Contacts of the helix formed by residues 1016 - 1031 (chain A) in PDB entry 6C90
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 ASN1016 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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892A MET* 5.5 0.6 - - - +
898A ASN* 4.9 5.9 - - - +
1011A ALA* 3.0 22.3 + - + +
1014A ILE* 2.9 22.8 + - + +
1015A GLY* 1.3 72.0 - - - +
1017A THR* 1.3 60.3 + - - +
1018A GLU* 3.0 15.8 + - - +
1019A LEU* 3.1 38.4 + - - +
1020A GLU* 3.1 18.5 + - - +
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Residues in contact with THR1017 (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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1015A GLY* 2.7 18.6 + - - -
1016A ASN* 1.3 71.2 - - - +
1018A GLU* 1.3 61.8 + - - +
1020A GLU* 3.9 19.5 + - - +
1021A ASN* 3.1 43.5 + - - +
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Residues in contact with GLU1018 (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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898A ASN* 3.8 39.6 + - - +
1016A ASN* 3.0 11.8 + - - +
1017A THR* 1.3 79.7 - - - +
1019A LEU* 1.3 66.5 + - + +
1021A ASN* 3.8 4.3 - - - +
1022A LYS* 3.1 28.4 + - - +
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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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892A MET* 3.6 38.1 - - + +
897A PHE* 3.8 26.2 - - + -
898A ASN* 3.7 24.5 - - - +
1011A ALA* 3.8 8.5 - - + -
1016A ASN* 3.1 25.3 + - - +
1018A GLU* 1.3 78.2 - - + +
1020A GLU* 1.3 57.8 + - - +
1022A LYS* 3.4 22.4 - - + +
1023A PHE* 2.7 56.6 + - + -
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Residues in contact with GLU1020 (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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1008A CYS* 3.6 25.0 - - + +
1011A ALA* 3.6 13.1 - - + +
1012A LYS* 3.7 42.5 - - - +
1015A GLY* 5.6 1.0 - - - -
1016A ASN 3.1 14.8 + - - +
1017A THR* 3.9 21.6 + - - +
1019A LEU* 1.3 77.2 - - - +
1021A ASN* 1.3 62.4 + - - +
1024A ALA* 2.9 31.5 + - + +
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Residues in contact with ASN1021 (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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1017A THR* 3.1 37.2 + - - +
1018A GLU* 3.8 4.1 - - - +
1020A GLU* 1.3 81.6 - - - +
1022A LYS* 1.3 57.5 + - - +
1024A ALA* 3.5 7.0 + - - +
1025A GLU* 3.0 29.2 + - - +
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Residues in contact with LYS1022 (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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897A PHE* 2.4 37.2 + - + +
898A ASN* 3.1 19.8 + - - +
900A LEU 2.8 23.5 + - - +
901A SER* 4.4 4.7 - - - +
902A ALA* 3.6 22.5 - - + +
905A ALA* 4.6 11.7 - - + -
1018A GLU* 3.1 22.6 + - - +
1019A LEU* 3.0 22.2 + - + +
1021A ASN* 1.3 74.5 - - - +
1023A PHE* 1.3 68.9 + - + +
1025A GLU* 3.1 19.2 + - - +
1026A GLY* 3.1 9.5 + - - -
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Residues in contact with PHE1023 (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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892A MET* 4.3 7.0 - - + -
897A PHE* 3.9 42.0 - + + -
905A ALA* 4.3 10.5 - - + -
909A LEU* 4.2 9.9 - - + -
1004A LEU* 3.8 28.3 - - + +
1007A MET* 3.5 53.2 - - + -
1008A CYS* 3.6 18.4 - - - -
1011A ALA* 4.6 0.4 - - + -
1019A LEU* 2.7 43.8 + - + +
1020A GLU 4.5 0.2 - - - -
1022A LYS* 1.3 76.0 - - + +
1024A ALA* 1.3 61.4 + - - +
1026A GLY* 3.2 3.9 + - - +
1027A ILE* 3.2 23.7 + - - +
