Contacts of the helix formed by residues 976 - 989 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947A GLU* 2.8 42.5 + - - +
782B LEU* 3.9 23.8 - - + -
974B PHE 3.8 0.4 - - - -
975B SER* 1.3 83.2 - - - +
977B LYS* 1.3 64.3 + - - +
978B THR* 3.5 3.5 - - - -
979B HIS* 3.1 22.3 + - + +
980B LEU* 3.0 17.3 + - - +
1007B ILE* 4.1 0.9 - - - +
1011B ILE* 3.4 11.0 - - - +
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Residues in contact with LYS 977 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976B THR* 1.3 70.2 - - - +
978B THR* 1.3 66.9 + - - +
980B LEU* 3.2 12.5 + - + +
981B SER* 2.9 32.2 + - - +
1008B GLN* 6.0 1.3 - - - +
1011B ILE* 3.5 19.7 - - + +
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Residues in contact with THR 978 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946A LYS* 4.2 23.4 + - + +
947A GLU* 3.3 31.2 + - - +
986A PHE* 4.0 31.4 - - + -
976B THR* 3.5 2.6 + - - -
977B LYS* 1.3 80.3 - - - +
979B HIS* 1.3 62.7 + - + +
981B SER* 3.3 5.2 + - - -
982B GLU* 3.1 22.8 + - + +
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Residues in contact with HIS 979 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943A ASP* 3.2 28.6 + - - -
946A LYS* 5.4 2.0 - - - -
947A GLU* 3.3 12.6 + - - -
938B HIS* 5.3 1.8 - - - -
939B LEU* 4.2 7.9 - - + +
974B PHE* 3.5 62.8 - + + -
975B SER 4.7 0.9 - - - -
976B THR* 3.1 30.0 + - + +
978B THR* 1.3 77.0 - - + +
980B LEU* 1.3 66.9 + - - +
982B GLU* 3.1 27.0 + - - +
983B VAL* 3.0 29.1 + - - +
1007B ILE* 4.8 0.7 - - - -
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Residues in contact with LEU 980 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976B THR 3.0 14.0 + - - +
977B LYS* 3.2 19.0 + - + +
979B HIS* 1.3 76.7 - - - +
981B SER* 1.3 57.3 + - - +
983B VAL* 4.1 0.9 - - - +
984B GLN* 3.0 52.4 + - - +
1004B LEU* 3.5 41.7 - - + +
1007B ILE* 3.8 21.6 - - + +
1008B GLN* 3.5 30.7 - - + +
1011B ILE* 4.1 5.4 - - + -
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Residues in contact with SER 981 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989A ASN* 3.5 29.0 + - - +
977B LYS* 2.9 29.0 + - - +
978B THR* 3.7 5.8 - - - -
980B LEU* 1.3 74.1 - - - +
982B GLU* 1.3 60.2 + - - +
984B GLN* 3.6 15.2 + - - +
985B ALA* 2.8 32.3 + - - +
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Residues in contact with GLU 982 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946A LYS* 4.2 17.6 + - - +
982A GLU* 4.4 17.2 - - + +
985A ALA* 6.4 0.4 - - - -
942B TRP* 2.9 23.3 + - - +
946B LYS* 2.6 34.8 + - + +
978B THR* 3.1 13.0 + - + +
979B HIS* 3.1 35.5 + - - +
981B SER* 1.3 75.0 - - - +
983B VAL* 1.3 51.7 + - - +
985B ALA* 3.1 6.8 + - - +
986B PHE* 2.8 34.8 + - + +
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Residues in contact with VAL 983 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942B TRP* 3.9 27.8 - - + +
971B THR* 4.3 7.2 - - + -
974B PHE* 4.1 17.0 - - + -
979B HIS 3.0 15.9 + - - +
980B LEU 4.1 0.7 - - - +
982B GLU* 1.3 71.1 - - + +
984B GLN* 1.3 67.8 + - - +
986B PHE* 3.3 0.9 + - - +
987B PHE* 3.2 45.0 + - + -
1000B VAL* 5.6 0.2 - - + -
1003B ALA* 5.3 5.2 - - + -
1004B LEU* 3.6 21.5 - - + -
1007B ILE* 4.0 20.6 - - + -
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Residues in contact with GLN 984 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
980B LEU* 3.0 47.0 + - - +
981B SER* 3.6 19.2 + - - +
983B VAL* 1.3 75.8 - - - +
985B ALA* 1.3 58.8 + - - +
987B PHE* 3.3 1.0 + - - -
988B GLU* 2.9 40.3 + - - +
995B PHE* 4.0 14.9 - - + -
1004B LEU* 3.7 28.5 - - + +
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Residues in contact with ALA 985 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982A GLU* 6.3 1.1 - - - -
985A ALA* 4.1 26.2 - - + -
989A ASN* 6.1 1.1 - - - +
981B SER 2.8 22.4 + - - +
982B GLU* 3.5 5.6 - - - +
984B GLN* 1.3 73.8 - - - +
986B PHE* 1.3 64.4 + - - +
988B GLU* 3.4 9.2 + - - +
989B ASN* 3.3 31.4 + - - +
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Residues in contact with PHE 986 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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978A THR* 4.1 17.5 - - + -
942B TRP* 4.1 11.4 - + + -
946B LYS* 3.8 49.8 - - + -
949B TRP* 3.7 33.2 - + + -
982B GLU* 2.8 19.3 + - + +
983B VAL 3.9 3.8 - - - +
984B GLN 3.3 0.6 - - - -
985B ALA* 1.3 74.4 - - - +
987B PHE* 1.3 98.8 + + - +
989B ASN* 3.5 9.2 + - + +
990B GLN* 3.0 49.7 + - + -
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Residues in contact with PHE 987 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942B TRP* 3.7 26.0 - + - -
949B TRP* 3.6 27.8 - + - -
967B VAL* 4.0 28.5 - - + -
983B VAL* 3.2 33.0 + - + +
986B PHE* 1.3 97.1 - + - +
988B GLU* 1.3 61.9 + - - +
989B ASN 3.2 0.7 - - - -
990B GLN* 3.4 13.0 + - + +
991B SER 3.0 17.7 - - - +
994B THR* 4.0 12.6 - - + -
995B PHE* 3.5 15.1 + - + +
1000B VAL* 3.8 45.5 - - + -
1003B ALA* 5.8 0.7 - - + -
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Residues in contact with GLU 988 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984B GLN* 2.9 22.6 + - - +
985B ALA* 4.0 8.5 + - - +
986B PHE 3.4 0.2 - - - -
987B PHE* 1.3 78.7 - - - +
989B ASN* 1.3 62.9 + - - +
990B GLN 3.3 0.2 - - - -
991B SER* 3.7 13.8 + - - +
992B GLU* 6.1 1.8 - - + -
995B PHE* 3.4 43.7 - - + -
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Residues in contact with ASN 989 (chain B).
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* 3.5 32.2 + - - -
985B ALA* 3.3 19.3 + - - +
986B PHE* 3.5 10.4 + - + +
987B PHE 3.2 0.6 - - - -
988B GLU* 1.3 79.0 - - - +
990B GLN* 1.3 74.0 + - - +
991B SER* 3.4 0.7 - - - -
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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
------------------------------------------------------------
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