Contacts of the helix formed by residues 937 - 948 (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 GLY 937 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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906B LEU* 4.1 9.6 - - - +
931B VAL* 3.3 35.9 + - - +
934B HIS* 3.4 3.6 + - - +
935B PHE 3.3 0.4 - - - -
936B PRO* 1.3 79.2 - - - +
938B HIS* 1.3 64.5 + - - +
939B LEU 3.5 1.8 - - - -
940B LEU* 3.4 9.8 - - - +
941B ALA* 2.9 22.5 + - - +
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Residues in contact with HIS 938 (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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781B LYS* 3.6 47.5 + - + +
932B GLY* 3.4 21.3 - - - -
934B HIS 3.2 17.0 + - - +
935B PHE* 3.2 13.2 + - + +
936B PRO 3.4 0.6 - - - -
937B GLY* 1.3 80.4 - - - +
939B LEU* 1.3 74.0 + - + +
941B ALA* 3.6 7.3 + - - +
942B TRP* 3.7 10.9 + - - +
970B SER 4.9 8.5 + - - +
973B LEU* 3.9 14.9 + - + +
974B PHE* 3.3 40.1 - + - -
979B HIS* 5.3 1.3 - - - -
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Residues in contact with LEU 939 (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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939A LEU* 3.7 31.8 - - + +
940A LEU* 4.0 19.7 - - + +
943A ASP* 3.6 45.5 - - + +
935B PHE 4.8 1.6 + - - +
936B PRO 5.2 0.6 + - - -
938B HIS* 1.3 91.0 - - + +
940B LEU* 1.3 63.3 + - - +
942B TRP* 3.5 6.7 + - + +
943B ASP* 3.0 23.2 + - - +
974B PHE* 4.4 5.4 - - + -
979B HIS* 4.2 14.6 - - + +
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Residues in contact with LEU 940 (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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935A PHE* 4.2 19.3 - - + +
939A LEU* 3.7 21.2 - - + +
903B VAL* 3.9 39.9 - - + +
906B LEU* 4.0 11.2 - - + -
907B TYR* 3.9 15.9 - - + +
910B MET* 3.7 23.6 - - + -
931B VAL* 4.3 3.4 - - + -
936B PRO 4.4 4.4 + - - +
937B GLY* 3.2 15.6 + - - +
938B HIS 3.2 0.4 - - - -
939B LEU* 1.3 78.8 - - - +
941B ALA* 1.3 58.1 + - - +
943B ASP* 3.4 4.6 + - + +
944B PHE* 3.0 27.2 + - - +
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Residues in contact with ALA 941 (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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910B MET* 4.3 11.2 - - - -
928B ILE* 3.9 23.0 - - + +
931B VAL* 4.0 6.2 - - + +
932B GLY* 3.8 22.7 - - - +
937B GLY 2.9 15.9 + - - +
938B HIS 4.2 1.8 - - - +
940B LEU* 1.3 74.9 - - - +
942B TRP* 1.3 67.0 + - - +
944B PHE* 3.2 2.8 + - - +
945B VAL* 3.0 28.9 + - - +
970B SER* 4.4 5.8 - - - -
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Residues in contact with TRP 942 (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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938B HIS 3.7 5.5 + - - +
939B LEU* 3.5 9.1 + - + +
940B LEU 3.4 0.4 - - - -
941B ALA* 1.3 77.8 - - - +
943B ASP* 1.3 63.4 + - - +
945B VAL* 3.4 21.7 + - + -
946B LYS* 3.0 51.8 + - + +
967B VAL* 5.2 2.7 - - - -
970B SER* 3.6 31.2 - - - +
971B THR* 3.7 19.3 - - + -
974B PHE* 3.6 25.1 - + + -
979B HIS* 6.0 0.2 - + - -
982B GLU* 2.9 33.1 + - - -
983B VAL* 3.9 26.3 - - + +
986B PHE* 4.1 7.6 - + + -
987B PHE* 3.7 30.7 - + - -
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Residues in contact with ASP 943 (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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781A LYS 5.7 1.0 - - - +
939A LEU* 3.6 27.3 - - + +
979A HIS* 3.2 32.2 + - - -
907B TYR* 6.1 1.0 - - - -
939B LEU 3.0 15.1 + - - +
940B LEU* 3.5 9.9 - - + +
942B TRP* 1.3 76.9 - - - +
944B PHE* 1.3 52.0 + - - +
946B LYS* 3.0 19.6 + - - +
947B GLU* 2.7 47.0 + - - +
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Residues in contact with PHE 944 (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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907B TYR* 4.1 23.1 - + + -
910B MET* 3.5 51.4 - - + -
911B LYS* 3.8 26.0 - - + -
914B LEU* 3.7 21.8 - - + -
924B LEU* 4.5 7.0 - - + -
928B ILE* 4.3 20.4 - - + -
940B LEU 3.0 14.3 + - - +
941B ALA 3.2 7.4 + - - +
943B ASP* 1.3 73.4 - - - +
945B VAL* 1.3 69.5 + - - +
947B GLU* 3.3 2.2 + - - -
948B ASN* 3.0 56.5 + - + +
952B LEU* 5.0 2.9 - - + -
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Residues in contact with VAL 945 (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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928B ILE* 4.0 15.0 - - + -
941B ALA 3.0 15.1 + - - +
942B TRP* 3.6 26.0 - - + +
944B PHE* 1.3 74.8 - - - +
946B LYS* 1.3 62.4 + - - +
948B ASN 3.5 0.9 + - - -
949B TRP* 3.2 47.1 + - + +
952B LEU* 3.9 9.0 - - + +
966B ILE* 3.5 34.5 - - + -
967B VAL* 5.0 2.7 - - + -
970B SER* 3.7 13.9 - - - +
986B PHE* 5.7 0.2 - - + -
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Residues in contact with LYS 946 (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* 4.3 18.0 + - + +
979A HIS* 5.6 1.8 - - - -
982A GLU* 4.4 20.4 + - - +
942B TRP* 3.0 60.5 + - + +
943B ASP* 3.3 22.2 + - - +
945B VAL* 1.3 78.8 - - - +
947B GLU* 1.3 64.8 + - + +
948B ASN 3.3 0.7 + - - -
949B TRP* 3.4 12.3 + - - +
982B GLU* 2.6 26.7 + - + +
986B PHE* 3.8 42.7 - - + -
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Residues in contact with GLU 947 (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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976A THR* 2.9 44.4 + - - +
978A THR* 3.6 18.6 + - - +
979A HIS* 3.5 15.4 + - - +
943B ASP* 2.7 36.8 + - - +
944B PHE* 4.0 4.5 - - - +
946B LYS* 1.3 74.7 - - + +
948B ASN* 1.3 70.7 + - - +
949B TRP 3.4 0.7 + - - -
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Residues in contact with ASN 948 (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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907B TYR* 5.7 1.4 + - - -
914B LEU* 3.8 28.6 - - + +
944B PHE* 3.0 56.1 + - + +
945B VAL 3.8 2.0 - - - -
947B GLU* 1.3 88.1 - - - +
949B TRP* 1.3 64.2 + - - +
950B ASN 3.3 2.7 - - - -
951B LYS* 3.1 11.2 + - + +
952B LEU* 2.9 28.5 + - + +
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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