Contacts of the helix formed by residues 123 - 132 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C LEU* 3.7 20.9 - - + +
114C HIS* 3.6 41.7 - - + +
130C GLU* 4.4 6.1 - - - +
134C LEU* 3.7 17.3 - - + -
7S ASN* 3.7 11.4 - - - +
121S VAL* 3.3 17.5 - - + +
122S ASP* 1.3 84.9 - - - +
124S HIS* 1.3 59.5 + - - +
126S CYS* 3.4 8.2 + - + +
127S ASP* 3.0 28.6 + - - +
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Residues in contact with HIS 124 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C LEU* 5.7 3.6 - - + -
134C LEU* 3.5 39.0 - - + +
135C GLU* 3.0 32.3 + - + +
138C VAL* 3.2 29.2 - - + +
68S TYR* 2.8 39.8 + + - -
71S LYS* 5.4 1.3 - - + -
72S ARG* 3.6 13.4 + - - +
122S ASP* 3.3 8.4 - - - +
123S PRO* 1.3 80.2 - - + +
125S LEU* 1.3 59.7 + - - +
127S ASP* 3.5 8.6 + - + +
128S PHE* 3.1 24.8 + - + +
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Residues in contact with LEU 125 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8S TYR* 4.4 7.4 - - + -
12S CYS* 4.0 28.7 - - + -
16S VAL* 4.3 13.7 - - + -
65S PHE* 5.3 0.4 - - + -
68S TYR* 3.2 33.6 + - + +
113S LEU* 4.4 11.9 - - + -
117S ALA* 3.9 21.1 - - + -
122S ASP* 2.9 23.2 + - - +
124S HIS* 1.3 74.5 - - - +
126S CYS* 1.3 66.1 + - - +
128S PHE* 3.6 13.0 - - + +
129S LEU* 3.1 35.6 + - + +
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Residues in contact with CYS 126 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C GLU* 5.7 3.1 - - - +
114S HIS* 3.6 21.5 - - - +
117S ALA* 3.6 19.1 - - - -
118S THR* 3.5 29.4 - - - -
122S ASP 3.4 15.1 + - - +
123S PRO* 3.5 12.6 - - + +
124S HIS 3.2 0.2 - - - -
125S LEU* 1.3 81.1 - - - +
127S ASP* 1.3 58.5 + - - +
129S LEU* 3.4 4.0 + - - +
130S GLU* 3.1 37.0 + - - +
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Residues in contact with ASP 127 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ASP* 5.7 0.7 - - - +
130C GLU* 3.7 47.7 + - + +
131C SER* 5.0 3.3 + - - -
134C LEU* 6.2 0.9 - - + -
135C GLU* 5.0 8.3 - - - +
127R ASP* 5.6 1.0 - - - +
123S PRO 3.0 17.0 + - - +
124S HIS* 3.8 8.9 - - + +
125S LEU 3.3 0.2 - - - -
126S CYS* 1.3 75.0 - - - +
128S PHE* 1.3 60.8 + - - +
130S GLU* 4.2 11.1 - - - +
131S SER* 2.9 50.5 + - - -
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Residues in contact with PHE 128 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C GLU* 5.8 3.8 - - - +
64S LYS* 3.7 24.2 - - + -
65S PHE* 3.5 20.9 - + - -
68S TYR* 3.6 39.3 - + + -
71S LYS* 6.2 2.7 - - - -
124S HIS* 3.1 18.8 + - + +
125S LEU* 3.6 9.9 - - + +
127S ASP* 1.3 77.0 + - - +
129S LEU* 1.3 69.4 + - + +
131S SER* 4.7 2.7 - - - -
132S GLU* 3.0 51.5 + - + +
133S TYR* 3.5 30.5 - + - -
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Residues in contact with LEU 129 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65S PHE* 4.0 33.0 - - + -
110S LEU* 4.2 16.2 - - + +
113S LEU* 3.9 18.6 - - + +
114S HIS* 3.8 40.8 - - + +
125S LEU* 3.1 26.4 + - + +
126S CYS 3.6 4.7 - - - +
128S PHE* 1.3 88.6 - - + +
130S GLU* 1.3 58.6 + - - +
133S TYR* 3.0 16.8 + - + +
134S LEU* 2.9 33.0 + - + +
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Residues in contact with GLU 130 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C GLU* 3.9 17.7 - - - +
123R PRO* 4.4 7.4 - - - +
126R CYS* 5.7 1.9 - - - +
127R ASP* 3.7 46.4 - - + +
130R GLU* 3.9 9.8 - - - +
114S HIS* 2.9 29.2 + - - +
126S CYS* 3.1 24.1 + - - +
127S ASP* 3.7 8.9 - - - +
129S LEU* 1.3 76.6 - - - +
131S SER* 1.3 63.4 + - - +
134S LEU* 3.9 17.5 - - + +
135S GLU* 4.1 18.7 + - - +
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Residues in contact with SER 131 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127R ASP* 5.3 4.4 + - - -
127S ASP* 2.9 35.4 + - - -
128S PHE* 4.2 2.2 - - - -
130S GLU* 1.3 78.2 - - - +
132S GLU* 1.3 74.5 + - - +
135S GLU* 5.8 2.8 - - - +
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Residues in contact with GLU 132 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61S HIS* 4.6 4.3 + - - -
64S LYS* 2.9 42.3 + - + +
128S PHE* 3.0 40.4 + - + +
131S SER* 1.3 90.0 - - - +
133S TYR* 1.3 80.3 + - + +
136S GLU* 4.2 12.0 - - - +
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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