Contacts of the helix formed by residues 123 - 132 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111F LEU* 3.7 18.6 - - + +
114F HIS* 3.5 47.1 - - + +
130F GLU* 4.4 5.5 - - - +
134F LEU* 3.8 14.6 - - + -
7O ASN* 3.7 11.9 - - - +
121O VAL* 3.3 17.0 - - + +
122O ASP* 1.3 84.4 - - - +
124O HIS* 1.3 58.4 + - + +
126O CYS* 3.4 8.0 + - + +
127O ASP* 3.0 28.4 + - - +
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Residues in contact with HIS 124 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F LEU* 5.7 3.6 - - + -
134F LEU* 3.5 39.2 - - + +
135F GLU* 3.1 32.9 + - + +
138F VAL* 3.3 28.4 - - + +
68O TYR* 2.8 40.4 + + - -
71O LYS* 5.4 0.7 - - + -
72O ARG* 3.6 13.6 + - - +
122O ASP* 3.3 9.0 + - - +
123O PRO* 1.3 79.4 - - + +
125O LEU* 1.3 60.7 + - - +
127O ASP* 3.5 9.2 + - + +
128O PHE* 3.1 25.0 + - + +
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Residues in contact with LEU 125 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8O TYR* 4.4 6.7 - - + -
12O CYS* 4.0 28.3 - - + -
16O VAL* 4.3 13.5 - - + -
65O PHE* 5.3 0.4 - - + -
68O TYR* 3.2 33.4 + - + +
113O LEU* 4.4 13.0 - - + -
117O ALA* 3.9 21.1 - - + -
122O ASP* 2.9 23.0 + - - +
124O HIS* 1.3 74.3 - - - +
126O CYS* 1.3 65.6 + - - +
128O PHE* 3.5 12.5 + - + -
129O LEU* 3.1 36.2 + - + +
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Residues in contact with CYS 126 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F GLU* 5.7 2.7 - - - +
114O HIS* 3.6 22.4 - - + +
117O ALA* 3.6 19.1 - - - -
118O THR* 3.5 29.6 - - - -
122O ASP 3.4 15.3 + - - +
123O PRO* 3.5 12.8 - - + +
125O LEU* 1.3 80.2 - - - +
127O ASP* 1.3 57.3 + - - +
129O LEU* 3.4 4.0 + - - +
130O GLU* 3.1 37.0 + - - +
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Residues in contact with ASP 127 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F ASP* 5.6 1.0 - - - +
130F GLU* 3.7 48.0 + - + +
131F SER* 5.0 3.6 + - - -
134F LEU* 6.4 0.7 - - + -
135F GLU* 5.1 7.8 - - - +
127G ASP* 5.6 1.0 - - - +
123O PRO 3.0 17.0 + - - +
124O HIS* 3.8 8.4 - - + +
126O CYS* 1.3 74.3 - - - +
128O PHE* 1.3 60.1 + - - +
130O GLU* 4.2 11.9 - - - +
131O SER* 2.9 49.3 + - - -
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Residues in contact with PHE 128 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F GLU* 5.7 3.6 - - - -
64O LYS* 3.7 23.8 - - + -
65O PHE* 3.5 20.9 - + - -
68O TYR* 3.6 38.1 - + + -
71O LYS* 6.2 2.5 - - - -
124O HIS* 3.1 19.8 + - + +
125O LEU* 3.6 9.2 - - + +
126O CYS 3.3 0.2 - - - -
127O ASP* 1.3 78.1 + - - +
129O LEU* 1.3 69.1 + - + +
131O SER* 4.7 2.5 - - - -
132O GLU* 3.0 52.1 + - + +
133O TYR* 3.5 30.7 - + - -
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Residues in contact with LEU 129 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65O PHE* 4.0 24.5 - - + -
110O LEU* 4.3 17.3 - - + +
113O LEU* 3.9 17.9 - - + +
114O HIS* 3.8 40.8 - - + +
117O ALA* 5.1 0.4 - - + -
125O LEU* 3.1 26.4 + - + +
126O CYS* 3.6 4.7 - - - +
128O PHE* 1.3 98.6 - - + +
130O GLU* 1.3 58.2 + - - +
133O TYR* 3.0 14.6 + - + +
134O LEU* 2.9 33.8 + - + +
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Residues in contact with GLU 130 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F GLU* 3.9 12.9 - - - +
123G PRO* 4.4 7.6 - - - +
126G CYS* 5.7 2.5 - - - +
127G ASP* 3.7 44.3 - - + +
130G GLU* 3.9 15.6 - - - +
114O HIS* 2.9 28.7 + - - +
126O CYS* 3.1 24.0 + - - +
127O ASP* 3.2 9.1 + - - +
129O LEU* 1.3 77.3 - - - +
131O SER* 1.3 62.8 + - - +
134O LEU* 3.9 25.0 + - + +
135O GLU* 4.1 12.1 + - - +
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Residues in contact with SER 131 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G ASP* 5.2 3.9 + - - -
127O ASP* 2.9 35.2 + - - -
128O PHE* 4.2 2.7 - - - -
130O GLU* 1.3 79.0 - - - +
132O GLU* 1.3 75.4 + - - +
135O GLU* 5.8 2.6 - - - +
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Residues in contact with GLU 132 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61O HIS* 4.6 3.6 + - - -
64O LYS* 2.9 41.5 + - + +
128O PHE* 3.0 39.4 + - + +
131O SER* 1.3 90.6 - - - +
133O TYR* 1.3 79.8 + - + +
136O GLU* 4.2 12.3 - - - +
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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