Contacts of the helix formed by residues 1011 - 1023 (chain A) in PDB entry 1MUK
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 ASP1011 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1006A PRO 3.5 12.8 - - - +
1007A PRO* 4.2 1.9 - - - +
1008A SER* 2.7 35.0 + - - +
1010A PHE* 1.3 80.2 - - - +
1012A VAL* 1.3 65.9 + - - +
1013A PRO 3.3 0.2 - - - -
1014A HIS* 3.1 12.2 + - - +
1015A LYS* 3.0 40.2 + - - +
1119A LEU* 4.5 6.7 - - + +
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Residues in contact with VAL1012 (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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978A LEU* 3.7 12.6 - - + -
1009A LEU* 2.9 22.3 + - - +
1011A ASP* 1.3 76.9 - - - +
1013A PRO* 1.3 65.6 - - + +
1015A LYS* 3.0 7.9 + - - +
1016A TRP* 2.8 64.0 + - + +
1116A VAL* 4.2 13.0 - - + -
1117A SER 3.9 4.9 - - - +
1118A GLY* 4.6 4.5 - - - -
1119A LEU* 3.6 31.9 - - + -
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Residues in contact with PRO1013 (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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971A THR* 3.7 33.0 - - + +
974A LEU* 3.6 18.6 - - + +
975A SER* 3.8 31.0 - - - +
978A LEU* 4.7 6.5 - - + -
979A MET* 6.3 0.9 - - + -
1009A LEU 3.3 9.0 - - - +
1010A PHE* 3.2 21.1 - - + +
1011A ASP 3.4 0.4 - - - -
1012A VAL* 1.3 92.1 - - + +
1014A HIS* 1.3 58.0 + - + +
1016A TRP* 3.4 4.0 + - + -
1017A TYR* 3.1 26.5 + - - +
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Residues in contact with HIS1014 (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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971A THR* 3.6 29.1 - - + +
1010A PHE 3.7 20.0 + - - -
1011A ASP* 3.1 9.2 + - - +
1013A PRO* 1.3 75.7 - - + +
1015A LYS* 1.3 67.1 + - + +
1017A TYR* 3.7 9.9 - + + +
1018A GLN* 3.0 30.2 + - - +
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Residues in contact with LYS1015 (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 ASP* 3.0 38.7 + - + +
1012A VAL* 3.4 9.4 - - - +
1014A HIS* 1.3 78.0 - - - +
1016A TRP* 1.3 62.5 + - - +
1018A GLN* 3.5 8.1 + - - +
1019A GLY* 3.1 18.7 + - - -
1118A GLY* 3.5 32.5 - - - +
1119A LEU* 4.9 7.0 - - + +
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Residues in contact with TRP1016 (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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453A SER* 3.7 17.5 - - - -
456A VAL* 3.6 38.2 + - + -
491A ILE* 3.3 30.4 - - + +
974A LEU* 3.6 46.9 - - + -
977A TYR* 4.1 17.5 - + - -
978A LEU* 3.9 23.8 - - + -
1012A VAL* 2.8 36.0 + - + +
1013A PRO* 3.7 5.4 - - + +
1015A LYS* 1.3 76.0 - - - +
1017A TYR* 1.3 66.4 + - - +
1019A GLY 3.1 1.7 + - - -
1020A ALA* 2.9 20.3 + - - +
1117A SER* 3.0 26.0 + - - -
1118A GLY* 4.5 7.0 - - - -
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Residues in contact with TYR1017 (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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483A LEU* 3.6 36.6 - - + +
484A PRO* 4.4 2.3 - - - +
485A VAL* 4.0 4.7 - - + -
967A ARG* 3.6 28.9 - - + -
970A PHE* 3.6 21.5 - + - -
971A THR* 4.2 15.5 - - - +
974A LEU* 4.2 8.9 - - + +
1013A PRO 3.1 17.7 + - - +
1014A HIS* 3.7 10.3 - + + +
1016A TRP* 1.3 76.2 - - - +
1018A GLN* 1.3 68.7 + - + +
1020A ALA* 3.1 9.0 + - - +
1021A GLN* 2.9 62.2 + - + +
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Residues in contact with GLN1018 (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 HIS* 3.0 20.9 + - - +
1015A LYS* 3.5 8.2 - - - +
1017A TYR* 1.3 83.7 - - + +
1019A GLY* 1.3 60.0 + - - +
1021A GLN* 2.9 9.5 + - + +
1022A GLU* 2.8 54.6 + - + +
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Residues in contact with GLY1019 (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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458A ALA* 4.2 8.5 - - - +
491A ILE* 4.5 8.1 - - - -
1015A LYS 3.1 8.5 + - - -
1016A TRP 3.1 7.2 + - - -
1018A GLN* 1.3 80.2 - - - +
1020A ALA* 1.3 60.4 + - - +
1022A GLU* 3.5 10.8 + - - +
1023A ALA* 3.2 23.7 + - - +
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Residues in contact with ALA1020 (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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458A ALA* 5.5 0.4 - - - -
485A VAL* 3.8 18.2 - - + -
486A LYS* 2.9 33.0 + - - +
489A THR* 4.3 14.6 - - - +
491A ILE* 3.8 23.2 - - + +
970A PHE* 4.8 3.8 - - + -
1016A TRP 2.9 12.1 + - - +
1017A TYR* 3.1 10.3 + - - +
1019A GLY* 1.3 76.0 - - - +
1021A GLN* 1.3 60.4 + - - +
1023A ALA* 3.7 5.8 + - - -
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Residues in contact with GLN1021 (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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484A PRO* 3.5 41.3 + - - +
485A VAL* 3.6 14.8 - - + -
1017A TYR* 2.9 41.7 + - + +
1018A GLN* 2.9 13.3 + - + +
1020A ALA* 1.3 75.7 - - - +
1022A GLU* 1.3 60.1 + - + +
1023A ALA 3.0 4.5 - - - -
1024A ALA* 3.0 27.9 + - - +
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Residues in contact with GLU1022 (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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954A ASN* 5.9 1.4 + - - -
956A LYS* 5.9 3.6 - - - +
1018A GLN* 2.8 41.3 + - + +
1019A GLY* 3.9 9.0 - - - +
1021A GLN* 1.3 73.7 - - + +
1023A ALA* 1.3 59.4 + - - +
1024A ALA 3.3 7.0 - - - +
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Residues in contact with ALA1023 (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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458A ALA* 4.3 18.2 - - + +
486A LYS* 3.4 33.1 + - + +
489A THR* 4.3 4.5 - - + -
1019A GLY 3.2 16.7 + - - +
1020A ALA 3.8 8.1 - - - +
1021A GLN 3.0 0.8 + - - -
1022A GLU* 1.3 75.2 - - - +
1024A ALA* 1.3 67.2 + - - +
1025A ILE* 3.9 5.0 + - - +
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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