Contacts of the helix formed by residues 933 - 945 (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 TYR 933 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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893A MET 3.4 15.3 - - - +
894A VAL 3.6 12.8 - - - -
895A ASP 3.9 5.6 - - - +
896A VAL* 3.4 38.8 - - + +
899A ASN* 3.8 17.5 - - - +
931A GLN* 2.6 16.9 + - - +
932A MET* 1.3 109.6 - - + +
934A GLY* 1.3 64.4 + - - +
935A CYS 3.3 0.2 - - - -
936A ARG* 3.1 21.2 + - - +
937A VAL 3.7 2.8 + - - -
845B GLN* 4.1 14.4 - - - -
847B ARG* 3.3 26.8 + - + +
19C U 3.3 41.1 - - + -
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Residues in contact with GLY 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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893A MET 3.3 12.5 + - - -
928A LEU* 3.1 32.0 - - - +
931A GLN* 2.6 18.0 + - - -
933A TYR* 1.3 73.8 - - - +
935A CYS* 1.3 61.0 + - - +
937A VAL* 3.0 16.1 + - - +
938A ILE* 3.1 15.9 + - - +
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Residues in contact with CYS 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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928A LEU 2.8 9.9 + - - -
929A ALA* 3.3 22.0 - - - +
931A GLN 2.9 21.6 + - - +
932A MET 3.4 12.1 - - - -
933A TYR 3.2 0.2 + - - -
934A GLY* 1.3 75.9 - - - +
936A ARG* 1.3 61.0 + - - +
938A ILE* 3.4 2.8 + - - +
939A GLN* 3.0 32.9 + - - +
969A ASN* 3.7 19.7 - - + +
973A VAL* 3.8 13.0 - - + +
18C A 3.8 25.6 - - - -
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Residues in contact with ARG 936 (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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899A ASN* 4.4 0.4 - - - +
903A GLN* 3.8 24.7 - - - +
932A MET 3.9 13.0 + - - +
933A TYR 3.1 12.9 + - - +
935A CYS* 1.3 77.9 - - - +
937A VAL* 1.3 63.4 + - - +
939A GLN* 3.9 6.9 - - - +
940A LYS* 3.1 22.9 + - - +
18C A 3.3 77.2 + - - +
19C U 3.1 63.4 + - + +
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Residues in contact with VAL 937 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A MET* 3.3 56.5 - - + +
899A ASN* 3.9 27.1 - - + +
902A ILE* 3.7 10.3 - - + -
903A GLN* 4.3 7.6 - - + -
906A PHE* 3.7 24.9 - - + -
921A ILE* 4.3 2.0 - - + -
933A TYR 4.1 2.0 - - - +
934A GLY 3.0 7.3 + - - +
936A ARG* 1.3 76.4 - - - +
938A ILE* 1.3 60.4 - - - +
940A LYS* 3.1 3.9 + - - +
941A ALA* 2.8 27.4 + - - +
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Residues in contact with ILE 938 (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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893A MET* 4.8 0.4 - - + -
921A ILE* 3.9 33.0 - - + -
925A VAL* 4.4 16.4 - - + +
928A LEU* 3.8 27.1 - - + -
929A ALA* 4.1 9.2 - - + +
934A GLY 3.1 13.4 + - - +
935A CYS 3.7 6.7 - - - +
937A VAL* 1.3 75.9 - - - +
939A GLN* 1.3 62.2 + - - +
941A ALA* 3.1 6.1 + - - +
942A LEU* 3.0 33.2 + - + +
953A MET* 4.5 11.4 - - + -
973A VAL* 3.5 33.0 - - + -
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Residues in contact with GLN 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 CYS* 3.0 30.7 + - - +
936A ARG* 3.9 9.8 - - - +
938A ILE* 1.3 78.0 - - - +
940A LYS* 1.3 62.2 + - - +
942A LEU* 3.4 13.6 + - - +
943A GLU* 3.5 8.1 + - - +
972A HIS* 3.5 24.8 - - - +
973A VAL* 4.1 9.0 - - - -
976A LYS* 3.7 39.1 - - + +
18C A 2.6 52.2 + - - +
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Residues in contact with LYS 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 GLN* 3.6 32.5 - - + +
906A PHE* 3.6 22.6 - - + +
907A GLU* 3.3 40.4 + - + +
936A ARG 3.1 14.1 + - - +
937A VAL* 3.1 5.2 + - - +
939A GLN* 1.3 79.9 - - - +
941A ALA* 1.3 64.4 + - - +
943A GLU* 3.1 21.1 + - - +
944A PHE* 3.4 32.1 - - + -
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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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906A PHE* 3.6 37.6 - - + -
921A ILE* 4.4 2.2 - - + -
937A VAL 2.8 20.0 + - - +
938A ILE* 3.1 7.4 + - - +
940A LYS* 1.3 73.2 - - - +
942A LEU* 1.3 61.7 + - - +
943A GLU 3.1 0.2 + - - -
944A PHE 3.2 1.0 + - - -
945A ILE* 3.0 32.3 + - + +
953A MET* 3.9 22.9 - - + -
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Residues in contact with LEU 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 ILE* 3.0 32.9 + - + +
939A GLN* 3.7 7.9 - - - +
940A LYS 3.3 0.2 - - - -
941A ALA* 1.3 75.1 - - - +
943A GLU* 1.3 58.7 + - - +
944A PHE 3.7 0.2 + - - -
945A ILE* 4.4 4.2 + - - -
950A GLN* 2.6 39.5 + - + +
953A MET* 4.3 26.5 - - + -
954A VAL* 4.5 3.1 - - + -
973A VAL* 4.0 2.9 - - + +
976A LYS* 3.9 21.3 - - + -
977A CYS* 3.6 31.2 - - - +
980A CYS* 3.7 14.8 - - + +
981A VAL* 4.3 19.7 - - + -
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Residues in contact with GLU 943 (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 7.0 + - - +
940A LYS* 3.1 21.4 + - - +
941A ALA 3.1 1.0 - - - -
942A LEU* 1.3 82.0 - - - +
944A PHE* 1.3 88.2 + - + +
945A ILE 4.7 2.0 - - - +
950A GLN* 4.9 1.9 + - - -
976A LYS* 3.2 28.2 + - - +
980A CYS* 4.2 10.1 - - - -
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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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906A PHE* 3.2 30.7 - - + +
907A GLU* 4.0 21.3 - - + -
914A LYS* 3.9 25.2 + - + +
940A LYS* 3.4 40.6 - - + +
941A ALA 3.2 3.8 + - - +
943A GLU* 1.3 106.5 - - + +
945A ILE* 1.3 65.7 + - - +
946A PRO* 4.4 1.6 - - - +
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Residues in contact with ILE 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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906A PHE* 4.0 24.7 - - + -
914A LYS* 4.5 9.9 - - + +
915A LEU* 5.8 0.7 - - + -
918A ALA* 4.4 12.1 - - + -
941A ALA 3.0 19.0 + - - +
942A LEU* 4.5 0.7 - - - +
943A GLU 3.8 1.6 - - - +
944A PHE* 1.3 80.3 - - - +
946A PRO* 1.3 73.8 - - + +
949A GLN* 3.6 27.6 - - + +
950A GLN* 3.7 30.6 + - + +
953A MET* 3.5 34.8 - - + -
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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