Contacts of the helix formed by residues 976 - 989 (chain A) in PDB entry 5MJ6
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 THR 976 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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782A LEU* 3.7 22.0 - - + -
974A PHE 3.8 1.2 - - - -
975A SER* 1.3 86.2 - - - +
977A LYS* 1.3 64.2 + - - +
978A THR* 3.9 3.8 - - - -
979A HIS* 3.0 23.8 + - + +
980A LEU* 3.0 18.0 + - - +
1007A ILE* 4.3 1.4 - - - +
1011A ILE* 3.4 10.3 - - - +
947B GLU* 2.9 40.4 + - - +
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Residues in contact with LYS 977 (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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976A THR* 1.3 72.1 - - - +
978A THR* 1.3 58.5 + - - +
980A LEU* 3.2 10.1 + - + +
981A SER* 2.9 38.0 + - - +
1008A GLN* 6.0 1.6 - - - +
1011A ILE* 3.3 23.1 - - + +
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Residues in contact with THR 978 (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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976A THR* 3.1 2.6 + - - -
977A LYS* 1.3 78.3 - - - +
979A HIS* 1.3 64.2 + - + +
981A SER* 3.6 6.1 + - - -
982A GLU* 3.0 21.8 + - + +
946B LYS* 4.3 24.7 + - + +
947B GLU* 3.6 26.5 + - - +
986B PHE* 4.1 31.2 - - + -
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Residues in contact with HIS 979 (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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781A LYS 5.9 1.0 + - - -
938A HIS* 5.4 1.6 + - - -
939A LEU* 4.3 8.0 - - + +
942A TRP* 6.1 0.2 - + - -
974A PHE* 3.8 54.3 - + + -
975A SER 4.8 2.2 - - - -
976A THR* 3.0 32.9 + - + +
978A THR* 1.3 76.3 - - + +
980A LEU* 1.3 61.0 + - - +
982A GLU* 3.0 24.2 + - - +
983A VAL* 2.8 35.4 + - - +
1007A ILE* 5.0 0.7 - - - -
943B ASP* 3.2 31.9 + - - -
946B LYS* 5.6 2.2 - - - -
947B GLU* 3.5 10.7 + - - +
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Residues in contact with LEU 980 (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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976A THR 3.0 13.1 + - - +
977A LYS* 3.2 17.0 + - + +
979A HIS* 1.3 76.6 - - - +
981A SER* 1.3 64.4 + - - +
983A VAL* 3.3 1.0 + - - +
984A GLN* 3.0 35.9 + - - +
1004A LEU* 3.5 42.0 - - + +
1007A ILE* 3.9 21.7 - - + +
1008A GLN* 3.7 28.7 - - + +
1011A ILE* 4.3 8.7 - - + -
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Residues in contact with SER 981 (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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977A LYS* 2.9 21.1 + - - +
978A THR* 3.9 6.0 - - - -
980A LEU* 1.3 77.2 - - - +
982A GLU* 1.3 58.0 + - - +
984A GLN* 3.7 8.8 - - - +
985A ALA* 2.9 32.1 + - - +
985B ALA* 6.5 0.2 - - - -
989B ASN* 3.5 28.3 + - - -
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Residues in contact with GLU 982 (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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942A TRP* 2.8 34.0 + - - -
946A LYS* 3.0 20.7 + - + +
978A THR* 3.0 17.6 + - + +
979A HIS* 3.0 33.0 + - - +
981A SER* 1.3 77.7 - - - +
983A VAL* 1.3 57.9 - - - +
985A ALA* 3.7 5.0 - - - +
986A PHE* 3.0 27.9 + - - +
946B LYS* 4.4 16.9 + - - +
982B GLU* 4.4 20.0 - - + +
985B ALA* 6.3 1.1 - - - -
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Residues in contact with VAL 983 (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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942A TRP* 3.8 26.9 - - + +
971A THR* 4.5 7.6 - - + -
974A PHE* 4.0 26.9 - - + -
979A HIS 2.8 19.0 + - - +
980A LEU 4.0 2.9 - - - +
982A GLU* 1.3 76.3 - - - +
984A GLN* 1.3 62.3 + - - +
986A PHE* 3.3 2.1 + - - +
987A PHE* 3.2 46.6 + - + -
1003A ALA* 5.2 3.6 - - + -
1004A LEU* 3.6 20.2 - - + -
1007A ILE* 4.0 13.5 - - + -
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Residues in contact with GLN 984 (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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980A LEU* 3.0 33.4 + - - +
981A SER* 3.7 6.9 - - - +
983A VAL* 1.3 77.4 - - - +
985A ALA* 1.3 58.4 + - - +
987A PHE* 3.3 2.1 + - - -
988A GLU* 2.9 31.0 + - + +
995A PHE* 3.7 28.6 - - + -
1004A LEU* 3.8 22.0 - - + +
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Residues in contact with ALA 985 (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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981A SER 2.9 19.2 + - - +
982A GLU* 3.7 4.9 - - - +
984A GLN* 1.3 74.0 - - - +
986A PHE* 1.3 65.7 + - - +
988A GLU* 3.5 6.8 + - - +
989A ASN* 3.2 32.1 + - - +
981B SER 6.5 0.2 - - - -
982B GLU* 6.4 0.4 - - - -
985B ALA* 4.1 25.6 - - + -
989B ASN* 6.4 0.2 - - - +
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Residues in contact with PHE 986 (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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942A TRP* 4.2 7.9 - + + -
946A LYS* 3.5 67.3 - - + -
949A TRP* 3.9 18.8 - + + -
982A GLU* 3.0 17.1 + - + +
983A VAL* 3.6 6.7 - - - +
984A GLN 3.2 0.2 - - - -
985A ALA* 1.3 76.9 - - - +
987A PHE* 1.3 94.0 + + - +
989A ASN* 3.2 14.9 + - + +
990A GLN* 3.5 41.3 + - + -
978B THR* 4.0 15.9 - - + -
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Residues in contact with PHE 987 (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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942A TRP* 3.8 21.1 - + - -
949A TRP* 3.8 25.4 - + - -
967A VAL* 3.9 31.2 - - + -
983A VAL* 3.2 42.9 + - + +
984A GLN 3.3 0.2 + - - -
986A PHE* 1.3 92.7 - + - +
988A GLU* 1.3 64.9 + - - +
990A GLN* 3.0 19.5 + - + +
991A SER 3.5 10.0 - - - +
994A THR* 4.1 11.7 - - + -
995A PHE* 3.7 14.7 + - + +
1000A VAL* 3.6 46.2 - - + -
1003A ALA* 5.5 0.9 - - + -
1004A LEU* 5.2 0.4 - - + -
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Residues in contact with GLU 988 (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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984A GLN* 2.9 18.8 + - + +
985A ALA* 3.7 8.5 - - - +
986A PHE 3.3 0.2 - - - -
987A PHE* 1.3 77.8 - - - +
989A ASN* 1.3 67.4 + - - +
990A GLN 3.2 0.9 + - - -
991A SER* 3.8 11.3 + - - -
992A GLU* 2.8 29.9 + - - +
995A PHE* 4.0 20.1 - - + -
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Residues in contact with ASN 989 (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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985A ALA* 3.2 19.4 + - - +
986A PHE* 3.2 10.6 + - + +
987A PHE 3.2 0.6 - - - -
988A GLU* 1.3 83.0 - - - +
990A GLN* 1.3 71.4 + - - +
981B SER* 3.5 34.7 + - - +
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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