Contacts of the helix formed by residues 1038 - 1050 (chain E) in PDB entry 5B2G
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 SER1038 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1025E TYR* 3.7 5.7 - - - -
1036E SER* 3.3 22.3 + - - -
1037E PRO* 1.3 77.8 - - - +
1039E LEU* 1.3 61.1 + - - +
1040E ASN* 4.5 5.2 - - - -
1041E ALA* 3.6 17.6 - - - +
1042E ALA* 3.1 26.0 + - - +
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Residues in contact with LEU1039 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025E TYR* 5.4 3.3 + - - -
1038E SER* 1.3 72.5 - - - +
1040E ASN* 1.3 96.0 + - - +
1042E ALA* 5.2 0.7 - - - -
1043E LYS* 3.7 38.2 + - + +
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Residues in contact with ASN1040 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038E SER* 3.4 3.3 - - - +
1039E LEU* 1.3 104.5 - - - +
1041E ALA* 1.3 58.0 - - - +
1043E LYS* 5.0 0.2 - - - +
1044E SER* 2.4 33.4 + - - -
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Residues in contact with ALA1041 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034E THR* 5.0 2.1 - - - +
1036E SER* 4.2 9.2 - - - +
1038E SER* 3.6 17.1 + - - +
1040E ASN* 1.3 80.2 - - + +
1042E ALA* 1.3 66.3 + - - +
1044E SER* 4.1 3.2 - - - -
1045E GLU* 3.7 25.8 + - - +
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Residues in contact with ALA1042 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025E TYR* 3.5 29.8 - - + -
1033E LEU* 6.1 0.9 - - - +
1034E THR* 4.1 18.8 - - + +
1036E SER* 4.0 8.7 + - - +
1038E SER 3.1 21.3 + - - +
1039E LEU* 5.2 0.2 - - - -
1041E ALA* 1.3 78.3 - - - +
1043E LYS* 1.3 66.6 + - + +
1044E SER 3.4 0.3 + - - -
1045E GLU* 3.7 2.3 + - - +
1046E LEU* 3.6 18.4 + - - +
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Residues in contact with LYS1043 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017E ILE* 3.8 31.3 - - + +
1025E TYR* 5.9 5.1 + - - -
1039E LEU* 3.7 32.5 + - + +
1040E ASN 5.0 0.2 - - - +
1041E ALA 3.6 0.2 - - - -
1042E ALA* 1.3 78.4 - - + +
1044E SER* 1.3 66.0 + - - +
1046E LEU* 3.5 22.0 + - + +
1047E ASP* 4.3 4.0 + - - +
1053E ASN* 5.2 7.1 + - - +
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Residues in contact with SER1044 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040E ASN 2.4 25.8 + - - -
1041E ALA* 4.1 5.6 - - - -
1042E ALA 3.3 0.8 - - - -
1043E LYS* 1.3 79.1 - - - +
1045E GLU* 1.3 60.2 + - - +
1047E ASP* 2.7 29.5 - - - +
1048E LYS* 5.1 0.5 - - - +
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Residues in contact with GLU1045 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034E THR* 5.9 7.0 - - + -
1041E ALA 3.7 17.0 + - - +
1042E ALA* 4.4 2.7 - - - +
1043E LYS 3.5 0.2 - - - -
1044E SER* 1.3 79.3 - - - +
1046E LEU* 1.3 58.5 + - - +
1047E ASP 3.3 0.9 - - - -
1048E LYS* 3.1 32.9 + - - +
1049E ALA* 3.0 25.5 + - - +
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Residues in contact with LEU1046 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017E ILE* 5.9 4.5 - - + -
1027E ILE* 3.6 44.4 - - + -
1033E LEU* 3.8 27.6 - - + -
1042E ALA 3.6 11.7 + - - +
1043E LYS* 3.5 18.1 + - + +
1044E SER 3.3 1.0 - - - -
1045E GLU* 1.3 78.5 - - - +
1047E ASP* 1.3 57.1 + - - +
1048E LYS 3.1 0.2 - - - -
1049E ALA* 3.3 4.1 + - + -
1050E ILE* 2.9 42.6 + - + +
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Residues in contact with ASP1047 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043E LYS 4.3 2.3 + - - +
1044E SER 2.7 27.6 + - - +
1046E LEU* 1.3 75.1 - - - +
1048E LYS* 1.3 63.7 + - - +
1050E ILE* 4.5 1.3 - - - -
1051E GLY* 3.2 30.3 - - - +
1052E ARG 4.3 10.8 - - - +
1053E ASN* 3.8 42.2 + - + +
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Residues in contact with LYS1048 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045E GLU* 3.1 31.1 + - - +
1047E ASP* 1.3 86.6 + - - +
1049E ALA* 1.3 60.8 + - + +
1050E ILE* 3.2 4.2 + - - -
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Residues in contact with ALA1049 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033E LEU* 4.5 23.6 - - + -
1045E GLU 3.0 12.2 + - - +
1046E LEU* 3.7 11.4 - - - +
1048E LYS* 1.3 79.6 - - + +
1050E ILE* 1.3 66.9 + - + +
1066E LEU* 5.3 1.7 - - - +
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Residues in contact with ILE1050 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1027E ILE* 3.9 16.6 - - + -
1033E LEU* 5.8 1.8 - - + -
1046E LEU* 2.9 35.0 + - + +
1047E ASP* 3.9 1.3 - - - -
1048E LYS 3.2 2.8 - - - +
1049E ALA* 1.3 86.0 - - + +
1051E GLY* 1.3 60.4 - - - +
1052E ARG* 4.1 17.5 - - + +
1058E ILE* 6.0 7.4 - - + -
1062E GLU* 5.1 13.2 - - + +
1066E LEU* 3.5 32.3 - - + -
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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