Contacts of the helix formed by residues 123 - 132 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7I ASN* 3.7 11.4 - - - +
121I VAL* 3.3 16.8 - - + +
122I ASP* 1.3 84.1 - - - +
124I HIS* 1.3 58.0 + - - +
126I CYS* 3.4 8.6 + - + +
127I ASP* 3.0 28.8 + - - +
111W LEU* 3.8 18.8 - - + +
114W HIS* 3.5 45.5 - - + +
115W LYS 5.9 0.2 - - - +
130W GLU* 4.4 6.5 - - - +
134W LEU* 3.9 13.5 - - + -
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Residues in contact with HIS 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68I TYR* 2.8 40.9 + + - -
71I LYS* 5.4 0.9 - - + -
72I ARG* 3.6 13.1 + - - +
122I ASP* 3.3 7.8 + - - +
123I PRO* 1.3 80.8 - - + +
125I LEU* 1.3 60.2 + - - +
127I ASP* 3.5 9.3 + - + +
128I PHE* 3.1 24.6 + - + +
111W LEU* 5.7 3.8 - - + -
134W LEU* 3.5 39.6 - - + +
135W GLU* 3.1 32.6 + - + +
138W VAL* 3.4 27.5 - - + +
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Residues in contact with LEU 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I TYR* 4.4 6.5 - - + -
12I CYS* 4.0 28.9 - - + -
16I VAL* 4.3 13.7 - - + -
65I PHE* 5.3 0.2 - - + -
68I TYR* 3.2 32.5 + - + +
113I LEU* 4.4 12.3 - - + -
117I ALA* 3.9 20.6 - - + -
122I ASP* 2.9 24.7 + - - +
124I HIS* 1.3 73.6 - - - +
126I CYS* 1.3 64.7 + - - +
128I PHE* 3.6 12.7 - - + +
129I LEU* 3.1 37.4 + - + +
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Residues in contact with CYS 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114I HIS* 3.6 22.4 - - + +
117I ALA* 3.6 18.6 - - - -
118I THR* 3.5 28.9 - - - -
122I ASP 3.4 14.7 + - - +
123I PRO* 3.5 12.1 - - + +
124I HIS 3.2 0.4 - - - -
125I LEU* 1.3 80.1 - - - +
127I ASP* 1.3 57.2 + - - +
129I LEU* 3.4 4.0 + - - +
130I GLU* 3.0 37.4 + - - +
130W GLU* 5.8 2.5 - - - +
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Residues in contact with ASP 127 (chain I).
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* 5.6 1.2 - - - +
123I PRO 3.0 16.6 + - - +
124I HIS* 3.8 9.1 - - + +
125I LEU 3.3 0.2 - - - -
126I CYS* 1.3 74.3 - - - +
128I PHE* 1.3 60.4 + - - +
130I GLU* 4.2 11.9 - - - +
131I SER* 2.9 50.1 + - - -
127W ASP* 5.6 1.0 - - - +
130W GLU* 3.7 46.8 + - + +
131W SER* 5.0 3.3 + - - -
134W LEU* 6.1 0.9 - - + -
135W GLU* 5.2 6.8 - - - +
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Residues in contact with PHE 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64I LYS* 3.7 25.1 - - + -
65I PHE* 3.5 20.6 - + - -
68I TYR* 3.6 39.3 - + + -
71I LYS* 6.2 2.0 - - - -
124I HIS* 3.1 18.8 + - + +
125I LEU* 3.6 9.6 - - + +
127I ASP* 1.3 78.1 + - - +
129I LEU* 1.3 69.3 + - + +
131I SER* 4.7 2.7 - - - -
132I GLU* 3.0 51.7 + - + +
133I TYR* 3.5 30.3 - + - -
135W GLU* 5.8 3.1 - - - -
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Residues in contact with LEU 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65I PHE* 4.0 33.0 - - + -
110I LEU* 4.3 17.0 - - + +
113I LEU* 3.9 18.6 - - + +
114I HIS* 3.8 41.5 - - + +
117I ALA* 5.1 0.2 - - + -
125I LEU* 3.1 26.7 + - + +
126I CYS* 3.6 4.7 - - - +
127I ASP 3.2 0.2 - - - -
128I PHE* 1.3 89.4 - - + +
130I GLU* 1.3 57.7 + - - +
133I TYR* 3.0 15.2 + - + +
134I LEU* 2.9 33.8 + - + +
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Residues in contact with GLU 130 (chain I).
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* 4.3 7.1 - - - +
126D CYS* 5.7 2.5 - - - +
127D ASP* 3.7 41.5 - - + +
130D GLU* 3.9 17.5 - - - +
114I HIS* 2.9 29.3 + - - +
126I CYS* 3.0 24.6 + - - +
127I ASP* 3.7 8.6 - - - +
129I LEU* 1.3 77.3 - - - +
131I SER* 1.3 62.2 + - - +
134I LEU* 3.9 24.9 + - + +
135I GLU* 4.1 11.6 + - - +
130W GLU* 4.0 12.1 - - - +
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Residues in contact with SER 131 (chain I).
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* 5.2 4.2 + - - -
127I ASP* 2.9 35.0 + - - -
128I PHE* 4.2 2.2 - - - -
130I GLU* 1.3 80.0 - - - +
132I GLU* 1.3 74.4 + - - +
135I GLU* 5.8 3.2 - - - +
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Residues in contact with GLU 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61I HIS* 4.6 4.2 + - - -
64I LYS* 2.9 42.7 + - + +
128I PHE* 3.0 39.9 + - + +
131I SER* 1.3 90.8 - - - +
133I TYR* 1.3 77.5 + - + +
136I 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