Contacts of the helix formed by residues 134 - 153 (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 LEU 134 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F ASN* 4.8 5.6 - - - +
110F LEU* 3.9 37.2 - - + +
111F LEU* 4.6 13.9 - - + -
114F HIS* 4.2 8.1 - - + -
129F LEU* 2.9 20.5 + - + +
130F GLU* 3.9 29.8 + - + +
133F TYR* 1.3 75.7 - - + +
135F GLU* 1.3 61.3 + - - +
137F GLN* 3.5 6.0 + - - +
138F VAL* 3.3 27.5 + - - +
123O PRO* 3.8 30.7 - - + -
124O HIS* 3.5 18.1 - - + +
127O ASP* 6.1 0.9 - - + -
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Residues in contact with GLU 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F GLU 4.1 11.0 + - - +
131F SER 5.8 2.7 - - - +
133F TYR 5.0 0.4 - - - +
134F LEU* 1.3 75.1 - - - +
136F GLU* 1.3 67.0 + - - +
138F VAL* 3.3 2.9 + - - +
139F LYS* 3.0 32.8 + - + +
68O TYR* 5.4 0.5 - - - -
71O LYS* 2.8 32.9 + - - -
124O HIS* 3.1 35.5 + - + +
127O ASP* 5.1 6.5 - - - +
128O PHE* 5.7 3.5 - - - -
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Residues in contact with GLU 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F HIS* 5.1 15.5 - - + +
132F GLU 4.2 12.9 - - - +
133F TYR* 3.3 13.6 + - - +
135F GLU* 1.3 78.9 - - - +
137F GLN* 1.3 57.8 + - + +
139F LYS* 3.5 7.9 - - - +
140F ASP* 3.1 35.1 + - - +
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Residues in contact with GLN 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F HIS* 5.1 1.4 - - - -
103F GLU* 3.0 47.0 + - - +
106F VAL* 3.9 9.1 - - - +
107F ASN* 3.6 23.2 - - - +
110F LEU* 3.7 20.6 - - + -
133F TYR* 3.0 19.7 + - + +
134F LEU* 3.7 3.6 - - - +
135F GLU 3.2 0.4 - - - -
136F GLU* 1.3 75.4 - - + +
138F VAL* 1.3 61.8 + - - +
140F ASP* 3.3 2.6 + - - +
141F ILE* 2.9 34.5 + - - +
176F MG 3.4 16.1 - - - -
177F MG 2.7 21.6 - - - -
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Residues in contact with VAL 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107F ASN* 5.0 11.7 - - - +
134F LEU 3.3 12.8 + - - +
135F GLU* 3.3 15.4 + - - +
137F GLN* 1.3 78.1 - - + +
139F LYS* 1.3 64.7 + - - +
141F ILE* 3.9 8.1 - - + +
142F LYS* 3.0 26.2 + - - +
71O LYS* 4.2 25.4 - - + +
72O ARG* 4.3 12.6 - - - +
124O HIS* 3.3 42.6 - - + +
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Residues in contact with LYS 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135F GLU* 3.0 34.7 + - + +
136F GLU* 3.5 12.6 - - - +
138F VAL* 1.3 78.8 - - - +
140F ASP* 1.3 60.8 + - - +
142F LYS* 3.5 5.0 + - - +
143F ARG* 3.0 33.3 + - - +
71O LYS* 4.6 11.9 - - - +
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Residues in contact with ASP 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F HIS* 3.7 19.5 - - + -
57F GLU* 4.1 10.0 - - - +
61F HIS* 5.6 0.7 - - - -
103F GLU* 4.4 12.8 - - + +
136F GLU* 3.1 17.8 + - - +
137F GLN 3.3 4.4 + - - +
139F LYS* 1.3 80.0 - - - +
141F ILE* 1.3 64.5 + - - +
143F ARG* 3.2 29.8 + - - +
144F ILE* 3.1 30.7 + - + +
177F MG 2.5 29.5 - - - -
