Contacts of the helix formed by residues 969 - 981 (chain B) in PDB entry 1M8X
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 ASN 969 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929B ALA 3.5 15.2 - - - +
930B LEU 3.7 13.7 + - - -
931B GLN 3.7 1.8 - - - +
932B MET* 3.5 42.8 - - - +
935B CYS* 3.7 19.2 - - - +
967B ASP* 2.9 11.3 + - - +
968B GLN* 1.3 85.2 + - - +
970B GLY* 1.3 67.2 + - - +
971B ASN 3.3 1.6 - - - -
972B HIS* 3.2 22.5 + - - +
973B VAL 3.7 2.6 + - - -
18D A 4.6 11.7 + - - +
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Residues in contact with GLY 970 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929B ALA* 3.2 19.3 + - - -
930B LEU* 4.6 1.6 - - - -
964B CYS* 3.1 23.9 - - - +
967B ASP* 3.3 9.1 + - - -
969B ASN* 1.3 79.8 - - - +
971B ASN* 1.3 56.9 + - - +
973B VAL* 2.8 23.8 + - - +
974B VAL* 2.9 14.6 + - - +
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Residues in contact with ASN 971 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964B CYS 2.7 12.1 + - - -
965B VAL* 2.9 30.3 - - - +
967B ASP 2.6 21.5 + - - +
968B GLN 3.1 19.8 + - - -
969B ASN 3.2 0.4 + - - -
970B GLY* 1.3 75.7 - - - +
972B HIS* 1.3 69.5 + - - +
974B VAL* 3.4 4.2 + - - +
975B GLN* 3.0 51.8 + - - +
1005B TYR* 3.4 34.2 - - + +
1008B ARG* 5.7 0.3 - - - -
1009B VAL* 4.0 5.0 - - + +
17D U 4.7 0.5 - - - +
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Residues in contact with HIS 972 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939B GLN* 3.5 10.4 - - - +
968B GLN 3.3 21.2 + - - -
969B ASN 3.5 5.8 - - - +
970B GLY 3.1 0.8 - - - -
971B ASN* 1.3 86.5 + - - +
973B VAL* 1.3 59.9 - - - +
975B GLN* 3.7 12.7 + - - +
976B LYS* 3.0 26.2 + - - +
1005B TYR* 5.8 1.4 - + - -
17D U 3.2 43.7 + + + -
18D A 3.1 74.5 + + + +
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Residues in contact with VAL 973 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929B ALA* 3.6 41.3 - - + +
935B CYS* 3.8 28.3 - - + +
938B ILE* 4.0 19.1 - - + -
939B GLN* 4.2 9.2 - - + -
942B LEU* 4.8 0.9 - - + -
957B LEU* 4.7 13.5 - - + -
964B CYS* 5.8 0.9 - - + -
969B ASN 4.1 1.1 - - - +
970B GLY 2.8 11.6 + - - +
972B HIS* 1.3 77.4 - - - +
974B VAL* 1.3 65.5 + - + +
976B LYS* 3.1 3.3 + - - +
977B CYS* 3.0 38.0 + - - -
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Residues in contact with VAL 974 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957B LEU* 6.0 3.8 - - + -
961B VAL* 4.6 3.4 - - + +
964B CYS* 3.6 23.6 - - + -
965B VAL* 3.8 31.2 - - + +
970B GLY 2.9 13.0 + - - +
971B ASN 3.7 5.6 - - - +
973B VAL* 1.3 78.4 - - + +
975B GLN* 1.3 62.9 + - - +
977B CYS* 3.4 8.1 + - - +
978B ILE* 3.1 44.2 + - + +
989B ILE* 4.0 19.7 - - + -
1009B VAL* 3.9 8.5 - - + -
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Residues in contact with GLN 975 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971B ASN* 3.0 45.6 + - - +
972B HIS* 3.7 13.9 + - - +
974B VAL* 1.3 74.7 - - - +
976B LYS* 1.3 64.7 + - - +
978B ILE* 3.4 10.7 + - - +
979B GLU* 3.1 28.5 + - - +
1005B TYR 4.8 0.6 + - - -
1008B ARG* 3.7 15.5 - - - +
1009B VAL* 3.8 14.1 - - + -
1012B ARG* 3.4 39.7 + - + +
17D U 3.0 29.0 + - - +
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Residues in contact with LYS 976 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939B GLN* 3.5 47.6 - - + +
942B LEU* 4.2 9.6 - - + -
943B GLU* 2.6 34.2 + - - +
972B HIS 3.0 16.7 + - - +
973B VAL 3.1 5.4 + - - +
975B GLN* 1.3 73.4 - - - +
977B CYS* 1.3 67.0 + - - +
979B GLU* 3.0 28.9 + - - +
980B CYS* 2.9 45.7 + - - +
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Residues in contact with CYS 977 (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 LEU* 3.7 18.8 - - - -
954B VAL* 4.0 19.5 - - + -
957B LEU* 4.7 8.3 - - - -
973B VAL* 3.0 30.8 + - - -
974B VAL* 3.6 9.9 - - - +
976B LYS* 1.3 75.3 - - - +
978B ILE* 1.3 56.8 + - - +
980B CYS* 2.8 8.7 + - - -
981B VAL* 2.8 48.1 + - + +
986B LEU* 4.0 13.7 - - + -
989B ILE* 4.8 4.7 - - + -
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Residues in contact with ILE 978 (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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974B VAL* 3.1 23.5 + - + +
975B GLN* 3.6 7.4 - - - +
976B LYS 3.3 0.2 - - - -
977B CYS* 1.3 80.0 - - - +
979B GLU* 1.3 57.1 + - - +
980B CYS 3.9 0.2 + - - -
981B VAL 4.8 2.4 - - - +
986B LEU* 3.6 18.9 - - + +
989B ILE* 4.4 12.1 - - + -
1009B VAL* 3.6 29.2 - - + +
1012B ARG* 3.3 42.4 - - + +
1013B ILE* 3.4 32.3 - - + +
1016B HIS* 3.0 21.5 - - + +
1017B CYS* 5.1 0.9 - - - -
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Residues in contact with GLU 979 (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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975B GLN* 3.1 19.2 + - - +
976B LYS* 3.1 43.2 + - + +
978B ILE* 1.3 76.8 - - - +
980B CYS* 1.3 63.2 + - - +
981B VAL 5.0 0.7 - - - -
1012B ARG* 4.8 10.1 - - - -
1016B HIS* 3.4 31.3 + - + +
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Residues in contact with CYS 980 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942B LEU* 4.1 8.5 - - + +
943B GLU* 4.1 18.2 - - - -
950B GLN* 3.5 25.0 + - - +
976B LYS* 2.9 46.3 + - - +
977B CYS* 2.8 5.2 + - - -
978B ILE 3.5 0.2 - - - -
979B GLU* 1.3 86.6 - - - +
981B VAL* 1.3 64.8 + - - +
982B GLN* 5.6 0.3 - - - +
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Residues in contact with VAL 981 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942B LEU* 4.4 6.3 - - + -
950B GLN* 3.8 17.7 - - + -
951B ASN* 3.5 15.3 - - - +
954B VAL* 3.4 32.8 - - + -
977B CYS* 2.8 33.0 + - + +
978B ILE 4.8 2.6 - - - +
979B GLU 5.0 0.3 - - - -
980B CYS* 1.3 77.9 + - + +
982B GLN* 1.3 77.4 + - - +
983B PRO* 3.3 6.9 - - - +
985B SER* 3.1 25.1 - - - +
986B LEU* 4.2 14.0 - - + +
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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