Contacts of the helix formed by residues 818 - 835 (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 ASP 818 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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814B LEU* 3.2 48.8 + - + +
816B ARG 3.6 1.2 + - - -
817B PHE* 1.3 80.4 - - - +
819B GLY* 1.3 70.8 + - - +
820B PRO* 3.2 5.9 - - - +
821B ALA* 3.3 13.5 + - - +
822B ARG* 3.9 2.2 - - - -
908B ARG* 3.6 20.6 + - - -
912B GLN* 2.6 33.5 + - - +
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Residues in contact with GLY 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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818B ASP* 1.3 79.3 + - - +
820B PRO* 1.4 70.2 - - - +
822B ARG* 3.3 11.2 + - - +
823B GLU* 3.2 25.4 + - - +
912B GLN* 4.4 4.0 - - - +
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Residues in contact with PRO 820 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818B ASP 3.6 5.2 - - - +
819B GLY* 1.4 82.2 - - - +
821B ALA* 1.3 58.3 + - - +
823B GLU* 3.5 7.8 + - + +
824B GLU* 3.2 25.6 + - - +
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Residues in contact with ALA 821 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814B LEU 4.4 0.4 - - - +
815B ALA 3.2 29.4 - - - +
816B ARG* 2.9 43.5 + - - +
818B ASP 3.3 8.8 + - - +
820B PRO* 1.3 76.5 - - - +
822B ARG* 1.3 60.7 + - - +
824B GLU* 3.4 5.0 + - - +
825B LEU* 3.0 15.9 + - - +
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Residues in contact with ARG 822 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816B ARG 3.6 7.6 + - - -
817B PHE 3.6 17.0 - - - +
818B ASP 3.5 5.5 + - - -
819B GLY* 3.3 13.5 + - - +
821B ALA* 1.3 75.6 - - - +
823B GLU* 1.3 74.8 + - - +
825B LEU* 3.3 2.0 + - - +
826B GLN* 3.0 46.8 + - - +
912B GLN* 3.6 30.4 + - - +
915B GLU* 2.6 47.5 + - - +
916B ILE* 3.7 23.7 - - + +
919B TYR* 5.5 1.0 - - - +
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Residues in contact with GLU 823 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819B GLY 3.2 12.7 + - - +
820B PRO* 3.8 10.1 - - + +
821B ALA 3.4 0.2 - - - -
822B ARG* 1.3 88.5 + - + +
824B GLU* 1.3 63.0 + - - +
826B GLN* 3.5 22.3 - - - +
827B GLN* 3.0 47.7 + - - +
919B TYR* 5.6 2.1 + - - -
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Residues in contact with GLU 824 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788B ILE* 3.5 16.8 - - + +
816B ARG* 2.7 33.3 + - - -
820B PRO 3.2 15.0 + - - +
821B ALA* 3.5 10.0 - - - +
823B GLU* 1.3 75.0 - - - +
825B LEU* 1.3 63.2 + - - +
827B GLN* 3.9 3.2 - - - +
828B VAL* 3.1 33.2 + - + +
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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
----------------------------------------------------------
785B LEU* 5.7 2.2 - - + -
788B ILE* 4.1 29.2 - - + -
789B HIS* 4.7 15.0 - - + +
816B ARG* 3.9 15.7 - - - +
817B PHE* 3.8 35.9 - - + -
821B ALA 3.0 15.9 + - - +
822B ARG 3.8 3.1 - - - +
823B GLU 3.3 0.2 - - - -
824B GLU* 1.3 77.6 - - - +
826B GLN* 1.3 57.2 + - - +
828B VAL* 3.1 2.3 + - - +
829B ALA* 2.7 44.0 + - + +
878B GLU* 4.7 6.7 - - - +
882B LEU* 4.6 14.6 - - + -
885B TYR* 5.2 1.3 - - + -
916B ILE* 4.2 15.7 - - + -
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Residues in contact with GLN 826 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822B ARG* 3.0 48.4 + - - +
823B GLU* 3.5 30.6 - - - +
825B LEU* 1.3 80.2 - - - +
827B GLN* 1.3 60.4 + - - +
829B ALA* 4.5 0.4 - - - -
830B ALA* 2.9 30.7 + - - +
916B ILE* 3.8 27.6 - - + +
919B TYR* 3.2 54.5 - - + +
920B VAL* 4.1 5.6 - - - +
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Residues in contact with GLN 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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823B GLU* 3.0 36.8 + - - +
824B GLU* 3.9 3.4 - - - +
826B GLN* 1.3 80.7 - - + +
828B VAL* 1.3 62.0 + - + +
830B ALA* 3.3 4.9 + - - +
831B GLN* 3.1 29.3 + - - +
