Contacts of the helix formed by residues 1019 - 1026 (chain A) in PDB entry 2RD0
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 ILE1019 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540A LEU* 4.1 6.0 - - + +
938A LEU* 4.4 2.5 - - - -
999A ILE* 4.0 26.4 - - + +
1002A PHE* 3.8 20.4 - - + +
1003A SER* 3.1 38.1 - - - +
1006A LEU* 4.2 3.4 - - + -
1013A LEU* 4.2 14.6 - - + -
1015A SER 4.1 8.1 - - - +
1016A PHE* 3.3 35.2 - - + +
1018A ASP* 1.3 71.5 - - - +
1020A ALA* 1.3 63.0 + - - +
1021A TYR 3.3 0.7 - - - -
1022A ILE* 3.1 26.0 - - + +
1023A ARG* 3.3 9.5 + - - +
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Residues in contact with ALA1020 (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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540A LEU* 4.0 9.0 - - + -
1016A PHE 3.3 3.8 + - - +
1017A ASP* 2.9 29.4 - - + +
1018A ASP 2.9 0.6 - - - -
1019A ILE* 1.3 76.4 - - - +
1021A TYR* 1.3 57.2 + - - +
1023A ARG* 2.7 32.5 + - + +
1024A LYS* 2.8 13.8 + - - +
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Residues in contact with TYR1021 (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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909A PHE* 4.6 3.4 + + - -
910A ILE 4.6 1.8 - - - -
912A GLY* 4.1 20.9 - - - -
938A LEU* 3.1 27.1 - - + +
939A ASP* 3.1 41.5 - - + +
940A HIS* 5.8 0.7 - - - -
951A ARG* 3.6 37.3 - - - +
952A VAL 4.9 0.3 + - - -
1017A ASP 4.3 0.8 + - - -
1018A ASP 3.4 13.5 + - - +
1020A ALA* 1.3 77.0 - - - +
1022A ILE* 1.3 60.8 + - - +
1024A LYS* 2.8 36.6 + - + +
1025A THR* 2.9 35.0 + - - -
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Residues in contact with ILE1022 (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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910A ILE* 3.9 31.6 - - + +
911A LEU* 4.9 4.0 - - + -
938A LEU* 3.4 27.1 - - + -
998A PHE* 4.4 20.0 - - + -
999A ILE* 4.3 13.2 - - + +
1002A PHE* 4.7 16.8 - - + -
1019A ILE* 3.1 32.8 - - + +
1021A TYR* 1.3 75.0 - - - +
1023A ARG* 1.3 60.6 + - - +
1025A THR* 4.1 1.3 - - - -
1026A LEU* 3.3 52.6 + - + +
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Residues in contact with ARG1023 (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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538A ASP* 3.5 39.2 + - - +
540A LEU* 3.7 27.9 + - + -
541A SER* 4.7 11.0 + - - +
999A ILE* 4.6 5.8 - - + -
1019A ILE 3.3 9.5 + - - +
1020A ALA* 2.7 26.7 + - - +
1022A ILE* 1.3 72.9 - - - +
1024A LYS* 1.3 63.3 + - - +
1026A LEU* 3.6 5.3 + - - +
1027A ALA 3.4 20.6 - - - +
1028A LEU* 3.3 61.7 + - - +
1029A ASP* 4.1 4.2 - - - +
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Residues in contact with LYS1024 (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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951A ARG* 3.2 32.7 - - - +
1020A ALA 2.8 8.6 + - - +
1021A TYR* 2.8 22.9 + - + +
1023A ARG* 1.3 76.1 - - - +
1025A THR* 1.3 58.9 + - - +
1027A ALA* 2.8 28.4 + - - -
1028A LEU* 3.7 35.4 - - + +
1038A TYR* 4.0 20.0 - - + +
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Residues in contact with THR1025 (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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909A PHE* 3.4 26.9 + - + +
910A ILE* 3.3 43.3 - - + +
988A TYR* 2.9 20.8 + - - -
1021A TYR* 2.9 39.6 + - - -
1022A ILE 4.2 2.5 - - - -
1024A LYS* 1.3 77.0 - - - +
1026A LEU* 1.3 56.2 + - - +
1038A TYR* 3.8 17.3 + - - -
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Residues in contact with LEU1026 (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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910A ILE* 3.9 36.1 - - + -
988A TYR* 3.2 14.7 + - + +
991A ILE* 4.3 5.2 - - + +
992A ARG* 2.5 64.8 + - + +
995A ALA* 3.8 30.5 - - + +
998A PHE* 5.6 1.1 - - + -
999A ILE* 5.4 2.7 - - + -
1022A ILE* 3.3 40.0 + - + +
1023A ARG* 4.2 3.8 - - - +
1024A LYS 3.0 1.2 + - - -
1025A THR* 1.3 74.4 - - - +
1027A ALA* 1.3 55.9 - - - +
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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