Contacts of the helix formed by residues 878 - 898 (chain A) in PDB entry 4XEK
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 878 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873A LEU* 5.7 0.3 - - - +
874A ASP 4.6 4.4 - - - +
875A ARG* 3.1 54.8 + - - +
876A THR 3.4 0.6 + - - -
877A ASP* 1.3 74.3 - - - +
879A LEU* 1.3 55.2 + - - +
880A VAL* 3.3 5.9 + - - +
881A TYR* 3.0 27.7 + - + +
882A LEU* 3.0 28.1 + - - +
991A LEU* 5.2 0.7 - - - +
995A ASP* 4.4 1.0 - - - +
998A LYS* 3.1 31.5 + - - +
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Residues in contact with LEU 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877A ASP 3.2 9.2 + - - +
878A ASP* 1.3 70.5 + - - +
880A VAL* 1.3 66.1 + - + +
882A LEU* 3.4 17.8 + - + -
883A ASN* 3.0 42.6 + - - +
923A SER* 3.6 27.1 - - - +
926A ASP* 5.4 5.4 - - + +
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Residues in contact with VAL 880 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A ASP* 3.3 7.7 + - - +
879A LEU* 1.3 76.5 - - + +
881A TYR* 1.3 58.3 + - - +
883A ASN* 3.2 2.3 + - - +
884A VAL* 2.8 37.4 + - + +
920A LEU* 3.8 6.9 - - + +
923A SER* 3.7 35.2 - - - +
924A VAL* 3.9 17.0 - - + -
927A LEU* 4.1 21.3 - - + -
990A LEU* 5.5 0.7 - - + -
991A LEU* 4.4 8.5 - - + -
994A VAL* 4.1 29.8 - - + -
998A LYS* 4.9 0.7 - - - +
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Residues in contact with TYR 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A ARG* 3.2 60.3 - - + +
878A ASP* 3.0 31.0 + - - +
880A VAL* 1.3 74.6 - - - +
882A LEU* 1.3 70.5 + - + +
884A VAL* 3.3 2.1 + - - +
885A MET* 3.0 50.6 + - + +
991A LEU* 3.7 26.4 - - + +
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Residues in contact with LEU 882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A ASP 3.0 16.7 + - - +
879A LEU* 3.6 19.1 - - + +
881A TYR* 1.3 83.2 - - + +
883A ASN* 1.3 69.1 + - - +
885A MET* 3.3 4.4 + - - +
886A GLU* 3.0 44.5 + - + +
919A LYS* 6.1 0.2 - - - +
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Residues in contact with ASN 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A LEU* 3.0 34.4 + - - +
880A VAL 3.8 3.1 - - - +
882A LEU* 1.3 87.8 - - - +
884A VAL* 1.3 66.1 + - - +
886A GLU* 3.7 6.6 - - - +
887A LEU* 3.0 24.4 + - - +
916A THR* 4.8 4.3 - - - +
919A LYS* 3.6 32.0 + - - +
920A LEU* 3.8 29.9 - - + +
923A SER* 3.3 23.0 + - - -
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Residues in contact with VAL 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A VAL* 2.8 27.0 + - + +
881A TYR* 3.3 5.4 + - - +
883A ASN* 1.3 74.6 - - - +
885A MET* 1.3 64.0 + - - +
887A LEU* 3.2 4.8 + - - +
888A VAL* 2.9 33.8 + - + +
920A LEU* 3.6 26.5 - - + -
987A ALA* 3.7 36.1 - - + +
988A LYS* 4.3 4.0 - - + +
990A LEU* 5.3 1.1 - - + -
991A LEU* 4.0 31.9 - - + +
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Residues in contact with MET 885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881A TYR* 3.0 55.5 + - + +
882A LEU* 3.9 4.3 - - - +
884A VAL* 1.3 89.5 - - - +
886A GLU* 1.3 57.9 + - - +
888A VAL* 3.4 20.6 + - + +
889A ARG* 2.9 47.4 + - + +
988A LYS* 6.0 2.9 - - - -
991A LEU* 4.9 5.2 - - - -
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Residues in contact with GLU 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882A LEU* 3.0 36.2 + - + +
883A ASN* 3.7 7.5 - - - +
885A MET* 1.3 74.1 - - - +
887A LEU* 1.3 58.6 + - - +
889A ARG* 3.3 8.5 + - + +
890A ALA* 2.8 29.0 + - + +
916A THR* 3.5 25.9 - - + +
919A LYS* 2.9 32.7 + - - -
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Residues in contact with LEU 887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883A ASN 3.0 17.8 + - - +
884A VAL* 3.5 4.9 - - - +
886A GLU* 1.3 74.8 - - - +
888A VAL* 1.3 66.4 + - - +
890A ALA* 3.2 1.6 + - - +
891A VAL* 3.0 24.7 + - + +
913A VAL* 3.6 28.5 - - + +
916A THR* 3.0 31.8 + - - +
917A LEU* 4.0 22.4 - - + +
920A LEU* 3.8 18.2 - - + -
946A LEU* 5.0 0.4 - - + -
983A LEU* 4.6 16.4 - - + +
984A ALA* 5.5 0.7 - - - -
987A ALA* 3.8 24.7 - - + -
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Residues in contact with VAL 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A VAL* 2.9 32.7 + - + +
885A MET* 3.8 21.3 - - + +
887A LEU* 1.3 74.2 - - - +
889A ARG* 1.3 59.0 + - + +
