Contacts of the helix formed by residues 932 - 940 (chain A) in PDB entry 1N35
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 ASP 932 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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914A MET* 4.6 0.4 - - - -
919A TYR* 2.7 36.1 + - + +
920A VAL 3.7 14.2 - - - +
921A THR* 4.1 12.9 - - - +
930A ASN 3.9 1.2 + - - -
931A ALA* 1.3 69.1 - - - +
933A TYR* 1.3 60.6 + - - +
934A ARG* 3.2 6.6 + - - +
935A ARG* 3.1 36.2 + - - +
936A CYS* 3.1 19.6 + - - +
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Residues in contact with TYR 933 (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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914A MET* 3.7 21.8 - - - -
925A SER* 3.8 23.6 - - - -
928A PHE* 3.7 34.3 - + + -
931A ALA 2.7 19.8 + - - +
932A ASP* 1.3 71.8 - - - +
934A ARG* 1.3 108.9 + - + +
937A PHE* 2.8 46.7 + + + -
943A TYR* 3.6 18.4 - - - -
1047A SER 4.2 3.8 + - - -
1048A SER* 5.5 1.3 - - - -
1049A PHE* 6.3 0.4 - + - -
1054A GLU* 5.5 5.8 - - - -
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Residues in contact with ARG 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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923A ARG* 5.6 9.4 - - - +
932A ASP* 3.2 6.3 + - - +
933A TYR* 1.3 115.2 + - + +
935A ARG* 1.3 62.7 + - - +
938A ASN* 3.0 31.9 + - - +
943A TYR* 4.0 6.6 - - - -
1046A TYR 4.8 1.8 - - - +
1047A SER* 3.2 49.6 + - - +
1048A SER* 5.9 0.6 - - - -
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Residues in contact with ARG 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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917A ASN 5.2 2.4 + - - -
918A GLY* 3.3 24.2 + - - -
919A TYR* 3.3 33.8 - - + +
932A ASP* 3.1 29.5 + - - +
934A ARG* 1.3 78.8 - - - +
936A CYS* 1.3 64.6 + - - +
938A ASN* 3.4 6.0 + - - +
939A GLU* 2.8 55.4 + - + +
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Residues in contact with CYS 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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881A PHE* 4.7 0.9 - - - -
913A TRP* 3.7 13.0 - - - -
914A MET* 3.6 37.5 - - - -
919A TYR* 3.6 23.2 - - + -
932A ASP 3.1 9.2 + - - +
933A TYR 3.3 6.5 + - - +
935A ARG* 1.3 76.9 - - - +
937A PHE* 1.3 65.4 + - + +
939A GLU* 3.2 3.5 + - - +
940A LEU* 2.9 57.6 + - - +
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Residues in contact with PHE 937 (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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881A PHE* 4.7 3.4 - + - -
903A ILE* 5.6 0.4 - - + -
910A MET* 4.1 14.8 - - + -
914A MET* 3.9 35.4 - - + -
928A PHE* 3.9 25.4 - + - -
933A TYR* 2.8 30.8 + + + +
936A CYS* 1.3 80.6 - - - +
938A ASN* 1.3 58.0 + - - +
940A LEU* 4.1 3.1 - - + +
942A LEU* 3.0 64.6 + - + -
943A TYR* 3.1 42.5 + + + -
944A GLN* 3.4 0.3 - - - +
1049A PHE* 4.0 15.7 - + - -
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Residues in contact with ASN 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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934A ARG* 3.0 23.2 + - - +
935A ARG* 3.9 5.1 - - - +
936A CYS 3.2 0.6 - - - -
937A PHE* 1.3 77.0 - - - +
939A GLU* 1.3 65.0 + - + +
941A LYS* 3.4 10.0 + - - +
943A TYR* 3.7 4.6 - - - -
944A GLN* 2.9 37.7 + - - +
1045A SER* 3.1 16.4 + - - -
1046A TYR 2.5 50.0 + - - +
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Residues in contact with GLU 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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25A ASP* 5.7 1.9 - - - +
919A TYR* 3.2 29.1 + - - +
935A ARG* 2.8 49.2 + - + +
936A CYS 3.7 2.5 - - - +
938A ASN* 1.3 76.9 - - + +
940A LEU* 1.3 62.5 + - + +
941A LYS* 3.1 13.9 + - - +
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Residues in contact with LEU 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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23A SER* 6.2 3.8 - - - -
24A ASN* 3.2 26.1 - - + +
25A ASP* 6.0 2.2 - - - +
868A TRP* 3.2 23.0 + - + +
881A PHE* 4.0 25.8 - - + -
913A TRP* 4.4 17.7 - - + -
919A TYR* 4.7 9.6 - - - +
936A CYS* 2.9 40.4 + - - +
937A PHE* 5.1 3.1 - - + -
939A GLU* 1.3 75.8 - - + +
941A LYS* 1.3 67.1 + - - +
942A LEU* 4.3 7.6 - - + +
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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