Contacts of the helix formed by residues 145 - 156 (chain M) in PDB entry 5MQF
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 HIS 145 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142M ILE* 3.9 14.1 + - - +
143M THR 3.2 5.8 + - - +
144M GLN* 1.3 77.6 - - - +
146M SER* 1.3 57.1 + - - +
147M ARG 3.1 0.7 - - - -
148M ILE* 3.1 5.1 + - - +
149M TRP* 2.9 35.3 + - + +
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Residues in contact with SER 146 (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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142M ILE 5.2 0.8 + - - -
144M GLN* 3.5 1.6 - - - +
145M HIS* 1.3 77.3 - - - +
147M ARG* 1.3 56.8 + - - +
149M TRP* 5.3 0.4 - - - -
150M PRO* 3.1 31.1 - - - +
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Residues in contact with ARG 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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114M LEU* 4.7 20.2 - - + +
117M CYS* 5.2 9.6 - - + -
133M PHE* 6.3 0.4 - - - -
136M ALA* 5.8 3.4 - - + -
144M GLN* 3.4 22.2 + - + +
145M HIS 3.1 0.8 - - - -
146M SER* 1.3 78.2 - - - +
148M ILE* 1.3 63.1 + - - +
149M TRP 3.6 0.2 - - - -
150M PRO* 5.0 0.2 - - - +
151M LEU* 3.2 21.8 + - - +
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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
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133M PHE* 5.1 16.6 - - + -
144M GLN 3.0 16.9 + - - +
145M HIS* 3.9 4.3 - - - +
147M ARG* 1.3 76.8 - - - +
149M TRP* 1.3 66.3 + - - +
151M LEU* 3.1 7.7 + - - +
152M TYR* 3.1 20.6 + - - +
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Residues in contact with TRP 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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145M HIS 2.9 13.8 + - - +
146M SER* 5.3 0.2 - - - -
148M ILE* 1.3 77.4 - - - +
150M PRO* 1.3 65.8 - - + +
152M TYR* 3.0 11.4 + - - +
153M LEU* 2.9 23.8 + - - +
182M GLU* 6.1 5.4 - - + -
183M TYR* 6.4 2.0 - - + +
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Residues in contact with PRO 150 (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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146M SER* 3.1 36.8 - - - +
147M ARG 5.0 0.4 - - - +
149M TRP* 1.3 92.7 - - + +
151M LEU* 1.3 56.1 + - - +
153M LEU* 3.5 11.2 - - + +
154M ARG* 2.9 29.1 + - - +
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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
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129M THR* 5.3 13.0 - - - -
147M ARG 3.2 21.4 + - - +
148M ILE* 3.1 8.4 + - - +
149M TRP 3.1 0.8 - - - -
150M PRO* 1.3 78.4 - - - +
152M TYR* 1.3 57.7 + - - +
154M ARG* 3.5 4.0 + - - +
155M PHE* 2.9 30.7 + - - +
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Residues in contact with TYR 152 (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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148M ILE 3.1 10.4 + - - +
149M TRP* 3.0 11.7 + - - +
151M LEU* 1.3 73.7 - - - +
153M LEU* 1.3 60.3 + - - +
155M PHE* 3.8 5.7 - - - +
156M LEU* 2.9 28.8 + - - +
162M PRO* 4.3 6.1 - - - +
163M GLU* 4.5 8.1 + - - +
166M VAL* 3.6 31.6 - - + -
167M ARG 5.5 0.2 - - - +
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Residues in contact with LEU 153 (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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149M TRP 2.9 12.3 + - - +
150M PRO* 3.6 14.1 - - + +
151M LEU 3.2 0.2 - - - -
152M TYR* 1.3 77.8 - - - +
154M ARG* 1.3 62.9 + - - +
156M LEU* 3.4 17.5 + - - +
157M ARG* 3.9 3.1 + - - +
186M TYR* 4.9 18.2 - - + -
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Residues in contact with ARG 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 PRO 2.9 16.3 + - - +
151M LEU* 4.1 4.5 - - - +
153M LEU* 1.3 75.3 - - - +
155M PHE* 1.3 64.2 + - - +
157M ARG* 3.3 21.2 + - - +
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Residues in contact with PHE 155 (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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151M LEU 2.9 20.5 + - - +
152M TYR* 4.2 2.9 - - - +
154M ARG* 1.3 71.6 - - - +
156M LEU* 1.3 57.0 + - - +
157M ARG 3.0 18.8 + - - +
159M HIS* 4.3 1.4 + - - +
162M PRO* 3.2 29.5 - - + +
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Residues in contact with LEU 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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152M TYR 2.9 20.7 + - - +
153M LEU* 3.4 13.2 - - - +
154M ARG 3.1 1.0 - - - -
155M PHE* 1.3 73.9 - - - +
157M ARG* 1.3 60.0 + - - +
158M SER 3.5 1.7 + - - -
159M HIS 2.8 24.0 + - - +
160M PRO* 4.9 0.5 - - - +
162M PRO* 3.8 5.1 - - - +
163M GLU* 3.6 24.0 - - + -
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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