Contacts of the helix formed by residues 1018 - 1025 (chain A) in PDB entry 3E0D
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 TYR1018 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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996A ILE* 2.5 51.3 - - + +
1014A PRO* 3.9 14.2 + - - +
1015A VAL* 3.1 24.2 - - + +
1017A ARG* 1.3 82.5 - - + +
1019A PRO* 1.3 62.2 - - + +
1020A GLY* 3.1 11.3 + - - +
1021A LEU* 3.8 31.1 + - + +
1022A ARG 4.6 1.2 + - - -
1125A LEU* 5.5 17.0 - - + -
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Residues in contact with PRO1019 (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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1015A VAL 4.8 0.2 - - - +
1016A LEU* 4.6 9.0 - - + +
1017A ARG 3.4 11.7 - - - +
1018A TYR* 1.3 81.9 - - - +
1020A GLY* 1.3 62.0 + - - +
1021A LEU 3.2 1.6 - - - -
1022A ARG* 3.2 17.7 + - + +
1023A GLU* 2.9 42.0 + - + +
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Residues in contact with GLY1020 (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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1018A TYR* 3.1 6.4 - - - +
1019A PRO* 1.3 81.2 - - - +
1021A LEU* 1.3 61.5 + - - +
1023A GLU* 3.7 11.7 + - - +
1024A VAL* 3.7 18.4 + - - +
1125A LEU* 5.7 7.6 - - - -
1200A PRO* 4.4 5.3 - - - +
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Residues in contact with LEU1021 (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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1015A VAL* 5.1 14.4 - - + -
1018A TYR* 3.8 30.4 + - + +
1019A PRO 3.2 0.4 - - - -
1020A GLY* 1.3 71.8 - - - +
1022A ARG* 1.3 67.6 + - - +
1023A GLU 3.1 3.1 + - - -
1024A VAL* 3.1 8.7 + - + +
1025A ALA* 3.1 24.5 + - - +
1048A SER* 4.8 15.6 + - - +
1098A PRO* 6.1 3.8 - - + -
1100A LEU* 6.5 1.1 - - + -
1121A LEU* 5.4 12.6 - - + -
1124A VAL* 3.2 35.4 - - + -
1125A LEU* 4.9 18.3 - - + +
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Residues in contact with ARG1022 (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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1015A VAL* 4.4 21.8 - - + +
1016A LEU* 4.1 19.3 - - + -
1018A TYR 4.6 0.4 + - - +
1019A PRO* 3.2 23.3 + - + +
1021A LEU* 1.3 79.0 - - - +
1023A GLU* 1.3 66.9 + - - +
1024A VAL 3.6 0.3 + - - -
1025A ALA* 3.7 20.9 + - - +
1027A CYS 3.4 24.9 + - - -
1028A THR* 4.4 8.6 + - - +
1048A SER* 5.6 2.4 + - - -
1072A ASP* 4.2 13.3 + - - -
1073A GLU* 3.6 24.7 + - - -
1164A ARG* 4.2 3.5 + - - -
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Residues in contact with GLU1023 (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 PRO* 2.9 34.7 - - - +
1020A GLY* 3.9 7.6 - - - +
1021A LEU 3.1 0.8 + - - -
1022A ARG* 1.3 79.5 - - - +
1024A VAL* 1.3 60.9 + - - +
1132A GLU* 3.9 8.0 - - - +
1134A GLU* 4.5 5.9 - - - +
1164A ARG* 3.3 20.4 + - - +
1197A TYR* 3.0 49.8 - - + +
1199A VAL* 3.4 33.7 - - + +
1200A PRO* 5.3 0.2 - - + -
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Residues in contact with VAL1024 (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 GLY 3.8 7.6 - - - +
1021A LEU* 3.1 12.1 + - + +
1023A GLU* 1.3 73.8 - - - +
1025A ALA* 1.3 69.9 + - - +
1026A SER* 4.6 0.9 - - - -
1046A LEU* 4.2 20.0 - - + +
1100A LEU* 5.1 10.1 - - + -
1124A VAL* 6.1 4.3 - - + -
1164A ARG* 4.7 0.2 + - - -
1199A VAL* 4.8 2.2 - - - -
1200A PRO* 2.6 64.8 - - + +
1202A ARG* 4.7 13.1 + - + +
1205A PHE* 5.0 14.6 - - + -
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Residues in contact with ALA1025 (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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1021A LEU 3.1 13.3 + - - +
1022A ARG* 3.8 15.3 - - - +
1023A GLU 3.5 0.4 - - - -
1024A VAL* 1.3 81.2 - - - +
1026A SER* 1.3 57.9 + - - +
1027A CYS 3.6 11.2 - - - +
1046A LEU* 4.6 5.8 - - - +
1047A LEU* 5.5 0.2 - - - -
1048A SER* 3.6 31.9 - - - +
1100A LEU* 5.1 3.8 - - + +
1164A ARG* 2.7 31.9 + - - -
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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