Contacts of the helix formed by residues 123 - 132 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111E LEU* 3.7 28.3 - - + +
114E HIS* 3.5 44.0 - - + +
130E GLU* 4.4 6.4 - - - +
134E LEU* 3.7 17.0 - - + -
7V ASN* 3.7 1.8 - - - +
121V VAL* 3.3 17.5 - - + +
122V ASP* 1.3 84.0 - - - +
124V HIS* 1.3 58.3 + - - +
126V CYS* 3.4 8.8 + - + +
127V ASP* 3.0 28.6 + - - +
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Residues in contact with HIS 124 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E LEU* 5.7 3.6 - - + -
134E LEU* 3.4 39.6 - - + +
135E GLU* 3.0 31.9 + - + +
138E VAL* 3.3 29.1 - - + +
7V ASN* 6.3 0.2 - - - +
68V TYR* 2.8 39.6 + + - -
71V LYS* 5.4 1.1 - - + -
72V ARG* 3.6 13.4 + - - +
122V ASP* 3.3 7.5 + - - +
123V PRO* 1.3 78.8 - - + +
125V LEU* 1.3 60.3 + - - +
127V ASP* 3.5 8.9 + - - +
128V PHE* 3.1 25.7 + - + +
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Residues in contact with LEU 125 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8V TYR* 4.4 6.5 - - + -
12V CYS* 4.0 28.5 - - + -
16V VAL* 4.3 12.8 - - + -
65V PHE* 5.3 0.2 - - + -
68V TYR* 3.2 33.3 + - + +
113V LEU* 4.4 13.0 - - + -
117V ALA* 3.9 19.7 - - + -
122V ASP* 2.9 23.4 + - - +
124V HIS* 1.3 75.2 - - - +
126V CYS* 1.3 66.1 + - - +
128V PHE* 3.5 13.0 + - + -
129V LEU* 3.1 35.2 + - + +
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Residues in contact with CYS 126 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E GLU* 5.7 3.1 - - - +
114V HIS* 3.6 21.8 - - + +
117V ALA* 3.6 18.8 - - - -
118V THR* 3.5 29.4 - - - -
122V ASP 3.4 15.3 + - - +
123V PRO* 3.5 11.9 - - + +
124V HIS 3.2 0.2 - - - -
125V LEU* 1.3 80.2 - - - +
127V ASP* 1.3 57.2 + - - +
129V LEU* 3.4 3.8 + - - +
130V GLU* 3.1 38.4 + - - +
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Residues in contact with ASP 127 (chain V).
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* 5.7 0.7 - - - +
127E ASP* 5.6 1.2 - - - +
130E GLU* 3.7 49.7 + - + +
131E SER* 5.0 3.5 + - - -
134E LEU* 6.1 1.1 - - + -
135E GLU* 5.1 8.0 - - - +
123V PRO 3.0 17.0 + - - +
124V HIS* 3.8 8.6 - - + +
126V CYS* 1.3 75.2 - - - +
128V PHE* 1.3 60.6 + - - +
130V GLU* 3.7 11.0 - - - +
131V SER* 2.9 49.3 + - - -
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Residues in contact with PHE 128 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E GLU* 5.7 4.0 - - - -
64V LYS* 3.7 24.2 - - + -
65V PHE* 3.5 20.6 - + - -
68V TYR* 3.6 38.8 - + + -
71V LYS* 6.2 2.2 - - - -
124V HIS* 3.1 19.3 + - + +
125V LEU* 3.6 10.1 - - + +
127V ASP* 1.3 77.3 + - - +
129V LEU* 1.3 68.5 + - + +
131V SER* 4.7 2.5 - - - -
132V GLU* 3.0 52.4 + - + +
133V TYR* 3.5 30.3 - + - -
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Residues in contact with LEU 129 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65V PHE* 4.0 24.5 - - + -
110V LEU* 4.3 16.2 - - + +
113V LEU* 3.9 18.6 - - + +
114V HIS* 3.8 41.7 - - + +
117V ALA* 5.1 0.2 - - + -
125V LEU* 3.1 27.1 + - + +
126V CYS* 3.6 4.7 - - - +
128V PHE* 1.3 96.6 - - + +
130V GLU* 1.3 58.5 + - - +
133V TYR* 3.0 15.4 + - + +
134V LEU* 2.9 33.0 + - + +
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Residues in contact with GLU 130 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B PRO* 4.4 6.8 - - - +
126B CYS* 5.7 2.2 - - - +
127B ASP* 3.7 46.0 - - + +
130B GLU* 3.9 10.3 - - - +
130E GLU* 3.9 17.7 - - - +
114V HIS* 2.9 29.3 + - - +
126V CYS* 3.1 24.0 + - - +
127V ASP* 3.2 8.2 + - - +
129V LEU* 1.3 77.8 - - - +
131V SER* 1.3 62.7 + - - +
134V LEU* 3.9 18.5 + - + +
135V GLU* 4.1 18.5 + - - +
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Residues in contact with SER 131 (chain V).
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* 5.3 3.4 + - - -
127V ASP* 2.9 34.9 + - - -
128V PHE* 4.2 2.2 - - - -
130V GLU* 1.3 78.7 - - - +
132V GLU* 1.3 76.2 + - - +
135V GLU* 5.8 2.4 - - - +
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Residues in contact with GLU 132 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61V HIS* 4.6 4.0 + - - -
64V LYS* 2.9 42.4 + - + +
128V PHE* 3.0 41.2 + - + +
131V SER* 1.3 89.4 - - - +
133V TYR* 1.3 78.1 + - + +
136V 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