Contacts of the helix formed by residues 123 - 132 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D ASN* 3.7 11.2 - - - +
121D VAL* 3.3 17.7 - - + +
122D ASP* 1.3 83.8 - - - +
124D HIS* 1.3 58.8 + - - +
126D CYS* 3.4 8.6 + - + +
127D ASP* 3.0 28.2 + - - +
111I LEU* 3.8 19.3 - - + +
114I HIS* 3.5 44.0 - - + +
130I GLU* 4.3 6.2 - - - +
134I LEU* 3.7 17.5 - - + -
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Residues in contact with HIS 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D TYR* 2.8 39.6 + + - -
71D LYS* 5.4 0.9 - - + -
72D ARG* 3.6 13.3 + - - +
122D ASP* 3.3 7.6 - - - +
123D PRO* 1.3 79.8 - - + +
125D LEU* 1.3 61.2 + - - +
127D ASP* 3.5 8.2 + - + +
128D PHE* 3.1 25.8 + + + +
111I LEU* 5.8 2.9 - - + -
134I LEU* 3.5 36.4 - - + +
135I GLU* 2.9 36.8 + - + +
138I VAL* 3.3 28.6 - - + +
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Residues in contact with LEU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D TYR* 4.4 6.7 - - + -
12D CYS* 4.0 28.3 - - + -
16D VAL* 4.3 14.1 - - + -
65D PHE* 5.3 0.2 - - + -
68D TYR* 3.2 33.6 + - + +
113D LEU* 4.4 12.6 - - + -
117D ALA* 3.9 20.6 - - + -
122D ASP* 2.9 24.7 + - - +
124D HIS* 1.3 74.2 - - - +
126D CYS* 1.3 66.0 + - - +
128D PHE* 3.5 12.7 + - + +
129D LEU* 3.1 36.3 + - + +
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Residues in contact with CYS 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D HIS* 3.6 21.4 - - + +
117D ALA* 3.6 19.1 - - - -
118D THR* 3.5 28.9 - - - -
122D ASP 3.4 15.3 + - - +
123D PRO* 3.5 11.9 - - + +
125D LEU* 1.3 80.2 - - - +
127D ASP* 1.3 57.9 + - - +
129D LEU* 3.4 3.7 + - - +
130D GLU* 3.1 37.6 + - - +
130I GLU* 5.7 3.1 - - - +
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Residues in contact with ASP 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D PRO 3.0 16.9 + - - +
124D HIS* 3.8 9.2 - - + +
126D CYS* 1.3 74.9 - - - +
128D PHE* 1.3 60.8 + - - +
130D GLU* 4.2 11.8 - - - +
131D SER* 2.9 50.5 + - - -
127I ASP* 5.6 1.0 - - - +
130I GLU* 3.7 47.0 + - + +
131I SER* 4.9 4.2 + - - -
134I LEU* 6.2 0.7 - - + -
135I GLU* 5.0 8.3 - - - +
127W ASP* 5.6 0.7 - - - +
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Residues in contact with PHE 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D LYS* 3.7 24.7 - - + -
65D PHE* 3.5 20.0 - + - -
68D TYR* 3.6 39.9 - + + -
71D LYS* 6.2 2.7 - - - -
124D HIS* 3.1 19.2 + - + +
125D LEU* 3.6 9.6 - - + +
126D CYS 3.3 0.4 - - - -
127D ASP* 1.3 78.1 + - - +
129D LEU* 1.3 69.6 + - + +
131D SER* 4.7 2.7 - - - -
132D GLU* 3.0 52.1 + - + +
133D TYR* 3.5 30.7 - + - -
135I GLU* 5.7 3.8 - - - +
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Residues in contact with LEU 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D PHE* 4.0 33.0 - - + -
110D LEU* 4.3 17.3 - - + +
113D LEU* 3.9 18.6 - - + +
114D HIS* 3.8 41.3 - - + +
125D LEU* 3.1 26.9 + - + +
126D CYS* 3.6 4.7 - - - +
128D PHE* 1.3 88.7 - - + +
130D GLU* 1.3 58.1 + - - +
133D TYR* 3.0 16.0 + - + +
134D LEU* 2.9 32.5 + - + +
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Residues in contact with GLU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D HIS* 2.9 30.0 + - - +
126D CYS* 3.1 25.1 + - - +
127D ASP* 3.7 8.4 - - - +
129D LEU* 1.3 78.1 - - - +
131D SER* 1.3 63.2 + - - +
134D LEU* 3.9 23.8 + - + +
135D GLU* 4.1 11.8 + - - +
130I GLU* 3.9 17.7 - - - +
123W PRO* 4.4 7.5 - - - +
126W CYS* 5.7 2.5 - - - +
127W ASP* 3.7 44.2 - - + +
130W GLU* 3.9 9.6 - - - +
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Residues in contact with SER 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ASP* 2.9 34.3 + - - -
128D PHE* 4.2 2.2 - - - -
130D GLU* 1.3 80.8 - - - +
132D GLU* 1.3 75.3 + - - +
135D GLU* 5.8 2.4 - - - +
127W ASP* 5.3 4.0 + - - -
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Residues in contact with GLU 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D HIS* 4.6 3.8 + - - -
64D LYS* 2.9 41.4 + - + +
128D PHE* 3.0 41.2 + - + +
131D SER* 1.3 87.6 - - - +
133D TYR* 1.3 80.0 + - + +
136D GLU* 4.2 12.6 - - - +
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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