Contacts of the helix formed by residues 1018 - 1026 (chain A) in PDB entry 3H0G
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 THR1018 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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877A ASP* 6.1 0.2 - - - -
879A LEU* 6.3 0.9 - - + -
1000A LEU* 4.3 6.5 + - - +
1002A ILE* 3.7 22.2 - - + -
1014A GLN* 3.1 25.5 + - - +
1017A ALA* 1.3 89.8 - - - +
1019A LEU* 1.3 56.9 + - - +
1020A LEU* 3.2 3.6 - - - -
1021A PHE* 3.0 21.5 + - + +
1022A GLN* 2.8 42.7 + - - +
1056A PHE* 3.8 23.6 - - + -
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Residues in contact with LEU1019 (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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946A CYS* 5.8 6.1 - - - +
1015A ASN 3.7 4.4 + - - +
1016A ASN* 3.6 35.6 + - + +
1017A ALA 3.7 1.0 - - - -
1018A THR* 1.3 76.4 - - - +
1020A LEU* 1.3 66.5 + - - +
1022A GLN* 3.1 28.0 + - + +
1023A ILE* 3.3 20.3 + - + +
1026A ARG* 6.2 1.1 - - - +
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Residues in contact with LEU1020 (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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889A PHE* 2.9 41.6 - - + -
947A LYS* 5.7 0.2 - - - -
957A TRP* 5.4 9.4 - - + -
959A LEU* 3.8 21.8 - - + -
1018A THR 3.2 1.0 - - - -
1019A LEU* 1.3 76.8 - - - +
1021A PHE* 1.3 56.8 + - - +
1022A GLN 2.6 15.6 + - - -
1023A ILE* 3.0 34.5 - - + +
1024A LEU 3.7 0.5 + - - -
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Residues in contact with PHE1021 (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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959A LEU* 4.0 18.9 - - + +
960A PRO* 2.9 48.2 - - + -
961A VAL* 4.1 14.4 - - + -
963A VAL* 4.2 16.4 - - + -
1000A LEU* 3.8 14.1 - - + -
1018A THR* 3.0 16.0 + - + +
1020A LEU* 1.3 77.4 - - - +
1022A GLN* 1.3 61.6 + - + +
1024A LEU* 3.3 19.5 - - + +
1025A LEU* 3.5 28.0 + - + +
1052A VAL* 4.4 9.4 - - + -
1056A PHE* 3.6 36.8 - + + -
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Residues in contact with GLN1022 (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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997A ILE* 3.5 24.2 - - + +
1000A LEU* 5.8 4.0 - - + -
1015A ASN* 2.8 31.7 + - - +
1018A THR* 2.8 35.9 + - - +
1019A LEU* 3.2 14.3 - - + +
1020A LEU 2.6 5.5 + - - -
1021A PHE* 1.3 75.5 - - + +
1023A ILE* 1.3 57.6 + - - +
1024A LEU 2.9 4.9 - - - -
1025A LEU* 2.8 28.6 + - - +
1026A ARG* 3.2 44.8 + - - +
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Residues in contact with ILE1023 (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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889A PHE* 3.3 30.0 - - + -
891A SER* 5.0 2.1 + - - +
943A GLU* 3.2 47.3 - - + +
946A CYS 5.6 3.4 - - - +
947A LYS* 3.4 25.6 - - + +
1019A LEU* 3.3 26.2 - - + +
1020A LEU* 3.0 27.6 - - + +
1022A GLN* 1.3 74.9 - - - +
1024A LEU* 1.3 52.1 + - - +
1026A ARG* 3.6 2.6 + - - +
1027A SER* 2.6 30.1 + - - -
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Residues in contact with LEU1024 (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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887A GLN* 3.7 23.1 - - + -
888A VAL 4.1 9.4 - - - +
889A PHE* 3.7 34.3 - - + -
890A ASP 5.6 0.2 - - - +
959A LEU* 3.3 27.8 - - + -
961A VAL 5.9 0.2 - - - +
963A VAL* 4.6 11.9 - - + -
1021A PHE* 3.3 16.3 + - + +
1022A GLN 2.9 0.8 + - - -
1023A ILE* 1.3 79.5 - - - +
1025A LEU* 1.3 60.3 + - + +
1026A ARG 3.1 0.9 - - - -
1027A SER* 2.4 29.5 + - - +
1028A LYS* 2.9 47.0 + - - +
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Residues in contact with LEU1025 (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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963A VAL* 4.1 16.4 - - + -
993A LEU* 3.0 33.7 - - + +
996A LEU 5.1 2.5 - - - +
997A ILE* 4.2 17.3 - - + -
1000A LEU* 4.0 14.8 - - + -
1021A PHE* 3.5 37.0 - - + +
1022A GLN* 2.8 11.2 + - + +
1024A LEU* 1.3 77.9 - - + +
1026A ARG* 1.3 58.7 + - + +
1027A SER 3.4 1.1 - - - -
1029A PHE* 3.5 42.4 - - + +
1049A MET* 6.2 2.9 - - + -
1052A VAL* 4.4 16.4 - - + -
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Residues in contact with ARG1026 (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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903A TYR* 4.7 0.5 - - - -
939A VAL* 3.9 21.8 - - - +
940A ALA* 4.2 17.1 - - + +
943A GLU* 2.8 38.2 + - - +
993A LEU* 4.3 15.7 - - + -
994A ASN* 5.9 1.2 + - - -
997A ILE* 3.4 22.3 - - + +
1019A LEU* 6.2 1.2 - - - +
1022A GLN* 3.2 49.8 + - - +
1023A ILE* 3.6 2.9 + - - +
1024A LEU 3.1 1.0 - - - -
1025A LEU* 1.3 81.3 - - + +
1027A SER* 1.3 58.9 + - - +
1028A LYS 3.8 0.4 - - - -
1030A ALA* 3.1 27.5 - - - +
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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