Contacts of the helix formed by residues 123 - 132 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7R ASN* 3.7 11.4 - - - +
121R VAL* 3.3 17.0 - - + +
122R ASP* 1.3 85.1 - - - +
124R HIS* 1.3 58.6 + - - +
126R CYS* 3.4 8.6 + - + +
127R ASP* 3.0 28.4 + - - +
111S LEU* 3.7 19.1 - - + +
114S HIS* 3.5 44.2 - - + +
130S GLU* 4.4 6.0 - - - +
134S LEU* 3.8 15.9 - - + -
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Residues in contact with HIS 124 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7R ASN* 6.3 0.2 - - - +
68R TYR* 2.8 39.8 + + - -
71R LYS* 5.4 1.1 - - + -
72R ARG* 3.6 14.4 + - - +
122R ASP* 3.3 8.2 + - - +
123R PRO* 1.3 79.6 - - + +
125R LEU* 1.3 60.1 + - - +
127R ASP* 3.5 8.8 + - - +
128R PHE* 3.1 24.8 + - + +
111S LEU* 5.7 4.0 - - + -
134S LEU* 3.5 39.1 - - + +
135S GLU* 3.0 33.4 + - + +
138S VAL* 3.3 29.1 - - + +
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Residues in contact with LEU 125 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8R TYR* 4.4 7.0 - - + -
12R CYS* 4.0 28.5 - - + -
16R VAL* 4.3 13.7 - - + -
65R PHE* 5.3 0.2 - - + -
68R TYR* 3.2 34.7 + - + +
113R LEU* 4.4 13.2 - - + -
117R ALA* 3.9 20.9 - - + -
122R ASP* 2.9 23.5 + - - +
124R HIS* 1.3 74.3 - - - +
126R CYS* 1.3 65.2 + - - +
128R PHE* 3.6 12.3 - - + +
129R LEU* 3.1 35.9 + - + +
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Residues in contact with CYS 126 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114R HIS* 3.6 21.7 - - + +
117R ALA* 3.6 18.6 - - - -
118R THR* 3.5 29.4 - - - -
122R ASP 3.4 14.5 + - - +
123R PRO* 3.5 12.6 - - + +
124R HIS 3.2 0.2 - - - -
125R LEU* 1.3 80.2 - - - +
127R ASP* 1.3 56.2 + - - +
129R LEU* 3.4 4.2 + - - +
130R GLU* 3.1 36.6 + - - +
130S GLU* 5.7 3.4 - - - +
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Residues in contact with ASP 127 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ASP* 5.6 1.0 - - - +
123R PRO 3.0 17.5 + - - +
124R HIS* 3.8 9.2 - - + +
126R CYS* 1.3 75.1 - - - +
128R PHE* 1.3 60.6 + - - +
130R GLU* 4.2 12.2 - - - +
131R SER* 2.9 50.9 + - - -
127S ASP* 5.6 0.7 - - - +
130S GLU* 3.7 47.4 + - + +
131S SER* 5.0 3.5 + - - -
134S LEU* 6.1 0.6 - - + +
135S GLU* 5.1 8.0 - - - +
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Residues in contact with PHE 128 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64R LYS* 3.7 24.9 - - + -
65R PHE* 3.5 20.0 - + - -
68R TYR* 3.6 38.8 - + + -
71R LYS* 6.2 2.5 - - - -
124R HIS* 3.1 18.8 + - + +
125R LEU* 3.6 9.4 - - + +
126R CYS 3.3 0.2 - - - -
127R ASP* 1.3 78.9 + - - +
129R LEU* 1.3 68.8 + - + +
131R SER* 4.7 3.1 - - - -
132R GLU* 3.0 52.2 + - + +
133R TYR* 3.5 29.9 - + - -
135S GLU* 5.8 3.4 - - - -
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Residues in contact with LEU 129 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65R PHE* 4.0 32.8 - - + -
110R LEU* 4.2 17.0 - - + +
113R LEU* 3.9 18.6 - - + +
114R HIS* 3.8 42.0 - - + +
125R LEU* 3.1 27.3 + - + +
126R CYS* 3.6 4.7 - - - +
128R PHE* 1.3 88.9 - - + +
130R GLU* 1.3 58.1 + - - +
133R TYR* 3.0 15.4 + - + +
134R LEU* 2.9 33.7 + - + +
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Residues in contact with GLU 130 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C PRO* 4.4 8.3 - - - +
126C CYS* 5.7 2.5 - - - +
127C ASP* 3.7 45.3 - - + +
130C GLU* 3.9 15.5 - - - +
114R HIS* 2.9 28.7 + - - +
126R CYS* 3.1 22.9 + - - +
127R ASP* 3.2 9.4 + - - +
129R LEU* 1.3 77.8 - - - +
131R SER* 1.3 63.1 + - - +
134R LEU* 3.9 24.6 + - + +
135R GLU* 4.1 11.6 + - - +
130S GLU* 3.9 12.1 - - - +
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Residues in contact with SER 131 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ASP* 5.3 4.2 + - - -
127R ASP* 2.9 34.7 + - - -
128R PHE* 4.2 2.0 - - - -
130R GLU* 1.3 79.2 - - - +
132R GLU* 1.3 75.6 + - - +
135R GLU* 5.8 2.8 - - - +
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Residues in contact with GLU 132 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61R HIS* 4.6 3.8 + - - -
64R LYS* 2.9 42.1 + - + +
128R PHE* 3.0 40.7 + - + +
131R SER* 1.3 89.7 - - - +
133R TYR* 1.3 79.5 + - + +
136R GLU* 4.2 12.4 - - - +
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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