736B LEU* 3.4 33.2 - - + -
739B PHE* 3.6 28.3 - - + -
750B LEU* 3.7 30.5 - - - +
751B ILE* 4.0 22.0 - - + -
754B SER* 3.4 24.4 - - - +
758B LEU* 3.8 12.8 - - + +
822B LYS 3.4 8.0 + - - +
823B VAL 3.2 10.0 + - - +
825B LEU* 1.3 77.6 - - - +
827B LEU* 1.3 61.1 + - + +
828B ASN 3.6 2.1 + - - -
829B THR 5.1 0.5 - - - +
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Residues in contact with LEU 827 (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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739B PHE* 4.4 1.8 - - + -
750B LEU* 3.9 18.6 - - + -
823B VAL* 3.3 30.5 + - + +
824B LEU* 3.1 13.5 + - + +
825B LEU 3.1 1.0 - - - -
826B LEU* 1.3 85.6 - - + +
828B ASN* 1.3 54.4 + - - -
829B THR 3.5 3.8 + - - -
841B PHE* 3.3 44.2 - - + -
844B MET* 4.1 28.9 - - + -
845B ARG* 3.7 39.7 + - + +
848B TYR* 4.3 2.7 - - + -
928B LEU* 3.5 9.0 - - - +
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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