Contacts of the helix formed by residues 969 - 981 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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929A ALA 3.4 13.7 - - - +
930A LEU 2.8 22.9 + - - +
931A GLN 3.7 10.3 - - - +
932A MET* 3.4 26.4 - - - +
935A CYS* 3.7 21.1 - - - +
967A ASP* 2.4 24.2 + - - +
968A GLN* 1.3 83.6 + - - +
970A GLY* 1.3 65.6 + - - +
971A ASN 3.1 3.6 + - - -
972A HIS* 3.2 21.2 + - - +
973A VAL 3.8 2.6 + - - -
18C A 4.0 15.5 + - - +
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Residues in contact with GLY 970 (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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929A ALA* 3.1 18.9 + - - -
930A LEU* 4.6 1.3 - - - -
964A CYS* 3.0 21.5 - - - +
967A ASP* 2.6 19.2 + - - -
969A ASN* 1.3 74.1 - - - +
971A ASN* 1.3 61.0 + - - +
973A VAL* 3.1 7.8 + - - +
974A VAL* 3.1 23.9 + - - +
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Residues in contact with ASN 971 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964A CYS 2.9 9.9 + - - -
965A VAL* 3.2 28.5 - - - +
967A ASP 3.1 18.6 + - - +
968A GLN 3.2 18.6 + - - -
969A ASN 3.1 0.6 + - - -
970A GLY* 1.3 75.3 - - - +
972A HIS* 1.3 72.1 + - - +
974A VAL* 3.3 5.5 + - - +
975A GLN* 2.8 62.2 + - - +
1005A TYR* 3.5 31.8 - - + +
1009A VAL* 4.2 5.2 - - + +
17C U 3.9 1.9 + - - +
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Residues in contact with HIS 972 (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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939A GLN* 3.5 13.5 - - - +
968A GLN 3.2 17.1 + - - -
969A ASN 3.2 4.6 + - - +
971A ASN* 1.3 94.4 - - - +
973A VAL* 1.3 61.6 + - - +
975A GLN* 3.7 10.2 - - - +
976A LYS* 3.0 28.4 + - - +
1005A TYR* 5.9 0.9 - + - -
17C U 2.9 45.8 + + - -
18C A 3.2 70.9 + + + +
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Residues in contact with VAL 973 (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 VAL* 5.6 0.4 - - + -
929A ALA* 3.9 27.6 - - + +
935A CYS* 3.8 39.7 - - + +
938A ILE* 3.5 27.1 - - + -
939A GLN* 4.1 8.1 - - + -
942A LEU* 4.2 1.3 - - + -
957A LEU* 4.3 12.6 - - + -
964A CYS* 6.3 0.4 - - + -
969A ASN 4.4 0.4 - - - +
970A GLY 3.1 8.5 + - - +
972A HIS* 1.3 74.2 - - - +
974A VAL* 1.3 67.6 + - + +
976A LYS* 3.2 2.8 + - - +
977A CYS* 2.9 34.9 + - - -
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Residues in contact with VAL 974 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957A LEU* 5.1 9.2 - - + -
961A VAL* 4.9 3.1 - - + +
964A CYS* 3.7 23.8 - - + -
965A VAL* 4.2 17.5 - - + +
970A GLY 3.1 14.7 + - - +
971A ASN 3.6 6.7 - - - +
973A VAL* 1.3 76.8 - - - +
975A GLN* 1.3 64.8 + - - +
977A CYS* 3.1 9.2 + - - +
978A ILE* 3.1 22.3 + - + +
989A ILE* 4.0 24.9 - - + -
1009A VAL* 3.8 28.5 - - + -
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Residues in contact with GLN 975 (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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971A ASN* 2.8 41.9 + - - +
972A HIS* 3.7 13.9 - - - +
974A VAL* 1.3 76.2 - - - +
976A LYS* 1.3 63.1 + - - +
978A ILE* 3.2 9.4 + - - +
979A GLU* 3.0 33.7 + - - +
1008A ARG* 3.6 15.2 - - - +
1009A VAL* 4.0 13.2 - - + -
1012A ARG* 3.1 43.9 + - + +
17C U 3.1 28.4 + - - +
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Residues in contact with LYS 976 (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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939A GLN* 3.7 46.0 - - + +
942A LEU* 3.9 12.8 - - + -
943A GLU* 3.2 29.7 + - - -
972A HIS 3.0 16.1 + - - +
973A VAL 3.5 5.2 - - - +
974A VAL 3.2 0.2 - - - -
975A GLN* 1.3 74.9 - - - +
977A CYS* 1.3 55.5 + - - +
979A GLU* 3.3 22.8 + - - +
980A CYS* 2.8 69.9 + - - +
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Residues in contact with CYS 977 (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 LEU* 3.6 18.8 - - - +
954A VAL* 3.9 21.8 - - + -
957A LEU* 4.2 20.2 - - - -
973A VAL* 2.9 28.1 + - - -
974A VAL* 3.5 9.2 - - - +
976A LYS* 1.3 75.6 - - - +
978A ILE* 1.3 58.3 + - - +
981A VAL* 2.7 42.9 + - - +
986A LEU* 3.8 17.6 - - + +
989A ILE* 4.9 5.2 - - + -
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Residues in contact with ILE 978 (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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974A VAL* 3.1 20.4 + - + +
975A GLN* 3.5 6.3 - - - +
977A CYS* 1.3 78.7 - - - +
979A GLU* 1.3 61.5 + - - +
981A VAL 4.0 4.7 - - - +
983A PRO* 6.1 0.3 - - - +
986A LEU* 3.5 25.7 - - + +
989A ILE* 4.6 10.3 - - + -
1009A VAL* 3.4 35.9 - - + +
1012A ARG* 3.3 36.1 - - + +
1013A ILE* 3.6 21.5 - - + +
1016A HIS* 3.5 20.1 - - + +
1017A CYS* 4.4 4.3 - - - -
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Residues in contact with GLU 979 (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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975A GLN* 3.0 27.6 + - - +
976A LYS* 3.5 32.7 + - - +
977A CYS 3.2 0.2 - - - -
978A ILE* 1.3 79.8 - - - +
980A CYS* 1.3 63.3 + - - +
981A VAL 5.1 0.3 - - - +
1012A ARG* 3.8 19.8 - - - -
1016A HIS* 3.9 33.3 + - + +
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Residues in contact with CYS 980 (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 LEU* 3.7 29.2 - - + +
943A GLU* 4.2 11.2 - - - -
950A GLN* 3.5 14.4 + - - +
976A LYS* 2.8 55.1 + - - +
979A GLU* 1.3 78.8 - - - +
981A VAL* 1.3 61.5 + - + +
982A GLN 4.0 0.5 + - - -
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Residues in contact with VAL 981 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942A LEU* 4.3 7.0 - - + -
950A GLN* 4.0 22.4 - - + +
951A ASN* 3.5 25.6 - - - +
954A VAL* 3.5 28.7 - - + -
977A CYS* 2.7 29.4 + - - +
978A ILE 4.0 4.7 - - - +
979A GLU 5.1 0.3 - - - +
980A CYS* 1.3 77.5 - - + +
982A GLN* 1.3 79.6 + - - +
983A PRO* 3.1 5.5 - - - +
985A SER* 3.7 9.4 - - - -
986A LEU* 3.7 19.3 - - + +
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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