Contacts of the helix formed by residues 923 - 934 (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 LYS 923 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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439A ARG* 4.1 9.6 - - - +
441A GLU* 2.6 21.2 + - - +
881A TYR* 3.9 19.9 + - - +
887A GLU* 4.1 17.7 + - - -
890A LYS* 5.5 0.6 - - - +
891A ASN* 2.4 40.8 + - - +
894A LEU* 3.7 25.8 - - + -
913A SER* 3.9 1.8 - - - -
919A PHE* 4.9 1.8 - - + -
920A ARG* 3.0 21.3 + - + +
922A GLN* 1.3 96.6 - - + +
924A LEU* 1.3 57.6 + - - +
925A SER 3.5 1.6 - - - -
926A PHE* 3.4 12.9 + - + +
927A ILE* 2.9 34.1 + - + +
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Residues in contact with LEU 924 (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* 3.8 26.0 - - + +
913A SER* 3.6 17.4 + - - +
914A LEU* 3.6 38.4 - - + -
921A THR* 3.2 22.6 + - + +
922A GLN 3.3 0.8 - - - -
923A LYS* 1.3 75.3 - - - +
925A SER* 1.3 67.7 + - - +
927A ILE* 3.2 3.0 + - + +
928A ILE* 2.9 46.0 + - + +
944A PHE* 4.3 4.9 - - + -
952A LEU* 3.7 18.8 - - + -
956A PHE* 4.8 6.5 - - + -
966A ILE* 5.1 1.8 - - + -
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Residues in contact with SER 925 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A GLU* 4.5 8.0 + - - -
921A THR 4.8 0.6 + - - -
922A GLN 4.8 5.6 + - - -
924A LEU* 1.3 78.0 - - - +
926A PHE* 1.3 60.2 + - - +
928A ILE* 3.5 1.9 + - - +
929A ARG* 2.9 43.3 + - - +
956A PHE* 6.0 0.4 - - - -
962A THR* 4.1 17.8 - - - +
965A ASN* 3.9 18.3 - - - +
966A ILE* 3.9 26.8 - - - +
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Residues in contact with PHE 926 (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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439A ARG* 6.0 1.6 - - - +
891A ASN* 3.8 37.5 - - - -
894A LEU* 4.1 20.6 - - + -
895A GLU* 3.5 43.3 - - + -
922A GLN 5.5 0.9 - - - +
923A LYS* 3.4 14.5 + - + +
924A LEU 3.2 0.4 - - - -
925A SER* 1.3 80.1 + - - +
927A ILE* 1.3 66.2 + - - +
929A ARG* 3.5 32.0 - - + +
930A THR* 2.9 43.7 + - - -
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Residues in contact with ILE 927 (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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894A LEU* 3.9 35.0 - - + -
898A ALA* 4.4 7.8 - - + +
909A LEU* 3.9 24.9 - - + +
910A MET* 3.8 24.0 - - + +
913A SER* 3.6 30.5 - - - +
919A PHE* 4.4 6.7 - - + -
923A LYS* 2.9 29.0 + - + +
924A LEU* 3.7 4.3 - - + +
926A PHE* 1.3 73.6 - - - +
928A ILE* 1.3 58.5 + - - +
930A THR* 3.2 5.7 + - - -
931A VAL* 2.9 34.7 + - + +
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Residues in contact with ILE 928 (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* 4.0 21.1 - - + -
924A LEU* 2.9 44.2 + - + +
925A SER* 3.9 3.6 - - - +
927A ILE* 1.3 71.2 - - - +
929A ARG* 1.3 68.9 + - - +
931A VAL* 3.3 1.4 + - - +
932A GLY* 2.9 22.3 + - - -
941A ALA* 3.9 18.5 - - + +
944A PHE* 4.0 17.7 - - + -
945A VAL* 4.2 23.3 - - + -
952A LEU* 5.0 2.7 - - + -
966A ILE* 4.3 24.2 - - + +
969A GLY 5.1 1.5 - - - +
970A SER* 4.4 8.5 - - - +
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Residues in contact with ARG 929 (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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925A SER* 2.9 32.7 + - - +
926A PHE* 3.5 38.7 - - + +
928A ILE* 1.3 78.1 - - - +
930A THR* 1.3 66.2 + - - +
932A GLY* 3.4 7.3 + - - -
933A ARG* 3.4 15.0 + - - +
961A TYR* 6.0 0.4 - - - -
965A ASN* 3.0 42.8 + - - +
969A GLY* 4.7 22.3 - - - +
972A TYR* 6.4 1.1 - - + -
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Residues in contact with THR 930 (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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895A GLU* 3.9 11.7 - - + +
898A ALA* 3.4 31.8 - - + +
899A SER* 3.8 17.7 - - - +
926A PHE* 2.9 38.9 + - - -
927A ILE 3.7 3.8 - - - -
929A ARG* 1.3 77.5 - - - +
931A VAL* 1.3 62.9 + - - +
933A ARG* 3.5 17.8 + - - +
934A HIS* 3.7 14.6 + - + -
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Residues in contact with VAL 931 (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 ALA* 3.9 18.8 - - + +
906A LEU* 4.0 32.5 - - + +
909A LEU* 5.2 0.4 - - + -
910A MET* 4.0 25.1 - - + -
927A ILE* 2.9 32.5 + - + +
928A ILE 3.3 3.1 + - - +
930A THR* 1.3 77.9 - - - +
932A GLY* 1.3 60.4 + - - +
933A ARG 3.2 2.2 + - - -
934A HIS* 3.9 6.6 + - - +
937A GLY* 3.2 39.5 + - - +
938A HIS 3.8 0.3 + - - -
940A LEU* 4.4 0.9 - - + -
941A ALA* 4.1 4.9 - - + +
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Residues in contact with GLY 932 (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 2.9 12.6 + - - -
929A ARG 3.4 2.7 + - - -
930A THR 3.3 0.2 - - - -
931A VAL* 1.3 76.1 - - - +
933A ARG* 1.3 59.7 + - - +
934A HIS 3.5 2.1 + - - +
937A GLY 3.8 4.7 - - - -
938A HIS* 3.3 29.0 + - - -
941A ALA* 3.6 21.3 - - - +
969A GLY 4.8 12.2 - - - +
970A SER* 5.5 1.9 - - - -
973A LEU* 4.0 6.0 - - - +
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Residues in contact with ARG 933 (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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773A ASP* 3.8 24.2 + - - +
774A LEU* 6.0 0.8 - - - +
777A ASN* 3.4 34.1 - - - +
781A LYS* 2.8 20.7 + - - -
929A ARG 3.4 11.5 + - - +
930A THR* 3.6 15.5 - - - +
931A VAL 3.2 1.0 - - - -
932A GLY* 1.3 79.4 - - - +
934A HIS* 1.3 79.6 + - + +
972A TYR* 3.4 28.4 + - + +
973A LEU* 3.7 8.8 - - + +
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Residues in contact with HIS 934 (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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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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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