Contacts of the helix formed by residues 123 - 132 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7F ASN* 3.7 11.7 - - - +
121F VAL* 3.3 17.5 - - + +
122F ASP* 1.3 84.7 - - - +
124F HIS* 1.3 59.7 + - - +
126F CYS* 3.4 8.6 + - + +
127F ASP* 3.0 28.9 + - - +
111G LEU* 3.7 18.8 - - + +
114G HIS* 3.5 44.2 - - + +
130G GLU* 4.4 5.9 - - - +
134G LEU* 3.7 16.2 - - + -
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Residues in contact with HIS 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F TYR* 2.8 40.5 + + - -
71F LYS* 5.4 0.9 - - + -
72F ARG* 3.6 13.6 + - - +
122F ASP* 3.3 7.5 - - - +
123F PRO* 1.3 79.4 - - + +
125F LEU* 1.3 61.0 + - - +
127F ASP* 3.5 8.8 + - - +
128F PHE* 3.1 24.7 + - + +
111G LEU* 5.7 3.1 - - + -
134G LEU* 3.5 40.5 - - + +
135G GLU* 3.0 33.2 + - + +
138G VAL* 3.3 28.7 - - + +
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Residues in contact with LEU 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F TYR* 4.4 7.0 - - + -
12F CYS* 4.0 28.9 - - + -
16F VAL* 4.3 13.7 - - + -
65F PHE* 5.3 0.4 - - + -
68F TYR* 3.2 34.0 + - + +
113F LEU* 4.4 12.6 - - + -
117F ALA* 3.9 20.2 - - + -
122F ASP* 2.9 23.2 + - - +
124F HIS* 1.3 75.0 - - - +
126F CYS* 1.3 65.8 + - - +
128F PHE* 3.6 12.3 - - + +
129F LEU* 3.1 36.2 + - + +
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Residues in contact with CYS 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F HIS* 3.6 21.1 - - + +
117F ALA* 3.6 19.3 - - - -
118F THR* 3.5 29.2 - - - -
122F ASP 3.4 15.5 + - - +
123F PRO* 3.5 12.3 - - + +
125F LEU* 1.3 80.2 - - - +
127F ASP* 1.3 57.7 + - - +
129F LEU* 3.4 4.0 + - - +
130F GLU* 3.1 37.8 + - - +
130G GLU* 5.7 2.9 - - - +
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Residues in contact with ASP 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F PRO 3.0 17.7 + - - +
124F HIS* 3.8 9.3 - - + +
126F CYS* 1.3 74.9 - - - +
128F PHE* 1.3 60.0 + - - +
130F GLU* 4.2 11.5 - - - +
131F SER* 2.9 50.4 + - - -
127G ASP* 5.6 1.0 - - - +
130G GLU* 3.7 46.3 - - + +
131G SER* 5.0 4.4 + - - -
134G LEU* 6.4 0.4 - - + -
135G GLU* 5.1 8.0 - - - +
127O ASP* 5.6 1.0 - - - +
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Residues in contact with PHE 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F LYS* 3.7 24.7 - - + -
65F PHE* 3.5 20.4 - + - -
68F TYR* 3.6 40.6 - + + -
71F LYS* 6.2 2.2 - - - -
124F HIS* 3.1 19.2 + - + +
125F LEU* 3.6 9.4 - - + +
127F ASP* 1.3 78.8 + - - +
129F LEU* 1.3 69.1 + - + +
131F SER* 4.7 2.9 - - - -
132F GLU* 3.0 51.4 + - + +
133F TYR* 3.5 30.8 - + - -
135G GLU* 5.7 3.6 - - - -
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Residues in contact with LEU 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F PHE* 4.0 32.8 - - + -
110F LEU* 4.3 16.4 - - + +
113F LEU* 3.9 19.3 - - + +
114F HIS* 3.8 41.1 - - + +
117F ALA* 5.1 0.2 - - + -
125F LEU* 3.1 27.8 + - + +
126F CYS* 3.6 4.3 - - - +
128F PHE* 1.3 88.7 - - + +
130F GLU* 1.3 58.4 + - - +
133F TYR* 3.0 15.0 + - + +
134F LEU* 2.9 34.1 + - + +
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Residues in contact with GLU 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F HIS* 2.9 29.5 + - - +
126F CYS* 3.1 23.7 + - - +
127F ASP* 3.7 8.5 - - - +
129F LEU* 1.3 77.1 - - - +
131F SER* 1.3 62.6 + - - +
134F LEU* 3.9 17.0 + - + +
135F GLU* 4.1 18.7 + - - +
130G GLU* 3.9 12.2 - - - +
123O PRO* 4.4 7.4 - - - +
126O CYS* 5.7 2.2 - - - +
127O ASP* 3.7 46.3 - - + +
130O GLU* 3.9 15.1 - - - +
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Residues in contact with SER 131 (chain F).
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* 2.9 35.4 + - - -
128F PHE* 4.2 2.2 - - - -
130F GLU* 1.3 78.5 - - - +
132F GLU* 1.3 75.6 + - - +
135F GLU* 5.8 2.4 - - - +
127O ASP* 5.2 3.6 + - - -
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Residues in contact with GLU 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F HIS* 4.6 3.8 + - - -
64F LYS* 2.9 42.2 + - + +
128F PHE* 3.0 39.6 + - + +
131F SER* 1.3 89.5 - - - +
133F TYR* 1.3 79.1 + - + +
136F GLU* 4.2 11.8 - - - +
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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