Contacts of the helix formed by residues 1012 - 1024 (chain A) in PDB entry 1D1Z
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 SER1012 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1011A ILE* 1.3 77.1 - - - +
1013A ARG* 1.3 64.8 + - - +
1014A GLU* 3.4 9.7 + - - +
1015A THR* 3.0 29.9 + - - -
1016A GLY* 2.9 20.8 + - - -
1032A ARG* 4.2 3.8 - - - -
1035A GLU* 3.7 22.7 - - - -
2101B PRO 5.4 1.2 + - - -
2103B GLU* 4.4 15.8 + - - -
2104B LYS* 4.8 6.1 - - - +
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Residues in contact with ARG1013 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1012A SER* 1.3 71.2 - - - +
1014A GLU* 1.3 60.8 + - - +
1016A GLY 3.3 0.9 + - - -
1017A GLU* 2.8 59.2 + - - +
1032A ARG* 3.5 38.3 + - - +
1035A GLU* 2.9 22.7 + - - +
5001A SO4 4.0 18.5 + - - +
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Residues in contact with GLU1014 (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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1012A SER* 3.3 9.1 + - - +
1013A ARG* 1.3 81.6 - - - +
1015A THR* 1.3 66.3 + - - +
1017A GLU* 3.9 5.1 - - - +
1018A LYS* 2.9 64.0 + - + +
1035A GLU* 4.7 0.4 + - - -
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Residues in contact with THR1015 (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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1011A ILE* 4.1 15.7 - - + -
1012A SER* 3.0 27.1 + - - -
1014A GLU* 1.3 81.2 + - - +
1016A GLY* 1.3 62.4 + - - +
1018A LYS* 3.7 10.7 + - - +
1019A LEU* 3.0 22.7 + - - +
2099B GLN 5.1 0.2 - - - +
2100B TYR* 3.8 39.1 - - + -
2101B PRO* 3.8 26.7 + - + +
2103B GLU* 4.9 0.9 + - - -
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Residues in contact with GLY1016 (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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1011A ILE* 3.8 19.9 - - - +
1012A SER 2.9 13.5 + - - -
1013A ARG 3.8 1.8 - - - -
1015A THR* 1.3 76.4 - - - +
1017A GLU* 1.3 62.1 + - - +
1019A LEU* 3.3 4.8 + - - +
1020A LEU* 3.0 28.7 + - - +
1030A LEU* 3.8 16.0 - - - +
1032A ARG* 4.8 4.7 - - - -
1044A CYS* 6.2 1.1 - - - -
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Residues in contact with GLU1017 (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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1013A ARG* 2.8 53.1 + - + +
1014A GLU* 4.0 4.7 - - - +
1016A GLY* 1.3 69.9 - - - +
1018A LYS* 1.4 67.6 + - + +
1020A LEU* 3.2 3.9 + - + +
1021A LEU* 2.9 34.7 + - + +
1032A ARG* 4.8 5.0 + - - +
1044A CYS* 5.7 2.0 - - - -
1051A ILE* 4.1 40.9 - - + +
1053A THR* 4.3 8.1 + - - -
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Residues in contact with LYS1018 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1014A GLU* 2.9 61.7 + - + +
1015A THR* 3.7 10.2 + - - +
1017A GLU* 1.4 77.7 - - + +
1019A LEU* 1.3 64.1 + - - +
1021A LEU* 3.4 9.3 + - + +
1022A ALA* 3.0 23.9 + - - +
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Residues in contact with LEU1019 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1011A ILE* 5.1 0.9 - - + -
1015A THR 3.0 17.1 + - - +
1016A GLY* 3.6 4.9 - - - +
1018A LYS* 1.3 78.2 - - - +
1020A LEU* 1.3 63.8 + - - +
1022A ALA* 3.1 17.5 + - + +
1023A THR* 3.4 15.2 + - + +
1030A LEU* 4.0 14.4 - - + -
1102A VAL* 3.9 25.8 - - + -
1104A LYS 5.1 2.9 - - - +
2025B LEU* 3.8 39.7 - - + -
2100B TYR* 3.3 32.1 - - + +
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Residues in contact with LEU1020 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1016A GLY 3.0 17.2 + - - +
1017A GLU* 3.2 4.2 + - - +
1019A LEU* 1.3 75.2 - - - +
1021A LEU* 1.3 63.4 + - - +
1023A THR* 2.7 28.1 + - - -
1028A SER* 3.8 9.2 - - - +
1029A TYR* 3.8 32.1 - - - +
1030A LEU* 3.8 10.8 - - + -
1044A CYS* 3.5 41.3 - - + +
1045A VAL 4.2 0.9 - - - +
1046A LEU* 3.5 11.0 - - + +
1051A ILE* 3.6 27.8 - - + -
1102A VAL* 3.8 18.4 - - + -
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Residues in contact with LEU1021 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1017A GLU* 2.9 27.0 + - + +
1018A LYS* 3.9 8.3 - - + +
1020A LEU* 1.3 76.7 - - - +
1022A ALA* 1.3 63.4 + - - +
1024A GLY* 3.1 14.9 + - - -
1046A LEU* 3.8 18.3 - - + +
1049A GLY* 3.4 28.7 - - - +
1050A TYR* 5.0 0.2 - - - -
1051A ILE* 4.1 14.8 - - + -
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Residues in contact with ALA1022 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1018A LYS 3.0 14.9 + - - +
1019A LEU* 3.5 13.9 - - + +
1020A LEU 3.1 0.4 - - - -
1021A LEU* 1.3 77.3 - - - +
1023A THR* 1.3 62.7 + - + +
1024A GLY* 3.3 1.2 + - - -
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Residues in contact with THR1023 (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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1019A LEU* 3.6 18.6 - - + +
1020A LEU 2.7 17.3 + - - +
1022A ALA* 1.3 80.3 - - + +
1024A GLY* 1.3 62.4 + - - +
1025A LEU* 3.1 18.7 + - - +
1028A SER* 3.0 29.9 + - - +
1046A LEU* 3.9 0.5 - - - +
1102A VAL* 4.3 19.5 - - + -
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Residues in contact with GLY1024 (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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1020A LEU 3.7 1.6 + - - -
1021A LEU 3.1 15.5 + - - -
1022A ALA 3.2 1.3 - - - -
1023A THR* 1.3 79.4 + - - +
1025A LEU* 1.3 62.2 + - - +
1026A ASP* 4.2 1.3 + - - +
1046A LEU* 3.9 8.7 - - - -
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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