Contacts of the helix formed by residues 134 - 153 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F PRO* 3.7 30.7 - - + -
124F HIS* 3.5 17.7 - - + +
127F ASP* 6.2 0.9 - - + -
107G ASN* 4.8 5.6 - - - +
110G LEU* 3.9 37.9 - - + +
111G LEU* 4.6 14.4 - - + -
114G HIS* 4.2 8.3 - - + -
129G LEU* 2.9 20.5 + - + +
130G GLU* 3.9 29.1 + - + +
133G TYR* 1.3 75.7 - - + +
135G GLU* 1.3 62.7 + - - +
137G GLN* 3.5 6.1 + - - +
138G VAL* 3.3 26.7 + - - +
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Residues in contact with GLU 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F TYR* 5.3 1.0 - - - -
71F LYS* 2.8 32.6 + - - -
124F HIS* 3.0 36.1 + - + +
127F ASP* 5.1 6.7 - - - +
128F PHE* 5.7 3.3 - - - -
130G GLU 4.1 11.0 + - - +
131G SER 5.8 2.7 - - - +
133G TYR 3.5 0.4 - - - -
134G LEU* 1.3 75.9 - - - +
136G GLU* 1.3 67.4 + - - +
138G VAL* 3.3 2.8 + - - +
139G LYS* 3.0 30.7 + - + +
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Residues in contact with GLU 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G HIS* 5.1 15.0 - - + +
132G GLU 4.2 12.5 - - - +
133G TYR* 3.3 13.5 + - - +
134G LEU 3.3 0.2 - - - -
135G GLU* 1.3 79.0 - - - +
137G GLN* 1.3 59.2 + - + +
139G LYS* 3.5 7.6 - - - +
140G ASP* 3.1 34.6 + - - +
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Residues in contact with GLN 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G HIS* 5.1 1.4 - - - -
103G GLU* 3.0 47.7 + - - +
106G VAL* 3.9 9.5 - - - +
107G ASN* 3.6 22.3 - - - +
110G LEU* 3.7 20.0 - - + -
133G TYR* 3.0 19.9 + - + +
134G LEU* 3.7 4.3 - - - +
135G GLU 3.2 0.2 - - - -
136G GLU* 1.3 75.1 - - + +
138G VAL* 1.3 61.3 + - - +
140G ASP* 3.3 3.0 + - - +
141G ILE* 2.9 34.0 + - - +
176G MG 3.4 15.6 - - - -
177G MG 2.7 21.5 - - - -
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Residues in contact with VAL 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F LYS* 4.3 22.8 - - + +
72F ARG* 4.3 15.7 - - - +
124F HIS* 3.3 43.7 - - + +
107G ASN* 5.0 11.0 - - - +
134G LEU 3.3 12.7 + - - +
135G GLU* 3.3 15.0 + - - +
137G GLN* 1.3 78.0 - - + +
139G LYS* 1.3 65.0 + - - +
141G ILE* 3.9 7.7 - - + +
142G LYS* 3.0 26.2 + - - +
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Residues in contact with LYS 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F LYS* 4.6 12.1 - - - +
135G GLU* 3.0 32.5 + - + +
136G GLU* 3.5 12.3 - - - +
137G GLN 3.2 0.2 - - - -
138G VAL* 1.3 79.1 - - - +
140G ASP* 1.3 59.8 + - - +
142G LYS* 3.5 5.0 + - - +
143G ARG* 3.0 33.8 + - - +
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Residues in contact with ASP 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G HIS* 3.7 19.7 - - + -
57G GLU* 4.1 9.4 - - - +
61G HIS* 5.6 0.5 - - - -
103G GLU* 4.4 11.9 - - + +
136G GLU* 3.1 17.8 + - - +
137G GLN* 3.7 3.8 - - - +
139G LYS* 1.3 79.8 - - - +
141G ILE* 1.3 65.0 + - - +
143G ARG* 3.2 30.3 + - - +
144G ILE* 3.1 30.7 + - + +
177G MG 2.5 30.1 - - - -
