Contacts of the helix formed by residues 1029 - 1036 (chain A) in PDB entry 6A5T
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 ALA1029 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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898A TYR* 4.0 31.6 - - + +
933A GLU* 4.7 9.0 - - + +
937A LEU* 4.5 7.0 - - + -
1025A ARG 3.8 15.4 + - - +
1027A ARG 2.6 12.4 + - - +
1028A LEU* 1.3 80.6 - - - +
1030A THR* 1.3 66.2 + - - +
1031A ARG* 3.6 1.6 - - + +
1032A ARG* 3.4 8.4 + - + +
1033A ILE* 3.3 20.4 + - - +
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Residues in contact with THR1030 (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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900A VAL* 4.7 8.5 - - + -
930A LEU* 4.6 10.8 - - + -
933A GLU* 3.5 21.7 + - - -
985A ILE* 3.8 34.8 - - + -
988A ILE* 3.3 35.4 - - + +
989A ILE* 3.7 2.9 - - - +
1029A ALA* 1.3 72.8 - - - +
1031A ARG* 1.3 67.9 + - - +
1032A ARG 3.3 0.2 + - - -
1033A ILE* 3.4 1.9 + - - +
1034A LEU* 3.0 27.4 + - + +
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Residues in contact with ARG1031 (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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896A LYS* 2.8 25.2 + - - +
897A ARG* 2.8 28.6 + - - +
898A TYR* 3.2 15.6 + - - +
899A TYR 3.2 27.8 + - - -
900A VAL* 3.7 23.2 - - + +
907A ASN* 4.3 23.8 + - - +
908A SER 4.7 2.2 + - - -
1029A ALA* 4.8 1.2 - - + +
1030A THR* 1.3 78.0 - - - +
1032A ARG* 1.3 65.9 + - + +
1034A LEU* 5.0 1.6 - - - -
1035A GLU* 2.8 72.3 + - - +
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Residues in contact with ARG1032 (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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885A ASP* 2.9 26.7 + - - -
897A ARG* 2.8 57.2 - - + +
898A TYR* 4.0 10.3 - - + -
1026A ALA 3.2 16.0 + - - -
1027A ARG* 3.3 35.8 + - - +
1029A ALA* 3.4 9.9 + - + +
1030A THR 3.2 0.8 - - - -
1031A ARG* 1.3 75.0 - - + +
1033A ILE* 1.3 64.5 + - - +
1035A GLU* 4.8 2.7 - - - -
1036A GLU* 2.9 37.8 + - + +
1037A PHE* 3.4 33.0 + - + -
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Residues in contact with ILE1033 (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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983A LEU* 3.5 28.7 - - + -
988A ILE* 4.0 15.0 - - + -
1027A ARG 5.3 0.2 - - - +
1028A LEU* 4.1 34.5 - - + +
1029A ALA 3.3 15.3 + - - +
1030A THR 3.9 3.4 - - - +
1031A ARG 3.2 0.2 - - - -
1032A ARG* 1.3 78.6 - - - +
1034A LEU* 1.3 64.7 + - + +
1035A GLU 3.0 2.0 + - - -
1037A PHE* 4.5 9.6 - - + +
1038A ARG* 3.0 26.2 + - - -
1039A LEU* 4.5 22.7 - - + +
1044A PHE* 4.0 27.8 - - + -
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Residues in contact with LEU1034 (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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909A ILE* 3.6 40.2 - - + +
913A VAL* 3.6 27.9 - - + +
914A ILE* 4.3 13.5 - - + -
981A SER* 4.9 5.8 - - - +
983A LEU* 3.5 42.6 - - + +
985A ILE* 4.0 17.3 - - + -
988A ILE* 4.1 15.3 - - + -
1030A THR* 3.0 17.8 + - + +
1031A ARG* 3.6 2.0 - - - +
1033A ILE* 1.3 76.7 - - + +
1035A GLU* 1.3 63.0 + - + +
1038A ARG* 5.2 5.6 - - - +
1039A LEU 5.5 1.6 - - - +
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Residues in contact with GLU1035 (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 ARG* 4.1 4.7 - - - +
908A SER 4.1 12.9 - - - +
909A ILE* 5.6 4.9 - - + -
910A LYS* 5.2 20.0 + - - +
913A VAL* 5.5 5.2 - - - +
1031A ARG* 2.8 78.9 + - - +
1032A ARG* 4.4 1.4 - - - +
1034A LEU* 1.3 84.8 - - + +
1036A GLU* 1.3 61.9 + - + +
1038A ARG* 4.9 11.0 + - - +
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Residues in contact with GLU1036 (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 ARG* 5.8 2.8 - - - +
970A GLN* 5.4 1.6 + - - -
1032A ARG* 2.9 26.0 + - + +
1033A ILE 3.6 0.6 + - - -
1035A GLU* 1.3 82.2 - - + +
1037A PHE* 1.3 86.5 + - + +
1038A ARG* 3.4 12.9 + - - +
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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