Contacts of the helix formed by residues 148 - 166 (chain M) in PDB entry 3MQT
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 THR 148 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146M ASP 3.7 5.5 + - - +
147M ALA* 1.3 74.9 - - - +
149M LEU* 1.3 68.0 + - - +
150M SER* 4.0 7.8 + - - -
151M GLU* 3.1 37.4 + - - +
152M ILE* 2.9 25.9 + - - +
178M ASN* 5.7 1.1 - - - -
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Residues in contact with LEU 149 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148M THR* 1.3 73.4 - - - +
150M SER* 1.3 57.1 + - - +
152M ILE* 3.1 16.7 + - + +
153M VAL* 2.9 34.8 + - - +
175M ILE* 6.0 0.9 - - + -
176M ILE* 5.8 4.7 - - + +
178M ASN* 4.9 12.9 + - + +
181M VAL* 3.4 33.2 - - + -
185M GLU* 3.8 28.3 - - + +
186M ILE* 4.4 11.7 - - + -
189M TYR* 4.0 37.7 - - + -
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Residues in contact with SER 150 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148M THR* 3.1 8.4 + - - -
149M LEU* 1.3 80.2 - - - +
151M GLU* 1.3 61.3 + - - +
153M VAL* 3.4 10.1 + - - +
154M GLU* 3.2 26.1 + - - +
192M GLU* 5.8 2.6 + - - -
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Residues in contact with GLU 151 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M VAL* 4.5 3.8 - - + +
144M ALA* 5.9 1.2 - - - +
146M ASP 4.6 1.9 - - - +
147M ALA* 3.7 23.9 - - + +
148M THR* 3.1 29.4 + - - +
150M SER* 1.3 76.2 - - - +
152M ILE* 1.3 65.9 + - - +
154M GLU* 3.4 9.7 + - + +
155M ALA* 3.0 23.2 + - - +
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Residues in contact with ILE 152 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141M PRO* 3.9 15.3 - - + -
143M VAL* 4.2 14.6 - - + -
147M ALA* 3.8 30.1 - - + +
148M THR 2.9 20.4 + - - +
149M LEU* 3.1 20.2 + - + +
151M GLU* 1.3 75.8 - - - +
153M VAL* 1.3 57.1 + - - +
155M ALA* 3.2 4.0 + - - +
156M TYR* 2.8 36.6 + - + -
176M ILE* 3.8 31.0 - - + -
178M ASN* 5.7 2.5 - - + +
189M TYR* 3.6 25.1 - - + +
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Residues in contact with VAL 153 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149M LEU 2.9 18.8 + - - +
150M SER* 3.6 11.4 - - - +
152M ILE* 1.3 74.3 - - - +
154M GLU* 1.3 66.5 + - - +
156M TYR* 3.1 17.2 + - - +
157M LYS* 3.2 27.6 + - - +
189M TYR* 3.8 27.6 - - + +
192M GLU* 3.5 39.0 - - + +
193M LEU* 4.2 17.5 - - + -
196M VAL* 4.7 5.8 - - + +
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Residues in contact with GLU 154 (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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150M SER* 3.2 15.4 + - - +
151M GLU* 3.6 11.7 - - + +
152M ILE 3.4 0.2 - - - -
153M VAL* 1.3 79.0 - - - +
155M ALA* 1.3 62.1 + - - +
157M LYS* 3.1 50.4 + - - +
158M PRO* 3.2 10.9 - - - +
192M GLU* 5.7 0.3 - - - +
200X ASP* 5.5 0.2 - - - +
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Residues in contact with ALA 155 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141M PRO* 3.9 11.9 - - + -
142M SER 4.5 5.8 - - - +
143M VAL* 3.5 31.9 - - + -
151M GLU 3.0 10.3 + - - +
152M ILE 3.6 5.4 - - - +
154M GLU* 1.3 76.0 - - - +
156M TYR* 1.3 62.7 + - - +
157M LYS 3.3 0.7 + - - -
158M PRO* 3.4 17.3 - - - +
159M LEU* 4.1 11.3 - - - +
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Residues in contact with TYR 156 (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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139M LEU* 2.6 48.3 + - + -
141M PRO* 3.5 27.9 - - + +
152M ILE* 2.8 23.3 + - + +
153M VAL 3.1 9.8 + - - +
155M ALA* 1.3 77.7 - - - +
157M LYS* 1.3 63.2 + - + +
159M LEU* 3.2 10.7 + - + +
160M ILE* 3.0 33.3 + - + +
173M VAL* 3.8 22.0 - - + -
174M CYS* 2.9 23.3 + - - +
176M ILE* 5.5 0.4 - - + +
189M TYR* 3.4 26.0 - - - -
193M LEU* 3.9 25.6 - - + -
196M VAL* 6.0 0.2 - - + -
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Residues in contact with LYS 157 (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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153M VAL* 3.2 18.9 + - - +
154M GLU* 3.1 41.1 + - - +
156M TYR* 1.3 75.2 - - - +
158M PRO* 1.3 65.3 - - + +
160M ILE* 3.6 1.6 + - - +
161M ALA* 3.0 29.9 + - - +
192M GLU* 4.8 5.1 + - - -
196M VAL* 4.3 38.2 - - + +
