Contacts of the helix formed by residues 1055 - 1062 (chain E) in PDB entry 2FO1
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 THR1055 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1027E HIS* 3.9 2.9 - - - -
1045E VAL 4.5 0.5 - - - -
1046E ASN* 4.3 23.0 + - - -
1048E ILE 4.0 14.4 + - - -
1049E ASP* 4.5 5.0 + - - -
1054E ARG* 1.3 75.4 - - - +
1056E VAL* 1.3 63.9 + - - +
1057E LEU* 3.2 30.5 - - + +
1058E HIS* 2.7 48.7 - - + +
1059E TRP* 3.1 6.6 + - - -
1086E ASP* 5.4 4.7 + - - +
1089E ALA* 4.7 11.8 - - + +
1097E PRO* 4.7 4.0 - - + -
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Residues in contact with VAL1056 (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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1026E LEU* 3.7 26.9 - - + -
1027E HIS* 3.5 27.9 + - + +
1030E ALA* 4.3 2.5 - - + -
1040E ILE* 6.6 0.2 - - + -
1044E SER 4.4 0.7 - - - +
1045E VAL* 3.3 47.8 - - + -
1048E ILE 5.7 0.2 - - - +
1055E THR* 1.3 74.0 + - - +
1057E LEU* 1.3 54.1 + - - +
1059E TRP* 2.8 5.5 + - - +
1060E ILE* 2.6 59.4 + - + +
1080E CYS* 4.3 7.6 - - + -
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Residues in contact with LEU1057 (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 VAL* 4.9 3.8 - - + -
1046E ASN 5.8 0.2 - - - +
1055E THR* 3.2 21.5 - - + +
1056E VAL* 1.3 78.5 - - + +
1058E HIS* 1.3 54.9 + - - +
1060E ILE* 3.3 12.8 - - + -
1061E ALA* 2.4 40.3 + - + +
1077E ALA* 5.3 5.4 - - + +
1080E CYS* 4.4 17.9 - - + -
1081E ILE* 4.4 12.3 - - + -
1085E ALA* 4.0 30.3 - - + -
1086E ASP 5.5 2.2 - - - +
1087E VAL* 4.3 18.4 - - - -
1097E PRO* 4.1 14.1 - - + -
1113E LEU* 4.4 20.9 - - + -
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Residues in contact with HIS1058 (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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1053E ASN 4.3 2.0 - - - -
1054E ARG* 3.6 26.9 - - + +
1055E THR* 2.7 48.3 + - + +
1057E LEU* 1.3 83.0 - - - +
1059E TRP* 1.3 58.1 + - - +
1061E ALA* 3.3 6.3 - - - +
1062E SER* 3.0 18.9 + - - -
1089E ALA* 2.7 43.4 + - + +
1090E MSE 3.7 5.3 - - - -
1091E ASP* 3.9 3.7 - - + +
1095E ASN 2.9 21.7 + - - -
1097E PRO* 3.3 22.9 - - + +
1100E LEU* 3.7 14.1 - - - +
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Residues in contact with TRP1059 (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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659A LYS* 4.8 9.6 - - + -
661A LEU* 3.5 44.0 - - + -
1027E HIS* 3.6 43.0 + + + +
1030E ALA* 4.6 7.3 - - + +
1031E ALA* 4.5 25.3 - - + +
1050E PRO* 4.3 8.6 - - + +
1052E HIS* 4.1 28.9 - + - -
1054E ARG* 3.6 46.8 + - + +
1055E THR 3.1 13.9 + - - -
1056E VAL 2.8 6.2 + - - +
1058E HIS* 1.3 74.2 - - - +
1060E ILE* 1.3 69.2 + - - +
1062E SER* 3.1 28.2 - - - +
1065E SER* 4.5 4.0 + - - -
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Residues in contact with ILE1060 (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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1030E ALA* 3.2 36.8 - - + +
1056E VAL* 2.6 52.9 + - + +
1057E LEU* 3.3 9.4 - - + +
1059E TRP* 1.3 73.3 - - - +
1061E ALA* 1.3 68.8 + - - +
1062E SER 3.1 6.2 + - - +
1063E ASN* 3.8 3.1 + - - -
1065E SER* 4.8 1.3 + - - -
1073E ILE* 3.9 43.9 - - + +
1076E GLU* 4.1 17.0 - - + +
1077E ALA* 4.1 17.3 - - + +
1080E CYS* 4.3 8.3 - - - -
1109E LEU* 4.7 2.3 - - + +
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Residues in contact with ALA1061 (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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1057E LEU 2.4 32.9 + - - +
1058E HIS* 3.3 7.6 - - - +
1060E ILE* 1.3 67.5 - - - +
1062E SER* 1.3 51.1 - - - +
1063E ASN* 2.3 28.6 + - - +
1097E PRO* 3.8 25.8 - - + +
1100E LEU* 3.9 13.4 - - + +
1101E ALA* 4.4 4.3 - - + +
1104E ALA* 4.4 5.4 - - - +
1106E ARG* 5.5 0.2 - - - +
1109E LEU* 3.7 26.4 - - + +
1113E LEU* 5.8 2.2 - - + -
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Residues in contact with SER1062 (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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573A HIS* 4.3 7.5 - - - -
1054E ARG* 4.5 16.6 + - - -
1058E HIS 3.0 9.8 + - - -
1059E TRP* 3.1 28.6 - - - +
1060E ILE 3.5 2.5 - - - +
1061E ALA* 1.3 74.6 - - - +
1063E ASN* 1.3 53.0 + - - +
1064E SER* 2.4 38.8 + - - +
1065E SER* 3.2 11.1 + - - -
1100E LEU* 4.6 10.0 - - - +
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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