Contacts of the helix formed by residues 123 - 132 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111N LEU* 3.7 19.1 - - + +
114N HIS* 3.5 44.0 - - + +
130N GLU* 4.4 5.9 - - - +
134N LEU* 3.7 17.3 - - + -
7Q ASN* 3.7 11.9 - - - +
121Q VAL* 3.3 16.6 - - + +
122Q ASP* 1.3 84.1 - - - +
124Q HIS* 1.3 58.2 + - + +
126Q CYS* 3.4 8.6 + - + +
127Q ASP* 3.0 28.4 + - - +
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Residues in contact with HIS 124 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111N LEU* 5.7 3.6 - - + -
134N LEU* 3.4 40.1 - - + +
135N GLU* 3.0 33.8 + - + +
138N VAL* 3.3 28.6 - - + +
7Q ASN* 6.3 0.2 - - - +
68Q TYR* 2.8 40.8 + + - -
71Q LYS* 5.4 0.7 - - + -
72Q ARG* 3.6 13.8 + - - +
122Q ASP* 3.3 7.8 - - - +
123Q PRO* 1.3 80.8 - - + +
125Q LEU* 1.3 59.6 + - - +
127Q ASP* 3.5 8.6 + - + +
128Q PHE* 3.1 24.9 + - + +
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Residues in contact with LEU 125 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Q TYR* 4.4 6.7 - - + -
12Q CYS* 4.0 27.6 - - + -
16Q VAL* 4.3 13.2 - - + -
65Q PHE* 5.3 0.2 - - + -
68Q TYR* 3.2 33.4 + - + +
72Q ARG* 4.3 0.2 - - - +
113Q LEU* 4.4 13.0 - - + -
117Q ALA* 3.9 20.4 - - + -
122Q ASP* 2.9 24.3 + - - +
124Q HIS* 1.3 74.1 - - - +
126Q CYS* 1.3 65.2 + - - +
128Q PHE* 3.5 12.7 + - + -
129Q LEU* 3.1 36.2 + - + +
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Residues in contact with CYS 126 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130N GLU* 5.7 3.1 - - - +
114Q HIS* 3.6 23.3 - - - +
117Q ALA* 3.6 18.4 - - - -
118Q THR* 3.5 29.2 - - - -
122Q ASP 3.4 14.7 + - - +
123Q PRO* 3.5 11.9 - - + +
124Q HIS 3.2 0.2 - - - -
125Q LEU* 1.3 80.0 - - - +
127Q ASP* 1.3 56.8 + - - +
129Q LEU* 3.4 3.8 + - - +
130Q GLU* 3.1 37.6 + - - +
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Residues in contact with ASP 127 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J ASP* 5.6 1.2 - - - +
127N ASP* 5.6 0.9 - - - +
130N GLU* 3.7 46.4 - - + +
131N SER* 5.0 3.5 + - - -
134N LEU* 6.1 0.9 - - + -
135N GLU* 5.0 8.1 - - - +
123Q PRO 3.0 16.8 + - - +
124Q HIS* 3.8 9.0 - - + +
126Q CYS* 1.3 75.6 - - - +
128Q PHE* 1.3 59.8 + - - +
130Q GLU* 4.2 11.0 - - - +
131Q SER* 2.9 49.8 + - - -
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Residues in contact with PHE 128 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135N GLU* 5.7 3.6 - - - -
64Q LYS* 3.7 24.9 - - + -
65Q PHE* 3.5 20.6 - + - -
68Q TYR* 3.6 39.5 - + + -
71Q LYS* 6.2 2.5 - - - -
124Q HIS* 3.1 18.9 + - + +
125Q LEU* 3.6 10.1 - - + +
126Q CYS 3.3 0.2 - - - -
127Q ASP* 1.3 77.9 + - - +
129Q LEU* 1.3 69.2 + - + +
131Q SER* 4.7 2.5 - - - -
132Q GLU* 3.0 52.3 + - + +
133Q TYR* 3.5 30.9 - + - -
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Residues in contact with LEU 129 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65Q PHE* 4.0 24.0 - - + -
110Q LEU* 4.2 16.4 - - + +
113Q LEU* 3.9 17.7 - - + +
114Q HIS* 3.8 41.5 - - + +
117Q ALA* 5.1 0.2 - - + -
125Q LEU* 3.1 26.4 + - + +
126Q CYS* 3.6 4.7 - - - +
128Q PHE* 1.3 98.4 - - + +
130Q GLU* 1.3 57.2 + - - +
133Q TYR* 3.0 16.2 + - + +
134Q LEU* 2.9 33.2 + - + +
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Residues in contact with GLU 130 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J PRO* 4.3 7.1 - - - +
126J CYS* 5.7 2.7 - - - +
127J ASP* 3.7 46.4 - - + +
130J GLU* 3.9 10.4 - - - +
130N GLU* 3.9 17.9 - - - +
114Q HIS* 2.9 28.6 + - - +
126Q CYS* 3.1 24.8 + - - +
127Q ASP* 3.7 8.8 - - - +
129Q LEU* 1.3 76.7 - - - +
131Q SER* 1.3 62.6 + - - +
134Q LEU* 3.9 26.2 + - + +
135Q GLU* 4.1 12.0 + - - +
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Residues in contact with SER 131 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J ASP* 5.2 4.2 + - - -
127Q ASP* 2.9 35.4 + - - -
128Q PHE* 4.2 2.5 - - - -
130Q GLU* 1.3 78.8 - - - +
132Q GLU* 1.3 74.0 + - - +
135Q GLU* 5.8 2.8 - - - +
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Residues in contact with GLU 132 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61Q HIS* 4.6 4.0 + - - -
64Q LYS* 2.9 42.0 + - + +
128Q PHE* 3.0 40.1 + - + +
131Q SER* 1.3 89.9 - - - +
133Q TYR* 1.3 78.3 + - + +
136Q 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