Contacts of the helix formed by residues 848 - 859 (chain B) in PDB entry 1Z00
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 ASN 848 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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842B LEU 6.0 0.7 - - - -
846B GLY 3.2 9.3 - - - +
847B VAL* 1.3 74.8 - - - +
849B ALA* 1.3 57.1 + - - +
850B LYS* 3.1 18.7 - - - +
851B ASN* 2.8 41.9 + - - +
852B CYS* 2.6 33.5 + - - +
882B ASN* 3.6 8.5 + - - +
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Residues in contact with ALA 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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842B LEU* 5.5 6.6 - - + +
848B ASN* 1.3 72.5 - - - +
850B LYS* 1.3 66.1 + - + +
852B CYS* 3.8 6.9 - - - +
853B ARG* 3.3 22.3 + - - +
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Residues in contact with LYS 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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848B ASN* 3.1 15.6 - - - +
849B ALA* 1.3 81.7 - - + +
851B ASN* 1.3 65.8 - - - +
853B ARG* 3.3 6.9 + - - +
854B SER* 3.2 24.1 + - - -
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Residues in contact with ASN 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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846B GLY 4.0 2.8 + - - -
847B VAL* 3.8 2.2 - - + -
848B ASN* 2.8 40.6 + - - +
850B LYS* 1.3 82.3 - - - +
852B CYS* 1.3 52.0 + - - +
854B SER* 3.2 8.4 + - - -
855B LEU* 2.7 38.5 + - - +
876B ILE 5.0 1.0 - - - +
877B LEU* 3.3 47.0 + - + +
879B ASN* 5.4 0.6 - - - +
882B ASN* 3.5 18.0 - - - +
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Residues in contact with CYS 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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841B LEU* 3.4 26.7 - - - +
842B LEU* 3.4 47.6 - - + -
847B VAL* 3.4 15.0 - - + +
848B ASN 2.6 23.4 + - - +
849B ALA 3.8 4.9 - - - +
851B ASN* 1.3 71.1 - - - +
853B ARG* 1.3 57.2 + - - +
855B LEU* 3.1 3.4 + - - +
856B MET* 2.8 39.8 + - - +
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Residues in contact with ARG 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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823B ASP* 2.7 41.4 + - - -
824B SER* 3.3 11.8 + - - -
825B GLU 2.7 29.7 + - - -
826B THR* 3.7 14.6 - - - +
830B SER* 6.4 1.6 - - - -
833B TYR* 5.8 0.9 - - + -
849B ALA 3.3 10.3 + - - +
850B LYS* 3.5 10.6 + - - +
851B ASN 3.2 0.2 - - - -
852B CYS* 1.3 77.3 - - - +
854B SER* 1.3 82.0 + - - +
856B MET* 3.0 29.9 - - - +
857B HIS* 3.2 35.6 + - - +
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Residues in contact with SER 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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824B SER* 4.9 6.7 + - - -
850B LYS 3.2 11.7 + - - -
851B ASN* 3.2 13.7 + - - -
853B ARG* 1.3 100.4 + - - +
855B LEU* 1.3 63.3 + - - +
857B HIS* 3.5 4.3 + - - -
858B HIS* 3.0 37.1 + - - +
876B ILE* 4.6 11.7 - - - -
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Residues in contact with LEU 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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841B LEU* 3.6 19.3 - - + -
847B VAL* 3.6 35.2 - - + -
851B ASN 2.7 21.2 + - - +
852B CYS 3.1 4.9 + - - +
854B SER* 1.3 71.7 - - - +
856B MET* 1.3 59.9 + - - +
857B HIS 3.0 1.3 - - - -
858B HIS 2.8 4.5 + - - -
859B VAL* 2.7 41.0 + - + +
865B LEU* 4.4 11.0 - - + -
873B LEU* 5.2 3.6 - - + +
876B ILE* 3.4 36.1 - - + +
877B LEU* 3.5 21.8 - - + -
886B LEU* 4.5 6.5 - - + -
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Residues in contact with MET 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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293A PHE* 3.5 34.4 - - + -
294A LEU* 3.3 21.4 - - + +
830B SER* 4.7 4.3 - - - +
833B TYR* 3.4 33.4 - - - -
838B GLN* 4.1 28.9 - - + +
841B LEU* 3.8 2.6 - - + +
842B LEU* 4.5 8.5 - - + -
852B CYS* 2.8 39.8 + - - +
853B ARG* 3.0 31.4 - - - +
855B LEU* 1.3 71.5 - - - +
857B HIS* 1.3 63.4 + - + +
859B VAL 3.4 10.3 - - - +
860B LYS 5.3 0.2 - - - +
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Residues in contact with HIS 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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294A LEU* 4.0 16.9 - - + +
297A PRO* 5.8 1.9 - - - +
824B SER 2.7 25.5 + - - +
825B GLU* 3.0 24.9 + - + +
826B THR* 5.1 1.1 - - - -
827B LEU* 4.6 7.6 - - + -
833B TYR* 2.8 37.5 + + - -
853B ARG* 3.2 41.1 + - - +
854B SER* 3.7 7.2 - - - +
855B LEU 3.0 0.6 - - - -
856B MET* 1.3 90.5 - - + +
858B HIS* 1.3 65.6 + - + +
859B VAL 4.7 0.2 - - - -
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Residues in contact with HIS 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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300A LEU* 5.3 4.9 - - - +
824B SER* 3.5 27.1 + - - -
854B SER* 3.0 28.8 + - - +
855B LEU 2.8 3.6 + - - -
857B HIS* 1.3 89.4 - - + +
859B VAL* 1.3 61.7 + - - +
860B LYS 3.8 1.2 + - - -
876B ILE* 3.7 36.5 - - + +
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Residues in contact with VAL 859 (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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293A PHE* 3.6 17.8 - - + -
300A LEU* 5.2 0.8 - - - +
855B LEU* 2.7 46.0 + - + +
856B MET 3.4 17.2 - - - +
857B HIS 4.7 0.2 - - - -
858B HIS* 1.3 75.0 - - - +
860B LYS* 1.3 66.6 + - - +
861B ASN 3.3 20.2 - - - +
864B GLU* 3.4 17.7 - - + +
865B LEU* 3.7 22.9 - - + +
868B LEU* 4.6 7.2 - - + -
876B ILE* 4.9 12.3 - - + -
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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