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Residues in contact with ILE 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F LEU* 3.9 18.7 - - + +
103F GLU* 3.9 27.4 - - + +
104F LYS* 4.2 7.4 - - + -
107F ASN* 3.9 25.1 - - + +
137F GLN* 2.9 22.8 + - - +
138F VAL* 3.9 6.7 - - + +
140F ASP* 1.3 74.8 - - - +
142F LYS* 1.3 58.6 + - - +
144F ILE* 3.4 2.0 + - - -
145F GLY 2.9 24.8 + - - -
4O VAL* 3.5 39.9 - - + +
6O GLN* 3.9 21.5 - - + +
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Residues in contact with LYS 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASP* 2.9 29.9 + - - -
40C ASP* 4.0 17.0 - - + +
45C HIS* 4.0 5.9 - - - -
138F VAL 3.0 19.4 + - - +
139F LYS* 3.7 5.6 - - - +
141F ILE* 1.3 78.1 - - - +
143F ARG* 1.3 58.2 + - - +
145F GLY* 3.5 0.7 + - - -
146F ASP* 2.8 66.1 + - - +
4O VAL* 4.0 9.4 - - + +
67O LYS* 6.0 0.8 - - - +
70O ASN* 3.3 33.0 - - - +
71O LYS* 4.1 22.7 - - + +
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Residues in contact with ARG 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F PHE* 3.9 11.9 - - - -
54F HIS* 3.1 31.1 + - - -
57F GLU* 5.8 1.6 + - - -
139F LYS* 3.0 22.4 + - - +
140F ASP* 3.2 30.7 + - - +
141F ILE 3.2 0.4 - - - -
142F LYS* 1.3 76.1 - - - +
144F ILE* 1.3 61.0 + - + +
146F ASP* 3.4 10.7 + - + +
147F PHE* 3.0 58.4 + - + -
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Residues in contact with ILE 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F TYR* 4.3 4.3 - - + +
50F PHE* 4.5 23.1 - - + -
54F HIS* 4.9 5.6 - - + -
96F MET* 3.4 38.4 - - - +
99F ALA* 4.1 15.3 - - + +
100F LEU* 3.9 17.5 - - + +
103F GLU* 3.9 28.7 - - + +
140F ASP* 3.1 18.4 + - - +
141F ILE* 4.0 2.7 - - - +
143F ARG* 1.3 75.2 - - + +
145F GLY* 1.3 61.6 + - - +
147F PHE* 3.2 8.3 + - - +
148F ILE* 2.9 30.0 + - + +
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Residues in contact with GLY 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ASP* 4.3 3.1 - - - -
100F LEU* 4.5 2.4 - - - +
141F ILE 2.9 17.4 + - - -
142F LYS 3.9 1.3 - - - -
144F ILE* 1.3 75.6 - - - +
146F ASP* 1.3 61.4 + - - +
148F ILE* 3.1 6.5 + - - +
149F THR* 3.0 19.9 + - - -
3O GLN* 3.2 30.3 + - - -
4O VAL* 4.0 10.1 - - - -
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Residues in contact with ASP 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ARG 4.1 0.2 - - - +
40C ASP* 3.3 16.7 - - - +
43C ALA* 3.8 15.1 - - + +
45C HIS* 3.0 28.1 + - + +
142F LYS* 2.8 51.0 + - - +
143F ARG* 3.4 12.5 - - + +
145F GLY* 1.3 76.2 - - - +
147F PHE* 1.3 65.1 + - + +
149F THR* 3.4 1.7 + - - -
150F ASN* 3.0 31.2 + - - +
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Residues in contact with PHE 147 (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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50F PHE* 3.7 32.3 - + - -
96F MET* 3.9 27.1 - - + -
143F ARG* 3.0 39.7 + - + -
144F ILE* 3.2 13.4 + - - +
146F ASP* 1.3 80.2 - - + +
148F ILE* 1.3 51.6 - - - +
150F ASN* 3.2 3.6 + - + +
151F LEU* 2.7 43.3 + - + +
166F PHE* 3.6 22.7 - + + -
170F SER* 3.5 31.6 - - - -
171F VAL* 4.3 9.4 - - + -