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Residues in contact with ILE 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F VAL* 3.4 35.9 - - + +
6F GLN* 3.8 22.2 - - + +
71F LYS 5.9 0.2 - - - +
100G LEU* 3.9 22.3 - - + +
103G GLU* 3.9 25.4 - - + +
104G LYS* 4.2 7.6 - - + -
107G ASN* 3.9 24.9 - - + +
137G GLN* 2.9 23.3 + - - +
138G VAL* 3.9 6.1 - - - +
140G ASP* 1.3 74.6 - - - +
142G LYS* 1.3 58.8 + - - +
144G ILE* 3.4 1.8 + - - -
145G GLY 2.9 25.3 + - - -
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Residues in contact with LYS 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASP* 2.9 30.3 + - - -
40B ASP* 3.9 17.7 - - + +
45B HIS* 4.0 6.5 - - - -
4F VAL* 3.9 8.5 - - + +
67F LYS* 6.0 0.6 - - - +
70F ASN* 3.3 32.5 - - - +
71F LYS* 4.1 23.6 - - + +
138G VAL 3.0 19.4 + - - +
139G LYS* 3.7 5.4 - - - +
141G ILE* 1.3 79.1 - - - +
143G ARG* 1.3 56.6 + - - +
145G GLY* 3.5 0.7 + - - -
146G ASP* 2.8 65.6 + - - +
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Residues in contact with ARG 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G PHE* 3.9 12.1 - - - -
54G HIS* 3.1 31.1 + - - -
57G GLU* 5.8 1.6 + - - -
139G LYS* 3.0 22.0 + - - +
140G ASP* 3.2 31.5 + - - +
141G ILE 3.2 0.4 - - - -
142G LYS* 1.3 75.1 - - - +
144G ILE* 1.3 61.2 + - - +
146G ASP* 3.4 10.4 + - + +
147G PHE* 3.0 56.6 + - + -
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Residues in contact with ILE 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G TYR* 4.3 4.5 - - + +
50G PHE* 4.5 23.3 - - + -
54G HIS* 4.9 5.8 - - + -
96G MET* 3.4 37.9 - - - +
99G ALA* 4.1 14.4 - - + +
100G LEU* 3.9 18.4 - - + +
103G GLU* 3.9 28.7 - - + +
140G ASP 3.1 18.0 + - - +
141G ILE 4.0 2.5 - - - +
143G ARG* 1.3 75.8 - - + +
145G GLY* 1.3 61.2 + - - +
147G PHE* 3.2 7.7 + - - +
148G ILE* 2.9 29.1 + - + +
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Residues in contact with GLY 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ASP* 4.3 3.1 - - - -
3F GLN* 3.2 29.7 + - - -
4F VAL* 4.0 10.5 - - - -
100G LEU* 4.5 2.8 - - - +
141G ILE 2.9 17.5 + - - -
142G LYS 3.9 1.3 - - - -
144G ILE* 1.3 76.2 - - - +
146G ASP* 1.3 62.6 + - - +
148G ILE* 3.1 6.0 + - - +
149G THR* 3.0 20.3 + - - -
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Residues in contact with ASP 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ASP* 3.3 17.5 - - - +
43B ALA* 3.7 15.7 - - + +
45B HIS* 3.0 28.1 + - + +
142G LYS* 2.8 51.5 + - - +
143G ARG* 3.4 13.5 - - + +
145G GLY* 1.3 76.0 - - - +
147G PHE* 1.3 64.9 + - + +
149G THR* 3.4 1.9 + - - -
150G ASN* 3.0 30.8 + - - +
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Residues in contact with PHE 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G PHE* 3.7 33.2 - + - -
96G MET* 3.9 27.1 - - + -
143G ARG* 3.0 39.7 + - + -
144G ILE* 3.2 11.4 + - - +
146G ASP* 1.3 81.5 - - + +
148G ILE* 1.3 53.8 + - - +
150G ASN* 3.2 4.1 + - + +
