Contacts of the helix formed by residues 123 - 132 (chain E) in PDB entry 1MFR
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 PRO 123 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B LEU* 3.7 18.8 - - + +
114B HIS* 3.5 43.3 - - + +
130B GLU* 4.4 6.7 - - - +
134B LEU* 3.7 16.8 - - + -
7E ASN* 3.7 11.4 - - - +
121E VAL* 3.3 16.8 - - + +
122E ASP* 1.3 84.6 - - - +
124E HIS* 1.3 59.0 + - + +
126E CYS* 3.4 8.2 + - + +
127E ASP* 3.0 28.6 + - - +
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Residues in contact with HIS 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU* 5.7 3.1 - - + -
134B LEU* 3.4 36.9 - - + +
135B GLU* 2.9 37.2 + - + +
138B VAL* 3.3 29.5 - - + +
68E TYR* 2.8 40.3 + + - -
71E LYS* 5.4 0.9 - - + -
72E ARG* 3.6 13.8 + - - +
122E ASP* 3.3 8.2 + - - +
123E PRO* 1.3 79.2 - - + +
125E LEU* 1.3 60.2 + - - +
127E ASP* 3.5 8.7 + - + +
128E PHE* 3.1 24.6 + - + +
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Residues in contact with LEU 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E TYR* 4.4 6.3 - - + -
12E CYS* 4.0 28.3 - - + -
16E VAL* 4.3 14.4 - - + -
68E TYR* 3.2 32.9 + - + +
113E LEU* 4.4 12.8 - - + -
117E ALA* 3.9 20.4 - - + -
122E ASP* 2.9 24.7 + - - +
124E HIS* 1.3 73.3 - - - +
126E CYS* 1.3 65.4 + - - +
128E PHE* 3.5 13.2 + - + -
129E LEU* 3.1 36.1 + - + +
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Residues in contact with CYS 126 (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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130B GLU* 5.7 3.4 - - - +
114E HIS* 3.6 22.9 - - + +
117E ALA* 3.6 18.6 - - - -
118E THR* 3.5 29.2 - - - -
122E ASP 3.4 15.1 + - - +
123E PRO* 3.5 13.0 - - + +
124E HIS 3.2 0.2 - - - -
125E LEU* 1.3 80.2 - - - +
127E ASP* 1.3 57.5 + - - +
129E LEU* 3.4 3.6 + - - +
130E GLU* 3.1 37.3 + - - +
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Residues in contact with ASP 127 (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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127B ASP* 5.6 1.0 - - - +
130B GLU* 3.7 46.2 - - + +
131B SER* 5.0 3.6 + - - -
134B LEU* 6.2 0.7 - - + -
135B GLU* 5.0 7.6 - - - +
123E PRO 3.0 17.5 + - - +
124E HIS* 3.8 9.4 - - + +
126E CYS* 1.3 76.4 - - - +
128E PHE* 1.3 61.2 + - - +
130E GLU* 4.2 11.2 - - - +
131E SER* 2.9 50.2 + - - -
127V ASP* 5.6 0.9 - - - +
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Residues in contact with PHE 128 (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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135B GLU* 5.7 3.6 - - - -
64E LYS* 3.7 24.5 - - + -
65E PHE* 3.5 20.4 - + - -
68E TYR* 3.6 39.9 - + + -
71E LYS* 6.2 2.9 - - - -
124E HIS* 3.1 19.0 + - + +
125E LEU* 3.6 9.4 - - + +
126E CYS 3.3 0.2 - - - -
127E ASP* 1.3 77.0 + - - +
129E LEU* 1.3 69.1 + - + +
131E SER* 4.7 2.9 - - - -
132E GLU* 3.0 51.3 + - + +
133E TYR* 3.5 30.3 - + - -
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Residues in contact with LEU 129 (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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65E PHE* 4.0 33.0 - - + -
110E LEU* 4.2 15.9 - - + +
113E LEU* 3.9 19.1 - - + +
114E HIS* 3.8 41.1 - - + +
117E ALA* 5.1 0.2 - - + -
125E LEU* 3.1 26.3 + - + +
126E CYS* 3.6 4.5 - - - +
127E ASP 3.2 0.2 - - - -
128E PHE* 1.3 89.3 - - + +
130E GLU* 1.3 58.4 + - - +
133E TYR* 3.0 15.8 + - + +
134E LEU* 2.9 33.0 + - + +
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Residues in contact with GLU 130 (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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130B GLU* 3.9 12.9 - - - +
114E HIS* 2.9 29.0 + - - +
126E CYS* 3.1 26.3 + - - +
127E ASP* 3.7 8.9 - - - +
129E LEU* 1.3 76.4 - - - +
131E SER* 1.3 62.9 + - - +
134E LEU* 3.9 25.9 + - + +
135E GLU* 4.1 11.8 + - - +
123V PRO* 4.4 7.6 - - - +
126V CYS* 5.7 2.4 - - - +
127V ASP* 3.7 45.6 - - + +
130V GLU* 3.9 15.0 - - - +
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Residues in contact with SER 131 (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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127E ASP* 2.9 34.8 + - - -
128E PHE* 4.2 2.7 - - - -
130E GLU* 1.3 79.3 - - - +
132E GLU* 1.3 74.8 + - - +
135E GLU* 5.8 2.8 - - - +
127V ASP* 5.3 4.4 + - - -
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Residues in contact with GLU 132 (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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61E HIS* 4.6 4.2 + - - -
64E LYS* 2.9 41.5 + - + +
128E PHE* 3.0 40.4 + - + +
131E SER* 1.3 89.6 - - - +
133E TYR* 1.3 77.9 + - + +
136E GLU* 4.2 12.2 - - - +
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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