Contacts of the helix formed by residues 951 - 963 (chain E) in PDB entry 1ZXE
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 MSE 951 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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806E ASN 4.7 5.8 - - - +
809E ARG* 5.0 4.7 - - + -
812E TYR* 3.0 35.7 - - + +
919E ILE* 4.0 27.6 - - + +
946E PHE* 4.1 26.0 - - + -
947E ASP* 3.5 29.0 + - + +
948E ASP 5.0 0.2 - - - -
949E ASN 3.2 0.6 - - - -
950E LYS* 1.3 80.8 - - + +
952E LYS* 1.3 63.7 + - - +
953E VAL 3.3 2.9 - - - -
954E GLU* 3.2 20.4 - - + +
955E LYS* 3.1 24.3 + - - +
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Residues in contact with LYS 952 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948E ASP* 4.3 18.0 + - - +
949E ASN* 3.0 33.9 + - - +
950E LYS 3.3 3.2 + - - +
951E MSE 1.3 75.2 - - - +
953E VAL* 1.3 58.2 + - + +
954E GLU* 4.0 0.2 + - - -
955E LYS* 4.1 3.5 - - - +
956E LYS* 3.1 33.6 + - + +
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Residues in contact with VAL 953 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809E ARG* 5.7 4.3 - - - +
813E TRP* 3.8 17.5 - - + +
952E LYS* 1.3 77.6 - - + +
954E GLU* 1.3 73.1 + - - +
955E LYS 3.1 2.0 - - - -
956E LYS* 3.5 15.6 - - + +
957E ILE* 2.7 52.4 + - + +
980E TRP* 3.6 26.0 - - + +
982E PRO* 5.0 6.3 - - + -
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Residues in contact with GLU 954 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809E ARG* 4.2 12.4 + - - +
812E TYR* 2.6 26.0 + - - +
813E TRP* 3.5 35.9 + - + -
915E PHE* 3.9 15.4 - - + -
919E ILE* 4.4 8.1 - - + -
950E LYS 4.1 2.9 - - - +
951E MSE 3.2 48.9 - - + +
952E LYS 4.0 0.3 + - - -
953E VAL* 1.3 89.5 - - - +
955E LYS* 1.3 57.8 + - - +
957E ILE* 3.9 1.1 - - - -
958E ILE* 2.9 32.4 + - - +
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Residues in contact with LYS 955 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942E PHE* 3.5 50.1 - - + +
943E PRO 5.1 1.6 + - - -
946E PHE* 3.2 42.0 + - + +
948E ASP* 2.6 42.5 + - - +
951E MSE 3.1 17.9 + - - +
952E LYS* 4.1 4.5 - - - +
953E VAL 3.1 0.2 - - - -
954E GLU* 1.3 76.6 - - - +
956E LYS* 1.3 67.3 + - - +
957E ILE 3.2 0.2 - - - -
958E ILE* 3.4 8.2 + - - +
959E ARG* 3.1 23.7 + - - +
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Residues in contact with LYS 956 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952E LYS* 3.1 24.9 + - + +
953E VAL* 3.1 17.9 + - + +
955E LYS* 1.3 80.2 - - - +
957E ILE* 1.3 62.6 + - + +
959E ARG* 3.5 7.3 + - - +
960E LEU* 3.3 22.0 + - + +
980E TRP* 3.5 56.1 - - - +
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Residues in contact with ILE 957 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813E TRP* 4.6 4.9 - - + -
816E PHE* 4.1 29.4 - - + -
915E PHE* 4.6 6.7 - - + -
953E VAL* 2.7 32.9 + - + +
954E GLU* 4.1 6.3 - - - +
956E LYS* 1.3 77.1 - - - +
958E ILE* 1.3 66.4 + - - +
960E LEU* 3.1 18.5 + - + +
961E LEU* 3.2 21.9 + - + +
975E LEU* 4.0 27.4 - - + -
980E TRP* 4.1 28.3 - - + -
