Contacts of the helix formed by residues 134 - 153 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123L PRO* 3.7 31.4 - - + -
124L HIS* 3.7 18.6 - - + +
127L ASP* 6.4 0.9 - - + -
107M ASN* 4.8 5.8 - - - +
110M LEU* 3.9 37.2 - - + +
111M LEU* 4.6 13.5 - - + -
114M HIS* 4.2 7.9 - - + -
129M LEU* 2.9 20.3 + - + +
130M GLU* 3.9 29.8 + - + +
133M TYR* 1.3 74.2 - - + +
135M GLU* 1.3 61.6 + - - +
137M GLN* 3.5 5.8 + - - +
138M VAL* 3.3 27.2 + - - +
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Residues in contact with GLU 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68L TYR* 5.3 0.7 - - - -
71L LYS* 2.8 34.3 + - - -
124L HIS* 3.0 34.7 + - + +
127L ASP* 5.1 7.0 - - - +
128L PHE* 5.7 3.5 - - - -
130M GLU 4.1 11.0 + - - +
131M SER 5.8 2.5 - - - +
133M TYR 3.5 0.4 - - - -
134M LEU* 1.3 75.9 - - - +
136M GLU* 1.3 66.5 + - - +
138M VAL* 3.3 2.9 + - - +
139M LYS* 3.0 30.4 + - + +
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Residues in contact with GLU 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M HIS* 5.1 15.7 - - + +
132M GLU 4.2 12.1 - - - +
133M TYR* 3.3 13.1 + - - +
134M LEU 3.3 0.6 - - - -
135M GLU* 1.3 80.1 - - - +
137M GLN* 1.3 57.7 + - + +
139M LYS* 3.5 7.8 - - - +
140M ASP* 3.1 35.8 + - - +
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Residues in contact with GLN 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M HIS* 5.1 1.2 - - - -
103M GLU* 3.0 47.4 + - - +
106M VAL* 3.9 9.5 - - - +
107M ASN* 3.6 23.8 - - - +
110M LEU* 3.7 19.5 - - + -
133M TYR 3.0 19.9 + - - +
134M LEU 3.7 3.4 - - - +
135M GLU 3.2 0.2 - - - -
136M GLU* 1.3 75.1 - - + +
138M VAL* 1.3 61.1 + - - +
140M ASP* 3.3 2.5 + - - +
141M ILE* 2.9 33.8 + - - +
176M MG 3.4 16.1 - - - -
177M MG 2.7 20.8 - - - -
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Residues in contact with VAL 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71L LYS* 4.2 26.9 - - + +
72L ARG* 4.3 13.2 - - - +
124L HIS* 3.3 42.6 - - + +
107M ASN* 5.0 11.7 - - - +
134M LEU 3.3 13.0 + - - +
135M GLU* 3.3 15.6 + - - +
137M GLN* 1.3 77.4 - - + +
139M LYS* 1.3 63.9 + - - +
141M ILE* 3.9 8.4 - - + +
142M LYS* 3.0 26.0 + - - +
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Residues in contact with LYS 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71L LYS* 4.5 12.1 - - - +
135M GLU* 3.0 33.2 + - + +
136M GLU* 3.5 12.6 - - - +
138M VAL* 1.3 78.2 - - - +
140M ASP* 1.3 60.8 + - - +
142M LYS* 3.7 4.9 - - - +
143M ARG* 3.0 34.2 + - - +
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Residues in contact with ASP 140 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M HIS* 3.7 20.1 - - + -
57M GLU* 4.1 9.6 - - - +
61M HIS* 5.6 0.5 - - - -
103M GLU* 4.4 11.7 - - - +
136M GLU* 3.1 17.8 + - - +
137M GLN* 3.3 4.9 + - - +
139M LYS* 1.3 80.5 - - - +
141M ILE* 1.3 64.4 + - - +
143M ARG* 3.2 29.9 + - - +
144M ILE* 3.1 31.4 + - + +
177M MG 2.5 28.9 - - - -