919B TYR* 4.3 17.9 + - - +
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Residues in contact with VAL 828 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781B ASN* 2.8 37.3 + - + +
784B GLU* 4.4 14.6 - - + -
785B LEU* 3.8 34.1 - - + +
788B ILE* 3.9 19.3 - - + -
824B GLU* 3.1 21.4 + - + +
825B LEU* 3.9 1.3 - - + +
827B GLN* 1.3 79.1 - - + +
829B ALA* 1.3 66.0 + - - +
831B GLN* 3.4 0.7 + - - -
832B PHE* 3.1 11.1 + - - +
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Residues in contact with ALA 829 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785B LEU* 4.6 5.4 - - + +
825B LEU* 2.7 29.7 + - + +
826B GLN* 4.5 0.2 - - - -
828B VAL* 1.3 73.3 - - - +
830B ALA* 1.3 59.2 + - - +
832B PHE* 3.2 6.3 + - - +
833B CYS* 2.9 34.8 + - - +
878B GLU* 4.5 9.4 - - + -
882B LEU* 4.4 20.9 - - + -
920B VAL* 4.2 18.8 - - + -
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Residues in contact with ALA 830 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826B GLN 2.9 23.5 + - - +
827B GLN 3.5 4.5 - - - +
828B VAL 3.3 0.2 - - - -
829B ALA* 1.3 75.1 - - - +
831B GLN* 1.3 59.9 + - - +
833B CYS* 4.3 0.2 - - - +
834B SER* 2.7 35.3 + - - -
919B TYR* 3.8 19.1 - - + -
920B VAL* 4.2 13.2 - - + +
923B ALA* 3.9 18.2 - - + +
924B VAL* 5.5 0.2 - - - +
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Residues in contact with GLN 831 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780B PRO* 3.7 29.0 - - + +
781B ASN* 3.6 32.3 + - - +
784B GLU* 5.3 0.7 - - - +
827B GLN* 3.1 15.2 + - - +
829B ALA 3.3 0.2 - - - -
830B ALA* 1.3 78.1 - - - +
832B PHE* 1.3 62.2 - - - +
834B SER* 3.8 12.7 + - - -
835B TYR* 4.6 2.8 + - - +
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Residues in contact with PHE 832 (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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753B LEU* 5.3 1.3 - - + -
756B LEU* 4.7 7.6 - - + -
777B ARG 5.5 0.9 - - - +
778B LEU 4.4 4.8 - - - +
779B PHE* 4.2 17.3 - + + -
780B PRO* 3.9 21.4 - - + +
781B ASN* 3.3 23.5 + - - +
782B LEU* 4.2 22.9 - - + -
785B LEU* 3.5 30.5 - - + -
828B VAL 3.1 11.2 + - - +
829B ALA* 3.6 7.9 - - - +
831B GLN* 1.3 79.0 - - - +
833B CYS* 1.3 61.0 + - - +
835B TYR 4.9 0.5 + - - -
836B GLN* 3.6 32.8 + - - +
875B ILE* 4.0 27.6 - - + -
878B GLU* 4.3 15.5 - - + -
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Residues in contact with CYS 833 (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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829B ALA* 2.9 19.8 + - - +
830B ALA 4.3 0.4 - - - +
832B PHE* 1.3 82.7 - - - +
834B SER* 1.3 66.4 + - - +
835B TYR 3.6 0.4 - - - -
836B GLN* 3.4 25.6 + - - +
837B SER 4.8 0.7 + - - -
878B GLU* 4.3 15.3 - - - -
879B MET* 4.1 36.6 - - + -
882B LEU* 6.0 0.9 - - - -
920B VAL* 4.0 21.3 - - + -
924B VAL* 3.4 17.0 - - + +
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Residues in contact with SER 834 (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 ALA 2.7 22.7 + - - -
831B GLN* 4.0 9.0 - - - -
832B PHE 3.5 1.4 - - - -
833B CYS* 1.3 79.7 - - - +
835B TYR* 1.3 62.5 + - - +
836B GLN 3.5 0.2 + - - -
837B SER 4.8 1.4 + - - -
838B ILE* 4.7 5.2 - - - +
923B ALA* 3.8 14.2 - - - +
924B VAL* 3.9 22.1 - - - +
927B THR* 3.3 35.3 + - - -
928B GLU* 4.7 1.2 - - - +
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Residues in contact with TYR 835 (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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777B ARG* 3.6 64.1 + - + +
780B PRO* 5.9 1.6 - - + -
831B GLN 4.6 4.4 + - - +
832B PHE 4.9 0.4 + - - -
834B SER* 1.3 80.4 - - - +
836B GLN* 1.3 53.3 + - - +
837B SER 3.4 0.7 - - - -
838B ILE* 2.8 64.6 + - + +
839B ALA* 3.1 25.2 + - + -
842B LEU* 5.8 4.2 - - + +
927B THR* 4.2 18.6 - - + -
931B HIS* 4.3 18.2 + + + -
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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