Contacts of the helix formed by residues 850 - 863 (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 GLU 850 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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846B LYS* 2.7 49.8 + - + +
847B GLN 3.4 10.5 - - - +
848B ARG 5.1 0.2 - - - -
849B LYS* 1.3 86.5 - - + +
851B SER* 1.3 62.3 + - - +
852B ARG* 4.1 19.7 - - + +
853B PHE* 3.3 23.0 + - + +
854B GLN* 3.2 16.2 + - - +
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Residues in contact with SER 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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849B LYS 3.7 3.4 + - - -
850B GLU* 1.3 70.7 - - - +
852B ARG* 1.3 57.9 + - - +
854B GLN* 3.5 8.7 - - - +
855B LEU* 2.7 42.9 + - - +
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Residues in contact with ARG 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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767B GLU 4.5 8.5 + - - -
768B ASN 4.2 16.3 + - - -
769B LEU* 4.0 26.7 - - + +
850B GLU* 4.1 18.8 - - + +
851B SER* 1.3 83.3 + - - +
853B PHE* 1.3 61.3 + - + +
855B LEU* 3.9 5.1 - - - +
856B PHE* 3.2 22.3 + - - +
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Residues in contact with PHE 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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769B LEU* 3.5 52.3 - - + -
770B MET* 3.8 33.9 - - + -
774B GLU* 4.7 0.9 - - - -
843B ILE* 4.2 17.9 - - + -
846B LYS* 3.5 63.5 - - + +
847B GLN* 4.2 3.8 - - + +
850B GLU* 3.3 25.2 + - - -
851B SER 3.3 0.2 - - - -
852B ARG* 1.3 78.0 - - + +
854B GLN* 1.3 66.3 + - - +
856B PHE* 3.4 1.4 + - - +
857B MET* 3.0 37.4 + - + +
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Residues in contact with GLN 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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847B GLN* 3.4 42.2 + - - +
848B ARG* 5.3 0.3 - - - -
850B GLU 3.2 16.0 + - - +
851B SER* 3.5 10.5 - - - +
853B PHE* 1.3 78.1 - - - +
855B LEU* 1.3 65.9 + - - +
857B MET* 3.9 1.1 - - - +
858B GLN* 3.0 54.9 + - - +
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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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851B SER* 2.7 25.9 + - - +
852B ARG* 3.9 5.4 - - - +
854B GLN* 1.3 74.8 - - - +
856B PHE* 1.3 63.1 + - - +
858B GLN* 3.3 13.7 - - - +
859B GLU* 3.1 32.3 + - + +
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Residues in contact with PHE 856 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759B ILE 4.8 1.6 - - - -
760B PHE* 4.3 3.1 - + - -
763B ARG* 3.6 37.3 + - + +
764B MET* 3.6 48.0 - - + -
767B GLU* 3.6 28.9 - - + -
769B LEU* 3.9 27.1 - - + -
852B ARG 3.2 15.8 + - - +
853B PHE 3.7 4.3 - - - +
854B GLN 3.3 0.2 - - - -
855B LEU* 1.3 80.4 - - - +
857B MET* 1.3 66.4 + - - +
859B GLU* 3.2 7.6 + - - +
860B ALA* 2.9 36.9 + - + +
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Residues in contact with MET 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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760B PHE* 4.1 24.0 - - - -
764B MET* 3.6 27.4 - - + -
769B LEU* 4.8 3.6 - - + -
843B ILE* 3.7 31.9 - - + -
847B GLN* 3.7 33.9 - - + +
853B PHE* 3.0 27.4 + - + +
854B GLN* 4.0 1.8 - - - +
856B PHE* 1.3 78.3 - - + +
858B GLN* 1.3 57.1 + - - +
860B ALA* 4.2 2.5 - - - -
861B GLU* 2.8 49.1 + - - +
871B LEU* 4.0 9.6 - - + -
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Residues in contact with GLN 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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854B GLN* 3.0 45.9 + - - +
855B LEU* 3.3 15.1 - - - +
857B MET* 1.3 74.3 - - - +
859B GLU* 1.3 65.9 + - + +
861B GLU* 4.2 2.6 - - - +
862B SER* 3.3 25.5 + - - -
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Residues in contact with GLU 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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763B ARG* 3.7 23.3 + - - +
855B LEU* 3.1 22.1 + - + +
856B PHE* 3.6 8.5 - - - +
858B GLN* 1.3 78.6 - - + +
860B ALA* 1.3 64.0 + - - +
862B SER* 3.1 20.5 + - - -
863B HIS* 3.5 6.8 + - - +
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Residues in contact with ALA 860 (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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759B ILE* 3.5 7.0 - - - +
760B PHE* 3.7 28.7 - - + -
763B ARG* 3.5 21.5 - - - +
856B PHE* 2.9 26.7 + - + +
857B MET* 4.0 2.9 - - - +
859B GLU* 1.3 76.7 - - - +
861B GLU* 1.3 63.4 + - - +
863B HIS* 3.3 15.2 + - - +
866B CYS* 3.4 15.1 - - - -
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Residues in contact with GLU 861 (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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760B PHE* 4.0 17.5 - - + -
847B GLN* 4.9 10.0 + - - +
857B MET* 2.8 40.8 + - - +
858B GLN* 4.6 2.3 - - - +
860B ALA* 1.3 75.7 - - - +
862B SER* 1.3 59.6 + - - +
863B HIS 3.3 6.3 + - - +
866B CYS* 3.9 15.8 - - - +
868B ARG* 4.4 12.0 - - - -
869B LEU 4.1 11.0 - - - +
870B GLN* 3.4 30.1 - - + +
871B LEU* 3.2 22.7 + - - +
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Residues in contact with SER 862 (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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858B GLN 3.3 16.1 + - - -
859B GLU* 3.1 18.2 + - - -
860B ALA 3.2 0.6 - - - -
861B GLU* 1.3 74.6 - - - +
863B HIS* 1.3 66.4 + - - +
864B PRO* 3.7 0.9 - - - +
868B ARG* 5.6 5.4 - - - +
3F ALA* 5.8 3.4 - - - +
5F ARG* 3.1 28.9 + - - +
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Residues in contact with HIS 863 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758B LEU* 6.4 0.2 - - - +
759B ILE* 3.9 23.8 - - + +
763B ARG* 5.5 4.5 + - - +
859B GLU 3.5 5.3 + - - +
860B ALA* 3.3 16.0 + - - +
861B GLU 3.3 2.0 - - - +
862B SER* 1.3 81.3 + - - +
864B PRO* 1.3 79.7 - - + +
865B GLN* 3.1 44.9 - - + +
866B CYS* 3.1 21.6 + - - +
867B ARG 3.9 1.4 + - - -
868B ARG 4.9 0.2 + - - -
3F ALA* 4.5 16.3 - - + +
5F ARG* 4.3 0.9 + - - -
52F GLN* 5.3 14.9 - - + +
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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