Contacts of the helix formed by residues 934 - 948 (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 HIS 934 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776A TYR* 6.4 1.3 - + - -
777A ASN* 4.8 7.4 - - - -
780A GLU* 4.1 4.3 - - - -
781A LYS* 3.6 3.8 - - - +
829A THR* 4.7 19.2 + - + +
865A LYS* 5.5 8.1 + - + -
898A ALA 5.3 0.2 + - - -
899A SER* 4.2 28.3 + - - +
901A GLU* 5.6 0.9 - - - +
930A THR* 3.7 19.7 + - + -
931A VAL 3.9 5.1 + - - +
933A ARG* 1.3 105.6 + - + +
935A PHE* 1.3 68.1 + - - +
936A PRO* 3.6 9.6 - - + -
937A GLY 3.5 2.1 + - - +
938A HIS* 3.1 23.2 + - - +
904B ARG* 4.6 7.9 - - - +
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Residues in contact with PHE 935 (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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780A GLU* 3.5 33.3 + - - -
781A LYS* 4.1 24.2 - - + +
783A GLY* 5.3 1.1 - - - -
785A MET* 3.6 24.0 - - + -
934A HIS* 1.3 74.4 - - - +
936A PRO* 1.3 73.0 - - + +
937A GLY 3.1 0.9 + - - -
938A HIS* 3.3 17.0 + + + +
939A LEU* 4.7 1.2 + - - +
903B VAL* 3.8 36.9 - - + +
904B ARG* 3.7 33.4 - - + +
907B TYR* 4.0 25.4 - + + -
940B LEU* 4.2 11.3 - - + +
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Residues in contact with PRO 936 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900A SER 5.1 1.3 - - - +
901A GLU* 3.7 50.0 - - + +
903A VAL* 3.9 19.2 - - + +
906A LEU* 4.7 5.2 - - + -
934A HIS* 3.7 8.3 - - + -
935A PHE* 1.3 95.7 - - + +
937A GLY* 1.3 57.6 + - - +
938A HIS 3.8 0.2 + - - -
939A LEU* 5.0 1.2 + - - +
940A LEU* 4.6 6.2 + - - +
902B ASP* 5.5 2.5 - - - +
903B VAL* 4.0 30.6 - - + +
904B ARG* 3.8 15.0 - - + +
936B PRO 5.6 0.2 - - - +
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Residues in contact with GLY 937 (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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906A LEU* 4.1 10.3 - - - +
931A VAL* 3.2 34.3 + - - +
934A HIS* 3.5 3.0 + - - +
935A PHE 3.1 0.6 - - - -
936A PRO* 1.3 79.7 - - - +
938A HIS* 1.3 65.9 + - - +
939A LEU 3.4 2.0 - - - -
940A LEU* 3.5 8.2 - - - +
941A ALA* 3.0 23.0 + - - +
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Residues in contact with HIS 938 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781A LYS* 3.6 36.3 - - + +
932A GLY* 3.3 21.6 + - - -
934A HIS 3.1 16.4 + - - +
935A PHE* 3.3 14.5 + + + +
937A GLY* 1.3 78.8 - - - +
939A LEU* 1.3 76.7 + - + +
941A ALA* 3.7 7.1 + - - +
942A TRP* 3.8 11.6 + - - +
970A SER* 5.2 7.0 - - - +
973A LEU* 3.8 26.2 + - + -
974A PHE* 3.1 42.6 - + - -
979A HIS* 5.4 1.3 + - - -
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Residues in contact with LEU 939 (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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935A PHE 4.7 1.2 + - - +
936A PRO 5.0 1.4 + - - +
937A GLY 3.4 0.2 - - - -
938A HIS* 1.3 91.6 - - + +
940A LEU* 1.3 62.3 + - - +
942A TRP* 3.7 7.1 + - + +
943A ASP* 3.1 24.3 + - - +
974A PHE* 4.9 4.3 - - + -
979A HIS* 4.3 12.3 - - + +
939B LEU* 3.7 22.2 - - + +
940B LEU* 3.7 34.1 - - + -
943B ASP* 3.6 45.8 - - + +
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Residues in contact with LEU 940 (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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903A VAL* 3.7 43.3 - - + +
906A LEU* 3.8 11.7 - - + -
907A TYR* 3.7 16.5 - - + +
910A MET* 3.7 23.8 - - + -
931A VAL* 4.4 2.2 - - + -
936A PRO 4.6 4.4 + - - +
937A GLY* 3.1 15.8 + - - +
939A LEU* 1.3 76.7 - - - +
941A ALA* 1.3 59.3 + - - +
943A ASP* 3.5 2.5 + - + +
944A PHE* 2.8 29.3 + - - +
935B PHE* 4.3 17.5 - - + +
939B LEU* 4.0 17.7 - - + +
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Residues in contact with ALA 941 (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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910A MET* 4.2 12.1 - - - -