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Residues in contact with ILE 148 (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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93F LEU* 3.9 15.5 - - + -
96F MET* 3.7 34.3 - - + +
97F GLN* 4.0 17.5 - - + +
100F LEU* 3.7 32.5 - - + -
144F ILE 2.9 19.8 + - - +
145F GLY 3.5 6.7 - - - +
147F PHE* 1.3 73.3 - - - +
149F THR* 1.3 58.1 + - - +
151F LEU* 3.3 8.6 + - - +
152F LYS* 2.9 48.5 + - + +
3O GLN* 3.6 16.2 - - - +
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Residues in contact with THR 149 (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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40C ASP 2.8 28.6 + - - +
41C ASP* 3.5 28.4 - - - +
43C ALA* 3.8 6.1 - - + -
145F GLY 3.0 5.1 + - - -
146F ASP 3.6 5.2 - - - -
148F ILE* 1.3 76.4 - - - +
150F ASN* 1.3 58.9 + - - +
152F LYS* 3.4 9.1 + - - +
153F ARG* 3.0 45.9 + - - +
3O GLN* 3.6 11.4 + - - -
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Residues in contact with ASN 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ALA* 3.1 33.7 + - - +
44C LEU* 3.9 5.5 - - - +
164C TYR* 3.2 34.3 - - + -
168C LYS* 4.8 1.0 + - - -
146F ASP* 3.0 26.1 + - - +
147F PHE* 3.7 6.5 - - + +
149F THR* 1.3 75.1 - - - +
151F LEU* 1.3 65.1 + - - +
153F ARG* 3.3 23.0 + - - +
154F LEU* 3.1 29.5 + - - +
166F PHE* 4.6 6.3 - - + -
170F SER* 4.8 2.9 - - - +
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Residues in contact with LEU 151 (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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92F THR* 4.1 9.2 - - + +
93F LEU* 3.9 17.3 - - + +
96F MET* 3.8 29.6 - - + -
147F PHE 2.7 30.2 + - - +
148F ILE* 3.3 7.2 + - - +
150F ASN* 1.3 73.0 - - - +
152F LYS* 1.3 59.4 + - - +
154F LEU* 3.3 9.7 + - + +
155F GLY 3.3 0.2 + - - -
156F LEU* 3.0 62.3 + - + +
163F GLU* 5.3 0.2 - - - -
166F PHE* 3.5 42.2 - - + -
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Residues in contact with LYS 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F LEU* 4.3 18.2 - - + -
97F GLN* 4.1 15.0 + - - -
148F ILE* 2.9 38.3 + - + +
149F THR* 3.6 7.4 - - - +
151F LEU* 1.3 75.4 - - - +
153F ARG* 1.3 60.3 + - - +
155F GLY* 2.9 18.8 + - - +
156F LEU 4.3 4.3 - - - +
157F PRO* 5.7 1.1 - - + -
3O GLN* 5.0 4.2 + - - -
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Residues in contact with ARG 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ASP 5.5 0.6 + - - -
42C VAL* 2.5 35.5 + - - +
44C LEU* 3.4 24.5 - - - +
160C GLY* 3.3 50.3 + - - +
161C MET 3.6 0.9 + - - -
163C GLU* 3.4 20.7 + - - +
164C TYR* 4.1 14.4 - - - +
149F THR* 3.0 29.2 + - - +
150F ASN* 3.3 34.0 + - - +
151F LEU 3.3 0.4 - - - -
152F LYS* 1.3 71.7 - - - +
154F LEU* 1.3 59.9 + - + +
155F GLY 3.0 8.6 + - - -
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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
------------------------------------------------------------
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