981E LEU* 4.3 13.0 - - + -
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Residues in contact with ILE 958 (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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912E GLY* 3.5 14.4 - - - +
915E PHE* 3.5 17.5 - - + -
916E PHE* 3.5 44.9 - - + +
919E ILE* 3.6 19.3 - - + -
942E PHE* 4.6 7.4 - - + -
946E PHE* 5.4 0.4 - - + -
954E GLU 2.9 24.5 + - - +
955E LYS* 3.4 8.7 + - - +
957E ILE* 1.3 77.2 - - - +
959E ARG* 1.3 63.2 + - - +
961E LEU* 3.1 8.2 + - - +
962E ILE* 3.0 45.7 + - + +
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Residues in contact with ARG 959 (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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940E ILE* 3.2 49.4 - - + +
942E PHE* 3.6 24.0 - - + -
955E LYS 3.1 13.6 + - - +
956E LYS* 3.5 12.6 - - - +
957E ILE 3.1 0.2 - - - -
958E ILE* 1.3 77.8 - - - +
960E LEU* 1.3 69.9 - - - +
961E LEU 3.1 1.2 + - - -
962E ILE* 3.2 17.3 + - - +
963E ASP* 2.9 44.4 + - - +
964E HIS* 5.1 4.0 - - - +
968E LYS* 5.2 2.0 - - - +
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Residues in contact with LEU 960 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956E LYS* 3.3 11.1 + - + +
957E ILE* 3.1 14.6 + - + +
959E ARG* 1.3 90.7 - - - +
961E LEU* 1.3 58.2 + - - +
963E ASP* 4.0 6.1 - - - +
968E LYS* 3.3 27.2 - - + +
969E ARG* 3.6 7.4 - - - -
970E PRO* 3.2 41.6 - - + +
975E LEU* 5.8 0.2 - - + -
980E TRP* 3.3 37.0 - - + -
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Residues in contact with LEU 961 (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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816E PHE* 4.4 16.2 - - + -
908E MSE 3.5 30.1 - - + +
909E TYR* 3.4 10.3 - - - -
911E LEU* 4.1 16.6 - - + -
912E GLY* 3.7 27.4 - - - +
915E PHE* 5.7 0.4 - - + -
957E ILE* 3.2 17.7 + - + +
958E ILE* 3.1 6.6 + - - +
959E ARG 3.1 0.6 - - - -
960E LEU* 1.3 77.4 - - - +
962E ILE* 1.3 57.5 + - - +
963E ASP 3.2 4.9 - - - -
969E ARG* 3.1 26.6 + - - +
970E PRO* 3.8 25.6 - - + +
975E LEU* 4.0 19.3 - - + -
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Residues in contact with ILE 962 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909E TYR* 2.9 31.9 + - + +
912E GLY* 4.2 8.5 - - - +
913E ILE* 3.5 29.4 - - + -
935E LEU* 3.8 40.2 - - + +
936E ARG* 5.0 0.9 - - - +
937E SER 6.1 0.2 - - - +
942E PHE* 5.6 0.2 - - + -
958E ILE* 3.0 37.7 + - + +
959E ARG* 3.2 11.9 + - - +
961E LEU* 1.3 75.0 - - - +
963E ASP* 1.3 68.8 + - - +
964E HIS* 4.4 9.4 + - + +
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Residues in contact with ASP 963 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909E TYR* 3.5 1.0 - - - -
959E ARG* 2.9 41.7 + - - +
960E LEU* 4.0 14.3 - - + +
961E LEU 3.2 1.6 - - - -
962E ILE* 1.3 87.5 - - - +
964E HIS* 1.3 76.4 + - - +
965E ASP* 2.5 23.7 + - - +
968E LYS* 3.2 34.9 - - + +
969E ARG* 2.8 31.8 + - + -
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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