200X ASP* 3.8 29.2 + - - +
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Residues in contact with PRO 158 (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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154M GLU 3.2 13.9 - - - +
155M ALA* 3.4 14.1 - - - +
157M LYS* 1.3 90.9 - - + +
159M LEU* 1.3 60.8 + - + +
161M ALA* 3.9 5.6 - - + +
162M LYS* 2.9 30.8 + - - +
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Residues in contact with LEU 159 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139M LEU* 4.2 20.9 - - + -
140M TYR 3.8 32.3 - - - +
141M PRO* 3.9 16.8 - - + -
142M SER 5.3 0.4 - - - +
155M ALA 4.1 11.4 - - - +
156M TYR* 3.2 10.6 + - + +
158M PRO* 1.3 77.6 - - + +
160M ILE* 1.3 65.8 + - - +
162M LYS* 3.2 9.0 + - + +
163M ALA* 2.9 22.3 + - - +
339M ASP 4.9 2.9 - - - +
340M PHE* 3.8 36.2 - - + +
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Residues in contact with ILE 160 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139M LEU* 3.9 21.5 - - + +
156M TYR* 3.0 39.2 + - + +
157M LYS 3.9 3.1 - - - +
159M LEU* 1.3 75.2 - - - +
161M ALA* 1.3 62.8 + - - +
163M ALA* 3.1 5.5 + - - +
164M LYS* 3.1 30.9 + - - +
171M VAL* 5.2 0.2 - - + -
173M VAL* 4.9 1.3 - - + -
193M LEU* 4.3 10.3 - - + -
196M VAL* 3.6 42.6 - - + +
197M ILE* 3.8 32.5 - - + -
201M MET* 4.4 4.7 - - + +
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Residues in contact with ALA 161 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157M LYS 3.0 20.0 + - - +
158M PRO* 3.9 5.8 - - + +
160M ILE* 1.3 79.4 - - - +
162M LYS* 1.3 61.6 + - - +
164M LYS* 3.3 12.0 + - + +
165M GLU* 3.0 23.6 + - - +
161X ALA* 6.0 6.6 - - + +
164X LYS* 6.3 4.7 - - + -
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Residues in contact with LYS 162 (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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158M PRO 2.9 18.3 + - - +
159M LEU* 3.2 8.3 + - + +
161M ALA* 1.3 76.6 - - - +
163M ALA* 1.3 63.2 + - - +
165M GLU* 3.1 7.9 + - + +
166M ARG* 3.0 51.2 + - + +
339M ASP* 3.3 42.1 + - + +
340M PHE* 4.0 9.9 - - + -
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Residues in contact with ALA 163 (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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137M PHE* 5.6 0.2 - - + -
139M LEU* 4.6 1.8 - - + -
159M LEU 2.9 13.1 + - - +
160M ILE* 3.1 9.8 + - - +
162M LYS* 1.3 77.0 - - - +
164M LYS* 1.3 60.0 + - - +
166M ARG* 3.3 3.4 + - - +
167M GLY 3.2 3.5 + - - -
168M ALA* 2.9 34.3 + - + +
171M VAL* 3.7 30.7 - - + -
201M MET* 4.5 2.5 - - - -
340M PHE* 3.6 22.4 - - + -
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Residues in contact with LYS 164 (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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160M ILE* 3.1 26.0 + - + +
161M ALA* 3.7 11.4 - - - +
163M ALA* 1.3 75.1 - - - +
165M GLU* 1.3 63.9 + - - +
167M GLY* 3.1 14.5 + - - +
168M ALA 4.8 1.1 - - - +
196M VAL 2.8 24.8 + - - -
197M ILE 3.1 26.6 + - - -
198M GLY* 4.5 2.6 - - - +
201M MET* 3.9 19.5 - - + -
161X ALA* 6.4 2.7 - - + -
164X LYS* 3.7 21.8 - - - +
195X GLU 5.8 0.2 + - - -
196X VAL* 4.7 4.2 + - - +
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Residues in contact with GLU 165 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161M ALA 3.0 14.2 + - - +
162M LYS* 3.3 13.7 - - - +
164M LYS* 1.3 78.7 - - - +
166M ARG* 1.3 78.2 + - - +
167M GLY 3.5 0.5 + - - -
161X ALA* 6.2 3.8 - - + -
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Residues in contact with ARG 166 (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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162M LYS* 3.0 45.2 + - + +
163M ALA* 3.3 6.7 + - - +
164M LYS 3.3 0.2 - - - -
165M GLU* 1.3 97.5 + - - +
167M GLY* 1.3 57.7 + - - +
168M ALA* 3.3 1.3 - - + +
339M ASP* 3.0 42.4 + - - +
340M PHE* 4.8 2.5 - - + -
355M LYS* 3.2 31.4 - - - +
356M ILE* 3.6 40.0 - - + +
358M ASP 3.3 10.6 + - - -
359M GLY 2.9 20.3 + - - -
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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
------------------------------------------------------------
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