Contacts of the helix formed by residues 123 - 132 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C ASN* 3.7 11.4 - - - +
121C VAL* 3.3 16.6 - - + +
122C ASP* 1.3 85.9 - - - +
124C HIS* 1.3 58.0 + - - +
126C CYS* 3.4 8.6 + - + +
127C ASP* 3.0 28.6 + - - +
111R LEU* 3.7 18.8 - - + +
114R HIS* 3.6 43.7 - - + +
130R GLU* 4.4 5.7 - - - +
134R LEU* 3.7 17.3 - - + -
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Residues in contact with HIS 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TYR* 2.8 39.6 + + - -
71C LYS* 5.4 0.9 - - + -
72C ARG* 3.6 14.2 + - - +
122C ASP* 3.3 7.3 + - - +
123C PRO* 1.3 80.2 - - + +
125C LEU* 1.3 59.6 + - - +
127C ASP* 3.5 9.0 + - + +
128C PHE* 3.1 25.2 + - + +
111R LEU* 5.7 3.1 - - + -
134R LEU* 3.5 38.9 - - + +
135R GLU* 3.0 34.4 + - + +
138R VAL* 3.3 28.0 - - + +
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Residues in contact with LEU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C TYR* 4.4 6.3 - - + -
12C CYS* 4.0 28.5 - - + -
16C VAL* 4.3 13.5 - - + -
65C PHE* 5.3 0.4 - - + -
68C TYR* 3.2 33.4 + - + +
113C LEU* 4.4 12.6 - - + -
117C ALA* 3.9 19.7 - - + -
122C ASP* 2.9 24.3 + - - +
124C HIS* 1.3 73.5 - - - +
126C CYS* 1.3 65.9 + - - +
128C PHE* 3.5 12.7 + - + -
129C LEU* 3.1 36.5 + - + +
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Residues in contact with CYS 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C HIS* 3.6 21.1 - - - +
117C ALA* 3.6 18.2 - - - -
118C THR* 3.5 29.4 - - - -
122C ASP 3.4 15.1 + - - +
123C PRO* 3.5 12.6 - - + +
124C HIS 3.2 0.2 - - - -
125C LEU* 1.3 80.7 - - - +
127C ASP* 1.3 56.9 + - - +
129C LEU* 3.4 3.5 + - - +
130C GLU* 3.0 37.8 + - - +
130R GLU* 5.7 2.9 - - - +
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Residues in contact with ASP 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C PRO 3.0 16.4 + - - +
124C HIS* 3.8 8.8 - - - +
126C CYS* 1.3 75.4 - - - +
128C PHE* 1.3 61.1 + - - +
130C GLU* 4.2 10.9 - - - +
131C SER* 2.9 49.9 + - - -
127R ASP* 5.6 0.9 - - - +
130R GLU* 3.7 46.9 + - + +
131R SER* 5.0 3.5 + - - -
134R LEU* 6.4 0.7 - - + -
135R GLU* 5.1 8.3 - - - +
127S ASP* 5.7 0.9 - - - +
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Residues in contact with PHE 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C LYS* 3.7 24.2 - - + -
65C PHE* 3.5 20.4 - + - -
68C TYR* 3.6 38.4 - + + -
71C LYS* 6.2 2.7 - - - -
124C HIS* 3.1 19.0 + - + +
125C LEU* 3.6 9.4 - - + +
127C ASP* 1.3 77.5 + - - +
129C LEU* 1.3 68.3 - - + +
131C SER* 4.7 2.2 - - - -
132C GLU* 3.0 52.4 + - + +
133C TYR* 3.5 30.8 - + - -
135R GLU* 5.7 3.6 - - - -
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Residues in contact with LEU 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C PHE* 4.0 24.5 - - + -
110C LEU* 4.2 17.0 - - + +
113C LEU* 3.9 18.2 - - + +
114C HIS* 3.8 40.2 - - + +
117C ALA* 5.1 0.2 - - + -
125C LEU* 3.1 27.3 + - + +
126C CYS* 3.6 5.2 - - - +
128C PHE* 1.3 98.7 - - + +
130C GLU* 1.3 58.4 + - - +
133C TYR* 3.0 15.6 + - + +
134C LEU* 2.9 33.1 + - + +
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Residues in contact with GLU 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C HIS* 2.9 28.7 + - - +
126C CYS* 3.0 25.2 + - - +
127C ASP* 3.2 9.4 + - - +
129C LEU* 1.3 77.0 - - - +
131C SER* 1.3 63.0 + - - +
134C LEU* 3.9 17.9 + - + +
135C GLU* 4.1 18.5 + - - +
130R GLU* 3.9 17.7 - - - +
123S PRO* 4.4 7.9 - - - +
126S CYS* 5.7 2.5 - - - +
127S ASP* 3.7 44.4 - - + +
130S GLU* 3.9 10.5 - - - +
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Residues in contact with SER 131 (chain C).
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* 2.9 35.4 + - - -
128C PHE* 4.2 2.5 - - - -
130C GLU* 1.3 78.3 - - - +
132C GLU* 1.3 75.6 + - - +
135C GLU* 5.8 2.8 - - - +
127S ASP* 5.3 3.9 + - - -
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Residues in contact with GLU 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C HIS* 4.6 4.2 + - - -
64C LYS* 2.9 42.2 + - + +
128C PHE* 3.0 39.9 + - + +
131C SER* 1.3 90.5 - - - +
133C TYR* 1.3 79.4 + - + +
136C GLU* 4.2 12.3 - - - +
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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