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Residues in contact with ILE 141 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4L VAL* 3.5 39.3 - - + +
6L GLN* 3.9 22.0 - - + +
100M LEU* 3.9 18.7 - - + +
103M GLU* 3.9 26.5 - - + +
104M LYS* 4.2 8.7 - - + -
107M ASN* 3.9 24.7 - - + +
137M GLN* 2.9 23.7 + - - +
138M VAL* 3.9 7.0 - - + +
140M ASP* 1.3 75.6 - - - +
142M LYS* 1.3 59.6 + - - +
144M ILE* 3.4 1.8 + - - -
145M GLY* 2.9 24.6 + - - -
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Residues in contact with LYS 142 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4L VAL* 4.0 8.2 - - + +
67L LYS* 6.0 0.4 - - - +
70L ASN* 3.3 32.1 - - - +
71L LYS* 4.1 23.1 - - + +
138M VAL 3.0 18.3 + - - +
139M LYS* 3.7 5.8 - - - +
141M ILE* 1.3 78.3 - - - +
143M ARG* 1.3 56.0 + - - +
145M GLY* 3.9 0.2 - - - -
146M ASP* 2.8 66.4 + - - +
38V ASP* 3.0 30.1 + - - -
40V ASP* 4.0 16.6 - - + +
45V HIS* 3.9 6.9 - - - -
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Residues in contact with ARG 143 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M PHE* 3.9 12.7 - - - -
54M HIS* 3.1 30.5 + - - -
57M GLU* 5.8 1.8 + - - -
139M LYS* 3.0 21.9 + - - +
140M ASP* 3.2 30.3 + - - +
141M ILE 3.2 0.4 - - - -
142M LYS* 1.3 75.5 - - - +
144M ILE* 1.3 61.9 + - + +
146M ASP* 3.4 11.6 + - + +
147M PHE* 3.0 56.1 + - + -
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Residues in contact with ILE 144 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M TYR* 4.3 3.8 - - + +
50M PHE* 4.5 23.3 - - + -
54M HIS* 4.9 5.6 - - + -
96M MET* 3.4 38.1 - - - +
99M ALA* 4.1 14.6 - - + +
100M LEU* 3.9 16.8 - - + +
103M GLU* 3.9 29.4 - - + +
140M ASP 3.1 18.6 + - - +
141M ILE* 4.0 3.1 - - - +
143M ARG* 1.3 76.3 - - + +
145M GLY* 1.3 60.2 + - - +
147M PHE* 3.2 8.8 + - - +
148M ILE* 2.9 29.1 + - + +
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Residues in contact with GLY 145 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L GLN* 3.2 29.4 + - - -
4L VAL* 4.0 10.3 - - - -
100M LEU* 4.5 2.6 - - - +
141M ILE 2.9 18.0 + - - -
142M LYS 3.9 1.3 - - - -
144M ILE* 1.3 75.7 - - - +
146M ASP* 1.3 62.8 + - - +
148M ILE* 3.1 6.2 + - - +
149M THR* 3.0 20.3 + - - -
40V ASP* 4.4 3.1 - - - -
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Residues in contact with ASP 146 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142M LYS* 2.8 50.9 + - - +
143M ARG* 3.4 11.9 - - + +
145M GLY* 1.3 76.2 - - - +
147M PHE* 1.3 65.7 + - + +
149M THR* 3.4 1.9 + - - -
150M ASN* 3.0 31.8 + - - +
39V ARG 4.2 0.2 - - - +
40V ASP* 3.4 17.1 - - - +
43V ALA* 3.8 14.5 - - + +
45V HIS* 3.0 27.3 + - + +
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Residues in contact with PHE 147 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50M PHE* 3.7 33.0 - + - -
96M MET* 3.9 27.1 - - + -
143M ARG* 3.0 39.7 + - + -
144M ILE* 3.2 12.1 + - - +
146M ASP* 1.3 80.9 - - + +
