Contacts of the helix formed by residues 839 - 855 (chain A) in PDB entry 4YOZ
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 HIS 839 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A GLU* 3.4 45.2 + - + -
565A SER* 4.2 11.4 - - - -
835A MET* 3.8 7.6 - - - +
838A ARG* 1.3 74.2 - - - +
840A LEU* 1.3 67.2 + - - +
841A ASP* 2.9 54.8 + - + +
842A GLN* 2.8 47.1 + - - +
843A LEU* 3.7 4.0 + - - +
868A TYR* 4.1 4.9 - - - -
873A GLN* 4.9 3.2 + - + +
877A HIS* 5.0 8.5 - + + -
878A VAL* 4.1 21.6 - - + +
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Residues in contact with LEU 840 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563A LEU 4.2 9.2 - - - +
564A GLU* 2.7 29.4 + - + +
568A TRP* 4.1 13.5 - - + +
795A VAL* 4.0 39.3 - - + +
798A LEU* 4.5 14.6 - - + -
799A ALA* 4.3 12.8 - - + +
802A ARG* 5.0 2.7 - - - +
824A PHE* 3.9 17.3 - - + -
828A LEU* 4.4 3.4 - - + -
835A MET* 3.5 26.1 - - + +
839A HIS* 1.3 72.2 + - - +
841A ASP* 1.3 65.2 + - - +
843A LEU* 3.3 7.6 + - - +
844A LEU* 3.2 18.6 + - + +
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Residues in contact with ASP 841 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A ARG* 2.8 30.4 + - - -
839A HIS* 2.9 23.3 + - - +
840A LEU* 1.3 77.8 - - - +
842A GLN* 1.3 60.5 + - - +
844A LEU* 3.7 12.3 - - + +
845A LEU* 2.9 37.1 + - - +
868A TYR* 2.5 42.7 + - + +
873A GLN* 3.2 20.2 + - - +
878A VAL* 4.2 1.8 - - + -
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Residues in contact with GLN 842 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838A ARG* 3.5 12.5 - - + +
839A HIS* 2.8 43.1 + - + +
841A ASP* 1.3 79.5 - - - +
843A LEU* 1.3 67.0 + - + +
845A LEU* 3.7 1.0 + - - +
846A CYS* 3.2 31.2 + - - -
877A HIS* 5.7 0.8 + - - -
878A VAL* 2.7 39.0 + - + +
881A SER 3.8 8.3 + - - -
882A VAL* 3.5 25.9 - - + +
883A LEU 5.4 0.2 + - - -
927A ARG* 5.3 2.4 - - - +
930A LEU* 3.8 22.8 - - + +
933A PHE* 4.9 3.6 - - + -
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Residues in contact with LEU 843 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824A PHE* 4.0 12.5 - - + -
827A THR* 3.8 28.6 + - - +
828A LEU* 4.4 7.6 - - + -
831A CYS 5.2 0.2 - - - +
834A LEU* 4.1 31.6 - - + +
835A MET* 3.6 35.9 - - + -
838A ARG* 5.0 2.2 - - - -
839A HIS 3.7 3.1 + - - +
840A LEU 3.3 8.3 + - - +
841A ASP 3.3 0.2 - - - -
842A GLN* 1.3 81.8 - - + +
844A LEU* 1.3 60.8 + - - +
846A CYS* 3.9 5.0 - - - +
847A ALA* 3.0 28.9 + - - +
933A PHE* 4.2 21.3 - - + -
938A TYR* 4.2 11.1 + - + -
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Residues in contact with LEU 844 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799A ALA* 3.7 25.6 - - + +
802A ARG* 4.0 13.7 - - + -
803A LEU* 3.9 42.0 - - + +
806A LEU* 4.7 11.7 - - + -
820A ILE* 4.5 2.4 - - + +
821A TRP* 5.2 0.4 - - + -
824A PHE* 3.8 37.4 - - + -
840A LEU* 3.2 13.6 + - + +
841A ASP* 3.2 17.5 + - - +
843A LEU* 1.3 78.4 - - - +
845A LEU* 1.3 60.9 + - + +
847A ALA* 3.4 3.0 + - - +
848A PHE* 3.0 26.2 + - - +
868A TYR* 6.6 0.2 - - + -
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Residues in contact with LEU 845 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806A LEU* 3.5 30.3 - - + -
841A ASP* 2.9 22.4 + - + +
842A GLN* 4.2 0.7 - - - +
844A LEU* 1.3 74.4 - - + +
846A CYS* 1.3 66.1 + - - +
848A PHE* 3.2 13.2 + - - +
849A TYR* 3.2 10.7 + - - +
861A PHE* 3.6 10.1 - - + -
864A ILE* 3.7 22.6 - - + +
865A MET* 4.4 9.4 - - + -
868A TYR* 3.8 44.9 - - + -
878A VAL* 5.3 2.0 - - + -
879A TYR* 4.9 3.4 - - + -
930A LEU* 3.7 28.5 - - + -
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Residues in contact with CYS 846 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842A GLN 3.2 24.0 + - - +
843A LEU 3.9 0.7 - - - +
845A LEU* 1.3 76.3 - - - +
847A ALA* 1.3 64.6 + - - +
849A TYR* 3.4 1.2 + - - +
850A ILE* 3.1 27.4 + - - +
861A PHE* 3.7 21.3 - - - -
930A LEU* 4.0 9.6 - - - -
933A PHE* 3.7 28.9 - - - -
934A TYR* 4.1 13.9 - - + -
938A TYR* 3.7 29.9 - - + -
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Residues in contact with ALA 847 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820A ILE* 3.8 22.6 - - + +