151G LEU* 2.7 43.6 + - + +
166G PHE* 3.6 23.6 - + + -
170G SER* 3.5 33.2 - - - -
171G VAL* 4.3 8.7 - - + -
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Residues in contact with ILE 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F GLN* 3.6 16.2 - - - +
93G LEU* 3.9 14.8 - - + -
96G MET* 3.7 35.0 - - + +
97G GLN* 4.0 18.6 - - + +
100G LEU* 3.7 32.8 - - + -
144G ILE 2.9 19.3 + - - +
145G GLY 3.1 6.3 + - - +
147G PHE* 1.3 73.5 - - - +
149G THR* 1.3 58.3 + - - +
151G LEU* 3.3 8.3 + - - +
152G LYS* 2.9 49.1 + - + +
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Residues in contact with THR 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ASP 2.9 28.0 + - - +
41B ASP* 3.5 28.3 - - - +
42B VAL 3.9 1.8 - - - +
43B ALA* 3.9 3.8 - - + -
3F GLN* 3.5 12.3 + - - -
145G GLY 3.0 4.4 + - - -
146G ASP 3.6 6.1 - - - -
147G PHE 3.2 0.2 - - - -
148G ILE* 1.3 77.3 - - - +
150G ASN* 1.3 58.2 + - - +
152G LYS* 3.4 9.5 + - - +
153G ARG* 3.0 46.2 + - - +
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Residues in contact with ASN 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ALA* 3.2 32.9 + - - +
44B LEU* 3.9 5.7 - - - +
164B TYR* 3.1 34.4 - - + -
168B LYS* 4.8 1.4 + - - -
146G ASP* 3.0 26.7 + - - +
147G PHE* 3.7 6.5 - - + +
149G THR* 1.3 75.8 - - - +
151G LEU* 1.3 65.0 + - - +
153G ARG* 3.3 22.4 + - - +
154G LEU* 3.1 30.0 + - - +
166G PHE* 4.6 7.0 - - + -
170G SER* 4.8 2.5 - - - +
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Residues in contact with LEU 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G THR* 4.1 8.5 - - + +
93G LEU* 3.9 17.0 - - + +
96G MET* 3.8 29.4 - - + -
147G PHE 2.7 31.0 + - - +
148G ILE* 3.6 6.7 - - - +
150G ASN* 1.3 73.9 - - - +
152G LYS* 1.3 60.5 + - - +
154G LEU* 3.3 9.3 + - + +
155G GLY 3.3 0.2 + - - -
156G LEU* 3.0 63.4 + - + +
166G PHE* 3.5 41.7 - - + -
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Residues in contact with LYS 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F GLN* 4.9 4.8 + - - -
93G LEU* 4.3 17.5 - - + -
97G GLN* 4.1 14.6 + - - -
148G ILE* 2.9 37.5 + - + +
149G THR* 3.6 7.6 - - - +
151G LEU* 1.3 74.8 - - - +
153G ARG* 1.3 59.5 + - - +
155G GLY* 2.9 18.9 + - - +
156G LEU* 4.3 5.2 - - - +
157G PRO* 5.7 2.0 - - + -
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Residues in contact with ARG 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ASP 5.5 0.6 + - - -
42B VAL* 2.5 33.9 + - - +
44B LEU* 3.4 22.7 - - - +
160B GLY* 3.2 54.3 + - - +
161B MET 3.6 0.9 + - - -
163B GLU* 3.4 25.7 + - - +
164B TYR* 4.0 13.0 - - - +
149G THR* 3.0 28.7 + - - +
150G ASN* 3.3 34.4 + - - +
152G LYS* 1.3 72.9 - - - +
154G LEU* 1.3 59.4 + - + +
155G GLY* 3.0 9.4 + - - -
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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
------------------------------------------------------------
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