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Residues in contact with ALA1024 (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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1008A CYS* 3.5 12.9 - - - -
1020A GLU* 2.9 20.2 + - + +
1021A ASN* 3.7 8.5 - - - +
1023A PHE* 1.3 77.3 - - - +
1025A GLU* 1.3 62.8 + - - +
1027A ILE* 3.2 12.3 + - + +
1028A THR* 3.0 24.8 + - - -
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Residues in contact with GLU1025 (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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902A ALA* 3.8 16.5 - - + +
903A GLU* 4.8 1.0 - - - +
1021A ASN 3.0 18.3 + - - +
1022A LYS* 3.1 8.9 + - - +
1024A ALA* 1.3 74.7 - - - +
1026A GLY* 1.3 65.1 + - - +
1028A THR* 3.2 10.2 + - - +
1029A LYS* 2.9 54.9 + - - +
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Residues in contact with GLY1026 (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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902A ALA* 3.7 9.9 - - - +
906A THR* 3.2 26.5 - - - -
974A ALA* 6.1 0.4 - - - -
1004A LEU* 4.0 4.7 - - - -
1022A LYS 3.1 12.2 + - - -
1023A PHE 3.2 4.4 + - - -
1025A GLU* 1.3 75.3 - - - +
1027A ILE* 1.3 60.4 + - - +
1029A LYS* 3.0 16.3 + - - +
1030A ILE* 3.1 19.1 + - - +
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Residues in contact with ILE1027 (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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1001A GLU* 4.2 22.0 - - + +
1004A LEU* 3.4 35.4 - - + +
1005A ARG* 3.8 29.6 - - + +
1008A CYS* 4.2 11.0 - - - -
1023A PHE 3.2 10.5 + - - +
1024A ALA* 3.2 11.2 + - + +
1026A GLY* 1.3 75.3 - - - +
1028A THR* 1.3 65.0 + - - +
1029A LYS 3.1 0.3 + - - -
1030A ILE* 3.2 8.3 + - - +
1031A LYS* 3.0 41.6 + - + +
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Residues in contact with THR1028 (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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1024A ALA 3.0 14.1 + - - -
1025A GLU* 3.2 13.3 + - - -
1027A ILE* 1.3 78.2 - - - +
1029A LYS* 1.3 62.7 + - + +
1030A ILE 3.6 0.3 + - - -
1031A LYS* 4.1 11.7 + - - +
1032A ARG* 5.5 3.6 - - - +
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Residues in contact with LYS1029 (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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902A ALA* 4.6 4.5 - - + -
903A GLU* 2.8 39.0 - - + +
974A ALA* 3.5 32.6 - - + +
975A THR* 6.1 0.2 - - - +
1025A GLU* 2.9 52.2 + - + +
1026A GLY* 3.0 7.5 + - - +
1028A THR* 1.3 83.2 - - + +
1030A ILE* 1.3 52.7 + - - +
1032A ARG* 2.7 28.4 + - - -
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Residues in contact with ILE1030 (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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906A THR* 3.9 17.5 - - + -
970A VAL* 4.9 1.6 - - + -
973A TRP* 2.9 41.2 + - + +
974A ALA* 4.1 10.5 - - + +
997A MET* 4.1 16.8 - - + +
1000A LEU* 4.1 13.5 - - + -
1001A GLU* 4.1 23.6 - - + +
1004A LEU* 3.9 24.5 - - + -
1026A GLY 3.1 13.9 + - - +
1027A ILE* 3.6 6.3 - - - +
1029A LYS* 1.3 83.1 - - - +
1031A LYS* 1.3 61.7 + - + +
1032A ARG* 3.0 9.1 + - - -
1036A PHE* 3.1 14.7 - - + -
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Residues in contact with LYS1031 (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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215A ASP 6.0 0.2 - - - -
1001A GLU* 4.0 18.2 - - + +
1027A ILE* 3.0 28.9 + - + +
1028A THR* 4.1 8.5 + - - +
1029A LYS 3.8 1.0 - - - -
1030A ILE* 1.3 73.6 - - + +
1032A ARG* 1.3 62.2 + - - +
1036A PHE* 3.6 32.8 - - + -
677B ASN* 3.3 26.4 - - - +
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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