Contacts of the helix formed by residues 911 - 930 (chain E) in PDB entry 5ZCS
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 THR 911 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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875E HIS 4.8 11.4 - - - +
909E VAL* 3.0 12.7 + - - +
910E ARG* 1.3 80.0 - - - +
912E PRO* 1.3 62.1 - - - +
913E ASP 3.7 0.2 + - - -
914E LEU* 5.1 1.2 - - - +
915E ASP* 4.3 13.0 + - - +
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Residues in contact with PRO 912 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904E GLU* 3.5 31.5 - - + +
907E ARG* 4.3 16.1 - - + +
911E THR* 1.3 79.2 - - - +
913E ASP* 1.3 60.1 + - - +
914E LEU 3.5 0.2 - - - -
915E ASP* 4.0 6.9 - - + +
916E LYS* 3.0 29.3 + - - +
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Residues in contact with ASP 913 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904E GLU 4.1 5.7 + - - -
905E LEU* 5.4 5.4 - - - +
907E ARG 4.2 10.8 + - - +
908E ASN* 5.0 5.4 - - + -
910E ARG* 4.1 18.8 - - - +
911E THR 3.4 1.4 - - - -
912E PRO* 1.3 76.9 - - - +
914E LEU* 1.3 60.9 + - - +
916E LYS* 3.4 3.6 + - - +
917E TRP* 2.9 29.3 + - - +
961E VAL* 4.9 18.2 - - + +
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Residues in contact with LEU 914 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910E ARG 4.3 13.8 + - - +
911E THR 4.5 1.3 + - - +
913E ASP* 1.3 76.2 - - - +
915E ASP* 1.3 61.3 + - - +
917E TRP* 3.7 6.1 - - - +
918E GLU* 2.9 30.5 + - - +
961E VAL* 6.4 0.2 - - - -
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Residues in contact with ASP 915 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876E VAL* 6.4 2.2 - - - -
878E LEU* 5.5 11.2 - - + -
904E GLU* 6.1 0.7 - - + -
911E THR 4.3 11.7 + - - +
912E PRO* 3.7 9.3 + - + +
913E ASP 3.3 0.2 - - - -
914E LEU* 1.3 80.1 - - - +
916E LYS* 1.3 57.5 + - - +
918E GLU* 3.4 6.1 + - - +
919E GLU* 2.9 29.5 + - - +
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Residues in contact with LYS 916 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901E ILE* 4.2 20.4 - - + +
904E GLU* 3.8 21.0 - - + +
905E LEU* 4.2 10.8 - - + +
912E PRO 3.0 19.2 + - - +
913E ASP 3.8 3.8 - - - +
914E LEU 3.3 0.2 - - - -
915E ASP* 1.3 73.4 - - - +
917E TRP* 1.3 60.6 + - - +
919E GLU* 3.8 6.1 - - - +
920E ILE* 2.9 30.1 + - - +
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Residues in contact with TRP 917 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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913E ASP 2.9 18.0 + - - +
914E LEU* 3.7 7.6 - - - +
915E ASP 3.3 0.2 - - - -
916E LYS* 1.3 76.8 - - - +
918E GLU* 1.3 55.8 + - - +
920E ILE* 3.4 5.9 + - - +
921E LYS* 2.9 29.3 + - - +
961E VAL* 4.7 13.5 - - + +
964E ILE* 5.7 3.8 - - + -
965E ARG* 4.5 25.4 - - + +
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Residues in contact with GLU 918 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914E LEU 2.9 18.2 + - - +
915E ASP* 3.8 6.3 - - - +
917E TRP* 1.3 76.3 - - - +
919E GLU* 1.3 57.8 + - - +
921E LYS* 3.8 6.0 - - - +
922E LYS* 2.9 29.5 + - - +
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Residues in contact with GLU 919 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881E HIS* 4.7 20.0 - - + -
901E ILE* 5.8 6.5 - - + -
915E ASP 2.9 18.3 + - - +
916E LYS* 3.8 7.4 - - - +
918E GLU* 1.3 75.6 - - - +
920E ILE* 1.3 58.6 + - - +
922E LYS* 3.4 6.4 + - - +
923E LEU* 2.9 29.1 + - - +
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Residues in contact with ILE 920 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901E ILE* 6.0 6.0 - - + +
916E LYS 2.9 18.1 + - - +
917E TRP* 3.8 6.1 - - - +
919E GLU* 1.3 76.1 - - - +
921E LYS* 1.3 58.0 + - - +
923E LEU* 3.8 5.6 - - - +
924E LYS* 2.9 29.3 + - - +
947E ASN* 5.9 8.7 - - + +
951E ASP* 6.0 6.7 - - + -
965E ARG* 6.0 4.3 - - + -
