Contacts of the helix formed by residues 940 - 950 (chain A) in PDB entry 2ITY
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 THR 940 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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935A GLN* 3.7 2.1 + - - -
938A ILE 3.5 1.6 + - - -
939A CYS* 1.3 76.9 - - - +
941A ILE* 1.3 67.1 + - - +
942A ASP* 3.7 15.8 + - - +
943A VAL* 3.2 19.1 + - - +
944A TYR 3.2 16.3 + - - -
977A ARG 3.3 23.6 - - - +
978A TYR* 2.6 34.1 + - - +
979A LEU 4.4 0.2 - - - +
980A VAL* 4.7 14.3 - - + +
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Residues in contact with ILE 941 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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935A GLN* 3.7 21.0 - - - +
940A THR* 1.3 73.1 - - - +
942A ASP* 1.3 79.0 + - - +
944A TYR* 4.4 3.8 - - + -
945A MET* 2.8 48.1 + - + +
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Residues in contact with ASP 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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940A THR* 3.1 18.2 - - - +
941A ILE* 1.3 88.1 - - - +
943A VAL* 1.3 60.4 + - - +
945A MET* 3.4 8.4 - - - +
946A ILE* 3.4 24.6 + - - +
971A MET* 3.9 19.7 - - + +
977A ARG* 5.0 2.1 + - - +
978A TYR* 3.7 21.1 - - + -
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Residues in contact with VAL 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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815A LEU* 4.9 2.9 - - + -
908A MET* 4.4 16.2 - - + -
939A CYS* 3.9 11.7 - - - -
940A THR* 3.2 22.6 + - - +
941A ILE 3.1 0.6 - - - -
942A ASP* 1.3 74.1 - - - +
944A TYR* 1.3 60.0 + - - +
945A MET 3.0 1.8 - - - -
946A ILE* 2.8 26.7 + - - +
947A MET* 3.1 33.3 + - + +
968A PHE* 4.6 12.8 - - + -
971A MET* 3.8 23.3 - - - -
978A TYR* 3.4 15.3 - - + +
979A LEU* 4.4 4.7 - - + -
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Residues in contact with TYR 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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905A TRP* 5.0 0.2 - + - -
932A ARG* 4.6 4.0 - - - +
933A LEU 2.3 29.7 + - - -
934A PRO* 3.5 5.0 - - - +
935A GLN* 3.1 64.3 + - + -
936A PRO* 4.1 7.9 - - + -
939A CYS* 4.6 2.2 - - + +
940A THR 3.2 13.5 + - - +
941A ILE* 3.9 7.0 - - + +
943A VAL* 1.3 79.0 - - - +
945A MET* 1.3 58.0 + - - +
947A MET* 3.2 17.0 + - + +
948A VAL* 2.9 51.6 + - + +
951A TRP* 4.5 8.1 - + - -
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Residues in contact with MET 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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941A ILE* 2.8 40.7 + - + +
942A ASP* 3.4 9.9 - - - +
943A VAL 3.0 0.2 - - - -
944A TYR* 1.3 76.4 - - - +
946A ILE* 1.3 60.9 + - + +
948A VAL* 3.7 11.0 - - + +
949A LYS* 2.9 52.6 + - + +
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Residues in contact with ILE 946 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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900A TYR* 5.5 1.1 - - + -
904A VAL* 6.1 0.7 - - + -
942A ASP 3.4 16.1 + - - +
943A VAL* 2.8 9.9 + - - +
945A MET* 1.3 77.4 - - + +
947A MET* 1.3 70.1 + - + +
949A LYS* 2.9 22.6 + - + +
950A CYS* 2.9 16.3 + - - -
959A PRO* 5.2 3.1 - - + -
964A LEU* 3.7 29.2 - - + -
967A GLU* 4.4 21.5 - - + +
968A PHE* 3.9 24.5 - - + -
971A MET* 3.6 28.0 - - + -
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Residues in contact with MET 947 (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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901A GLY* 4.6 4.3 - - - +
904A VAL* 3.9 15.9 - - + -
905A TRP* 3.8 39.0 - - - -
908A MET* 3.7 14.6 - - + -
936A PRO* 4.3 2.7 - - + -
939A CYS* 3.4 33.4 - - - -
943A VAL* 3.1 25.7 + - + +
944A TYR* 3.5 14.8 - - + +
946A ILE* 1.3 79.2 - - + +
948A VAL* 1.3 63.3 + - - +
950A CYS* 3.0 19.2 + - - +
951A TRP* 3.2 38.0 - - + -
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Residues in contact with VAL 948 (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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932A ARG* 5.2 9.2 - - + -
944A TYR* 2.9 54.4 + - + +
945A MET* 4.0 12.1 - - + +
946A ILE 3.0 0.2 - - - -
947A MET* 1.3 75.0 - - - +
949A LYS* 1.3 61.3 + - + +
951A TRP* 2.7 36.7 + - + +
952A MET* 3.4 13.4 + - - +
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Residues in contact with LYS 949 (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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945A MET* 2.9 40.8 + - + +
946A ILE* 2.9 13.2 + - + +
948A VAL* 1.3 78.8 - - + +
950A CYS* 1.3 59.6 + - - +
951A TRP 3.1 0.9 + - - -
952A MET* 3.6 28.6 + - + +
957A SER 5.4 1.8 - - - +
958A ARG* 3.2 19.1 - - - +
959A PRO* 3.4 22.5 - - + +
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Residues in contact with CYS 950 (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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897A VAL* 3.5 34.8 - - - +
898A TRP* 3.4 17.0 - - - -
900A TYR* 4.3 11.4 - - - -
901A GLY* 3.8 20.2 - - - -
946A ILE* 2.9 19.8 + - - -
947A MET 3.0 10.0 + - - +
949A LYS* 1.3 75.1 - - - +
951A TRP* 1.3 65.1 + - + +
952A MET 3.5 0.7 - - - -
958A ARG* 3.5 16.9 - - - +
959A PRO* 3.9 7.6 - - - -
964A LEU* 4.3 11.4 - - - -
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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