891A VAL* 3.1 4.7 + - + +
892A LEU* 2.9 42.5 + - + +
984A ALA* 4.2 37.5 - - + +
987A ALA* 4.8 2.0 - - + -
988A LYS* 5.3 5.2 - - + +
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Residues in contact with ARG 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A MET* 2.9 41.1 + - + +
886A GLU* 3.6 8.0 - - - +
888A VAL* 1.3 78.1 - - + +
890A ALA* 1.3 57.1 + - - +
892A LEU* 3.1 19.7 + - + +
893A GLU* 2.9 27.7 + - - +
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Residues in contact with ALA 890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886A GLU 2.8 20.8 + - - +
887A LEU 3.2 5.1 + - - +
889A ARG* 1.3 73.3 - - - +
891A VAL* 1.3 63.0 + - - +
893A GLU* 3.2 8.8 + - - +
894A LEU* 3.0 22.9 + - - +
909A VAL 5.3 0.3 - - - +
912A ASN* 4.1 22.6 + - - +
913A VAL* 4.0 17.3 - - + +
916A THR* 4.2 17.5 - - + +
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Residues in contact with VAL 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A LEU* 3.0 19.0 + - + +
888A VAL 3.1 8.0 + - - +
890A ALA* 1.3 76.8 - - - +
892A LEU* 1.3 62.0 + - + +
894A LEU* 3.3 4.7 + - - +
895A LYS* 2.9 39.3 + - + +
913A VAL* 4.4 24.0 - - + -
980A SER* 3.5 44.9 - - - +
981A HIS* 4.3 1.8 - - - +
983A LEU* 4.8 2.2 - - + -
984A ALA* 3.9 24.0 - - + +
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Residues in contact with LEU 892 (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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888A VAL* 2.9 30.4 + - + +
889A ARG* 3.1 23.8 + - - +
891A VAL* 1.3 78.9 - - + +
893A GLU* 1.3 57.9 + - - +
895A LYS* 3.4 18.9 + - + +
896A ASN* 2.9 43.3 + - - +
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Residues in contact with GLU 893 (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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889A ARG 2.9 12.7 + - - +
890A ALA* 3.5 11.1 - - - +
891A VAL 3.2 0.2 - - - -
892A LEU* 1.3 74.5 - - - +
894A LEU* 1.3 65.7 + - - +
896A ASN* 3.2 8.0 + - - +
897A GLU* 3.0 52.5 + - - +
909A VAL* 5.5 4.0 - - + +
912A ASN* 3.7 21.3 + - - -
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Residues in contact with LEU 894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890A ALA 3.0 13.5 + - - +
891A VAL* 3.5 8.3 - - - +
893A GLU* 1.3 76.7 - - - +
895A LYS* 1.3 63.9 + - - +
897A GLU* 3.8 0.6 - - - -
898A LEU* 3.1 40.8 + - + +
909A VAL* 3.9 50.4 - - + +
910A VAL* 4.1 15.3 - - + -
913A VAL* 4.1 12.3 - - + -
953A LEU* 4.3 12.8 - - + -
976A MET* 4.7 8.3 - - + +
977A LEU* 4.0 15.3 - - + -
980A SER* 3.9 22.4 - - - +
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Residues in contact with LYS 895 (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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891A VAL* 2.9 33.8 + - + +
892A LEU* 3.7 18.1 - - + +
894A LEU* 1.3 77.1 - - - +
896A ASN* 1.3 65.2 + - - +
897A GLU 3.6 0.2 + - - -
898A LEU* 4.0 4.7 + - - +
899A SER 5.2 0.9 + - - -
977A LEU* 3.7 34.7 - - + +
980A SER* 3.8 15.3 - - - +
981A HIS* 3.1 39.4 + - + +
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Residues in contact with ASN 896 (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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892A LEU* 2.9 29.9 + - - +
893A GLU* 3.7 7.2 - - - +
894A LEU 3.2 0.2 - - - -
895A LYS* 1.3 81.0 - - - +
897A GLU* 1.3 60.7 + - + +
898A LEU 3.8 0.3 + - - -
899A SER* 4.5 8.8 + - - -
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Residues in contact with GLU 897 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A GLU* 3.0 40.4 + - - +
894A LEU 4.5 1.3 - - - +
896A ASN* 1.3 78.8 - - + +
898A LEU* 1.3 62.9 + - - +
899A SER 3.4 1.6 - - - -
900A GLN* 3.8 7.8 + - + +
901A LEU* 3.2 25.8 + - + +
909A VAL* 3.6 24.5 - - + +
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Residues in contact with LEU 898 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A LEU* 3.1 22.3 + - + +
895A LYS 4.0 3.3 + - - +
896A ASN 3.5 1.6 - - - -
897A GLU* 1.3 76.5 - - - +
899A SER* 1.3 67.3 + - - +
901A LEU* 3.3 17.3 + - + +
906A TYR* 3.8 29.8 - - + -
909A VAL* 5.1 7.6 - - + -
973A LYS* 3.7 40.1 - - + +
976A MET* 4.1 27.1 - - + -
977A LEU* 3.6 31.4 - - + -
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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