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Residues in contact with LYS 921 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917E TRP 2.9 17.4 + - - +
918E GLU* 3.8 7.6 - - - +
920E ILE* 1.3 78.1 - - - +
922E LYS* 1.3 56.3 + - - +
924E LYS* 3.4 6.4 + - - +
925E ALA* 2.9 29.6 + - - +
965E ARG* 5.3 5.1 - - + +
968E CYS* 4.1 28.9 - - + +
969E VAL* 5.2 4.3 - - - +
972E LEU* 5.6 1.9 - - - +
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Residues in contact with LYS 922 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881E HIS 6.1 1.1 - - - +
882E LEU* 6.3 2.9 - - - -
885E GLN* 5.0 12.3 - - + +
918E GLU 2.9 18.5 + - - +
919E GLU* 3.8 6.7 - - - +
921E LYS* 1.3 73.4 - - - +
923E LEU* 1.3 60.0 + - - +
925E ALA* 3.8 6.3 - - - +
926E SER* 2.9 30.0 + - - -
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Residues in contact with LEU 923 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885E GLN* 5.5 5.8 - - + +
919E GLU 2.9 17.8 + - - +
920E ILE* 3.8 7.6 - - - +
921E LYS 3.3 0.2 - - - -
922E LYS* 1.3 77.5 - - - +
924E LYS* 1.3 56.1 + - - +
926E SER* 3.4 5.7 + - - -
927E LEU* 2.9 30.1 + - - +
947E ASN* 6.0 6.5 - - + -
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Residues in contact with LYS 924 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
920E ILE 2.9 17.8 + - - +
921E LYS* 3.8 7.0 - - - +
923E LEU* 1.3 75.0 - - - +
925E ALA* 1.3 59.5 + - - +
927E LEU* 3.4 6.7 + - - +
928E TRP* 2.9 31.1 + - - +
969E VAL* 5.7 8.7 - - + -
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Residues in contact with ALA 925 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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921E LYS 2.9 17.9 + - - +
922E LYS* 3.8 6.7 - - - +
923E LEU 3.3 0.2 - - - -
924E LYS* 1.3 78.6 - - - +
926E SER* 1.3 56.3 + - - +
928E TRP* 4.1 3.8 - - - +
929E ALA* 2.9 33.8 + - - +
972E LEU* 4.7 19.5 - - + -
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Residues in contact with SER 926 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885E GLN* 3.8 26.5 - - - -
922E LYS 2.9 18.3 + - - -
923E LEU* 3.8 6.5 - - - -
924E LYS 3.3 0.2 - - - -
925E ALA* 1.3 75.9 - - - +
927E LEU* 1.3 61.0 + - - +
929E ALA* 4.6 3.5 - - - +
930E LEU* 3.5 24.3 + - - +
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Residues in contact with LEU 927 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923E LEU 2.9 18.5 + - - +
924E LYS* 3.4 6.7 + - - +
925E ALA 3.3 0.2 - - - -
926E SER* 1.3 77.7 - - - +
928E TRP* 1.3 60.4 + - - +
929E ALA 3.5 0.2 - - - -
930E LEU* 3.9 14.9 - - - +
944E GLN* 5.3 13.7 - - + -
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Residues in contact with TRP 928 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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924E LYS 2.9 17.8 + - - +
925E ALA* 4.1 4.3 - - - +
927E LEU* 1.3 77.4 - - - +
929E ALA* 1.3 62.2 + - - +
930E LEU 3.3 4.0 + - - -
931E GLY* 4.6 2.8 + - - -
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Residues in contact with ALA 929 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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925E ALA 2.9 18.8 + - - +
926E SER* 4.6 3.6 - - - +
928E TRP* 1.3 76.7 - - - +
930E LEU* 1.3 59.4 + - - +
931E GLY* 3.0 7.5 + - - -
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Residues in contact with LEU 930 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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926E SER 3.5 18.9 + - - +
927E LEU* 3.9 11.2 + - - +
928E TRP 3.3 3.2 - - - -
929E ALA* 1.3 73.1 - - - +
931E GLY* 1.3 62.7 + - - +
932E ASN 3.4 2.7 - - - +
933E ILE* 3.4 35.3 - - + +
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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
------------------------------------------------------------
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