823A CYS* 4.3 2.2 - - - -
824A PHE* 3.9 21.3 - - + +
843A LEU 3.0 19.3 + - - +
844A LEU 3.5 6.3 - - - +
846A CYS* 1.3 75.5 - - - +
848A PHE* 1.3 63.3 + - - +
850A ILE* 3.6 2.6 - - - +
851A MET* 3.2 30.1 + - - +
938A TYR* 3.3 15.4 + - - +
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Residues in contact with PHE 848 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803A LEU* 3.8 14.4 - - + -
806A LEU* 4.0 28.3 - - + -
807A CYS* 3.8 20.4 - - - -
810A LEU* 3.5 25.1 - - + -
812A VAL* 3.6 28.3 - - + -
820A ILE* 3.6 27.4 - - + +
844A LEU 3.0 12.7 + - - +
845A LEU* 3.3 13.9 - - - +
846A CYS 3.2 0.2 - - - -
847A ALA* 1.3 77.9 - - - +
849A TYR* 1.3 57.4 + - - +
852A ALA* 2.9 35.6 + - + +
859A ARG* 4.6 11.2 - - + -
864A ILE* 3.6 22.9 - - + -
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Residues in contact with TYR 849 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845A LEU 3.2 2.4 + - - +
846A CYS 4.1 0.2 - - - +
848A PHE* 1.3 75.7 - - - +
850A ILE* 1.3 59.4 + - - +
852A ALA* 3.2 3.6 + - - +
853A LYS* 2.4 87.3 + - + +
858A GLU* 6.0 2.2 - - + -
859A ARG 3.1 27.1 - - - -
860A THR* 4.2 1.1 - - - -
861A PHE* 3.3 46.7 - + + -
864A ILE* 3.6 15.3 - - + -
934A TYR* 3.7 22.9 - + - -
24B CYS* 3.9 19.9 - - + +
25B TYR 5.0 0.2 + - - -
26B GLU* 3.6 20.8 + - - +
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Residues in contact with ILE 850 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823A CYS* 3.9 11.9 - - - -
846A CYS 3.1 19.5 + - - +
847A ALA 3.6 6.1 - - - +
849A TYR* 1.3 78.4 - - - +
851A MET* 1.3 76.7 + - + +
853A LYS* 3.5 3.4 - - - +
854A VAL* 3.0 35.4 + - - +
934A TYR* 3.2 30.3 - - + +
938A TYR* 3.9 18.8 - - + -
939A VAL* 4.8 6.7 - - + -
942A VAL* 4.7 4.5 - - + -
943A LYS* 4.6 9.0 - - - -
946A ALA* 3.9 20.0 - - + -
22B LEU* 4.1 22.4 - - + -
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Residues in contact with MET 851 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816A LEU* 3.7 7.2 - - + -
819A LYS* 3.5 25.4 - - - +
820A ILE* 3.6 17.3 - - + -
823A CYS* 3.5 35.4 - - + -
847A ALA 3.2 18.5 + - - +
849A TYR 3.2 0.2 - - - -
850A ILE* 1.3 88.3 - - + +
852A ALA* 1.3 56.6 + - - +
854A VAL* 3.7 10.3 - - + -
855A THR* 2.7 40.2 + - - +
945A PHE* 4.6 4.0 - - + -
946A ALA* 3.3 41.5 - - + -
949A TYR* 4.8 13.7 - - - -
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Residues in contact with ALA 852 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816A LEU* 3.7 25.9 - - + +
848A PHE* 2.9 28.4 + - + +
849A TYR* 3.7 4.7 - - - +
851A MET* 1.3 75.2 - - - +
853A LYS* 1.3 62.1 + - - +
855A THR* 3.4 0.4 + - - -
856A LYS 3.2 1.4 + - - -
857A GLU 3.0 12.1 + - - +
858A GLU* 3.0 22.6 + - - -
859A ARG* 3.8 24.7 - - + +
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Residues in contact with LYS 853 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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849A TYR* 2.4 67.8 + - + +
850A ILE 3.5 6.7 - - - +
852A ALA* 1.3 71.6 - - - +
854A VAL* 1.3 58.4 + - - +
856A LYS* 2.9 28.1 + - - +
858A GLU* 3.4 24.1 - - + +
934A TYR* 4.3 0.7 - - - +
21B ASP 3.2 25.8 - - - -
22B LEU* 3.7 23.8 - - + +
23B TYR 3.7 12.2 + - - -
25B TYR* 5.9 1.0 - - - -
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Residues in contact with VAL 854 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850A ILE 3.0 18.6 + - - +
851A MET* 3.3 26.7 - - + +
853A LYS* 1.3 77.5 - - - +
855A THR* 1.3 69.1 + - + +
856A LYS* 3.3 21.3 + - - +
946A ALA* 4.3 17.3 - - + +
947A LEU* 4.6 8.7 - - + +
949A TYR* 3.8 25.3 - - + +
22B LEU* 3.6 32.1 - - + -
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Residues in contact with THR 855 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816A LEU* 3.5 14.1 - - + +
819A LYS* 3.8 38.1 - - + +
851A MET* 2.7 23.4 + - - +
852A ALA* 3.4 6.9 + - - -
854A VAL* 1.3 85.4 - - + +
856A LYS* 1.3 69.2 + - - +
857A GLU* 3.2 12.5 + - - +
949A TYR* 4.8 12.1 - - + -
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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