148M ILE* 1.3 52.8 + - - +
150M ASN* 3.2 4.1 + - + +
151M LEU* 2.7 44.2 + - + +
166M PHE* 3.6 23.2 - + + -
170M SER* 3.5 33.7 - - - -
171M VAL* 4.3 9.0 - - + -
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Residues in contact with ILE 148 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L GLN* 3.6 16.8 - - - +
93M LEU* 3.9 15.3 - - + -
96M MET* 3.7 34.8 - - + +
97M GLN* 4.0 17.0 - - + +
100M LEU* 3.7 32.5 - - + -
144M ILE 2.9 19.0 + - - +
145M GLY 3.5 6.1 - - - +
147M PHE* 1.3 74.2 - - - +
149M THR* 1.3 58.0 + - - +
151M LEU* 3.5 8.2 - - - +
152M LYS* 2.9 47.6 + - - +
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Residues in contact with THR 149 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3L GLN* 3.6 11.4 + - - -
145M GLY 3.0 4.9 + - - -
146M ASP 3.6 5.8 - - - -
148M ILE* 1.3 76.4 - - - +
150M ASN* 1.3 59.4 + - - +
152M LYS* 3.4 9.9 + - - +
153M ARG* 3.0 46.2 + - - +
40V ASP 2.8 28.2 + - - +
41V ASP* 3.5 26.0 - - - +
43V ALA* 3.8 6.3 - - + -
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Residues in contact with ASN 150 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146M ASP* 3.0 25.5 + - - +
147M PHE* 3.7 6.7 - - + +
149M THR* 1.3 74.5 - - - +
151M LEU* 1.3 67.1 + - - +
153M ARG* 3.3 21.1 + - - +
154M LEU* 3.1 29.6 + - - +
166M PHE* 4.6 6.3 - - + -
170M SER* 4.8 2.2 - - - +
43V ALA* 3.1 33.9 + - - +
44V LEU* 3.9 5.7 - - - +
45V HIS* 5.8 0.4 - - - -
164V TYR* 3.1 35.1 - - + -
168V LYS* 4.8 1.7 + - - -
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Residues in contact with LEU 151 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92M THR* 4.1 8.3 - - + +
93M LEU* 3.9 17.3 - - + +
96M MET* 3.8 29.2 - - + -
147M PHE 2.7 30.1 + - - +
148M ILE* 3.5 7.4 - - - +
150M ASN* 1.3 73.9 - - - +
152M LYS* 1.3 59.7 + - - +
154M LEU* 3.3 9.9 + - + +
155M GLY 3.3 0.2 + - - -
156M LEU* 3.0 63.9 + - + +
163M GLU* 5.3 0.2 - - - -
166M PHE* 3.5 42.6 - - + -
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Residues in contact with LYS 152 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L GLN* 4.9 4.4 + - - -
93M LEU* 4.3 17.5 - - + -
97M GLN* 4.1 14.9 + - - -
148M ILE* 2.9 39.6 + - + +
149M THR* 3.6 8.1 - - - +
151M LEU* 1.3 75.1 - - - +
153M ARG* 1.3 60.3 + - - +
155M GLY* 2.9 19.2 + - - +
156M LEU* 4.3 4.9 - - - +
157M PRO* 5.7 1.1 - - + -
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Residues in contact with ARG 153 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149M THR* 3.0 30.1 + - - +
150M ASN* 3.3 34.0 + - - +
151M LEU 3.3 0.2 - - - -
152M LYS* 1.3 70.8 - - - +
154M LEU* 1.3 59.8 + - + +
155M GLY* 3.0 9.2 + - - -
41V ASP 5.5 0.6 + - - -
42V VAL* 2.5 36.1 + - - +
44V LEU* 3.4 26.0 - - - +
160V GLY* 3.3 51.7 - - - +
161V MET 3.6 1.0 + - - -
163V GLU* 3.5 20.1 + - - +
164V TYR* 4.0 13.7 - - - +
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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