928A ILE* 3.9 19.6 - - + +
931A VAL* 4.1 4.9 - - + +
932A GLY* 3.6 34.3 - - - +
937A GLY 3.0 7.4 + - - +
938A HIS 4.2 1.6 - - - +
940A LEU* 1.3 72.2 - - - +
942A TRP* 1.3 68.2 + - - +
944A PHE* 3.0 4.0 + - - +
945A VAL* 2.9 28.4 + - - +
970A SER* 4.3 6.1 - - - -
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Residues in contact with TRP 942 (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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938A HIS 3.8 5.4 + - - +
939A LEU* 3.7 9.1 + - + +
940A LEU 3.4 0.2 - - - -
941A ALA* 1.3 77.6 - - - +
943A ASP* 1.3 63.1 + - - +
945A VAL* 3.0 26.2 + - + +
946A LYS* 2.9 52.1 + - + +
967A VAL* 5.1 2.2 - - - -
970A SER* 3.5 31.3 - - - +
971A THR* 3.6 18.4 - - + -
974A PHE* 3.6 25.8 - + + -
979A HIS* 6.1 0.2 - + - -
982A GLU* 2.8 32.0 + - - -
983A VAL* 3.8 26.8 - - + +
986A PHE* 4.2 5.6 - + + -
987A PHE* 3.8 31.6 - + - -
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Residues in contact with ASP 943 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907A TYR* 6.2 0.2 - - - -
939A LEU 3.1 18.5 + - - +
940A LEU* 3.7 3.8 - - + +
942A TRP* 1.3 76.8 - - - +
944A PHE* 1.3 63.0 + - - +
946A LYS* 3.9 18.0 + - - +
947A GLU* 3.0 39.3 + - - +
781B LYS 5.8 0.2 - - - +
939B LEU* 3.6 28.9 - - + +
979B HIS* 3.2 29.6 + - - -
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Residues in contact with PHE 944 (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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907A TYR* 4.0 26.9 - + + -
910A MET* 3.6 52.0 - - + -
911A LYS* 3.8 15.3 - - + -
914A LEU* 3.9 20.6 - - + -
924A LEU* 4.3 7.6 - - + -
928A ILE* 4.0 25.1 - - + -
940A LEU 2.8 15.5 + - - +
941A ALA 3.0 8.5 + - - +
943A ASP* 1.3 77.7 - - - +
945A VAL* 1.3 64.5 + - - +
947A GLU* 5.0 0.9 - - - -
948A ASN* 3.0 55.9 + - + +
952A LEU* 5.1 3.6 - - + -
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Residues in contact with VAL 945 (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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928A ILE* 4.2 13.9 - - + -
941A ALA 2.9 19.0 + - - +
942A TRP* 3.0 26.7 + - + +
944A PHE* 1.3 78.1 - - - +
946A LYS* 1.3 61.4 + - - +
949A TRP* 3.2 44.7 + - + +
952A LEU* 3.7 10.5 - - + +
966A ILE* 3.5 33.7 - - + -
967A VAL* 5.1 2.9 - - + -
970A SER* 3.7 15.5 - - - +
986A PHE* 5.9 0.2 - - + -
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Residues in contact with LYS 946 (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* 2.9 56.4 + - + +
943A ASP* 3.9 21.4 + - - +
945A VAL* 1.3 77.3 - - - +
947A GLU* 1.3 63.9 + - + +
949A TRP* 3.2 17.2 + - - +
982A GLU* 3.0 22.5 + - + +
986A PHE* 3.5 48.3 - - + -
978B THR* 4.2 17.1 + - + +
979B HIS* 5.4 1.2 - - - -
982B GLU* 4.2 22.2 + - - +
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Residues in contact with GLU 947 (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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943A ASP* 3.0 35.3 + - - +
944A PHE* 5.0 0.4 - - - -
946A LYS* 1.3 77.4 - - + +
948A ASN* 1.3 71.1 + - - +
949A TRP 3.3 1.0 + - - -
976B THR* 2.8 45.4 + - + +
978B THR* 3.3 22.0 + - - +
979B HIS* 3.3 19.8 + - - +
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Residues in contact with ASN 948 (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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907A TYR* 5.4 3.0 + - - -
914A LEU* 3.5 32.3 - - + +
944A PHE* 3.0 55.5 + - + +
945A VAL 3.8 2.2 - - - -
947A GLU* 1.3 86.8 - - - +
949A TRP* 1.3 64.5 + - - +
950A ASN 3.3 2.9 - - - -
951A LYS* 3.1 9.6 + - + +
952A LEU* 3.0 25.9 + - + +
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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