Contacts of the helix formed by residues 146 - 160 (chain N) 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 MET 146 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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836 A 4.1 25.7 - - + +
846 A 3.9 16.1 + - - +
144N PRO 3.0 2.2 + - - +
145N ASP* 1.3 78.4 - - + +
147N GLU* 1.3 58.7 + - - +
149N TYR* 3.8 1.6 - - - +
150N GLU* 2.9 33.9 + - - +
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Residues in contact with GLU 147 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C LYS* 5.7 8.1 - - + -
144N PRO* 3.7 9.8 + - + +
145N ASP 3.4 0.2 - - - -
146N MET* 1.3 78.8 - - - +
148N THR* 1.3 58.3 + - - +
150N GLU* 3.4 4.3 + - - +
151N ARG* 2.9 30.3 + - - +
310O ASN* 5.9 9.8 - - + +
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Residues in contact with THR 148 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140N LYS* 6.4 2.5 - - - -
141N GLN 6.3 0.7 - - - -
142N ILE* 5.5 4.7 - - - -
144N PRO* 3.6 29.2 + - - +
145N ASP* 2.9 10.1 + - - -
147N GLU* 1.3 79.8 - - - +
149N TYR* 1.3 58.2 + - - +
151N ARG* 3.3 5.6 + - - +
152N LEU* 2.9 32.1 + - - +
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Residues in contact with TYR 149 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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846 A 4.0 36.9 - - - +
856 U 4.1 7.2 + - - +
145N ASP* 2.5 25.4 + - - +
146N MET* 4.1 1.8 - - - +
148N THR* 1.3 72.9 - - - +
150N GLU* 1.3 55.8 + - - +
152N LEU* 4.4 3.8 - - - +
153N ARG* 2.8 31.4 + - - +
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Residues in contact with GLU 150 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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846 A 5.2 8.0 + - - +
146N MET 2.9 20.2 + - - +
147N GLU* 3.8 4.9 - - - +
149N TYR* 1.3 76.3 - - - +
151N ARG* 1.3 59.0 + - - +
153N ARG* 3.8 5.0 - - - +
154N GLU* 2.9 30.5 + - - +
310O ASN* 5.8 1.1 - - + +
314O TYR* 4.5 22.0 - - + +
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Residues in contact with ARG 151 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147N GLU 2.9 18.3 + - - +
148N THR* 3.3 5.6 + - - +
150N GLU* 1.3 77.1 - - - +
152N LEU* 1.3 56.9 + - - +
154N GLU* 3.4 4.4 + - - +
155N LYS* 2.9 30.1 + - - +
344O GLN* 5.5 11.7 - - + -
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Residues in contact with LEU 152 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866 U 5.9 2.2 - - - +
140N LYS* 5.5 11.2 - - + -
148N THR 2.9 17.0 + - - +
149N TYR* 4.4 3.8 - - - +
151N ARG* 1.3 77.6 - - - +
153N ARG* 1.3 57.0 + - - +
155N LYS* 3.8 6.2 - - - +
156N HIS* 2.9 30.8 + - - +
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Residues in contact with ARG 153 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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846 A 5.9 2.5 - - - -
856 U 3.6 19.1 - - - +
149N TYR 2.8 23.7 + - - +
150N GLU* 3.9 6.1 - - - +
152N LEU* 1.3 76.7 - - - +
154N GLU* 1.3 58.4 + - - +
156N HIS* 3.8 4.8 - - - +
157N GLY* 2.9 25.3 + - - -
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Residues in contact with GLU 154 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150N GLU 2.9 18.6 + - - +
151N ARG* 3.9 4.0 - - - +
153N ARG* 1.3 74.3 - - - +
155N LYS* 1.3 60.2 + - - +
157N GLY* 4.9 0.7 - - - -
158N GLU* 2.9 30.8 + - - +
314O TYR* 5.9 5.2 - - + -
317O THR* 5.0 16.8 - - - -
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Residues in contact with LYS 155 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151N ARG 2.9 18.8 + - - +
152N LEU* 4.1 6.5 - - - +
154N GLU* 1.3 76.0 - - - +
156N HIS* 1.3 57.6 + - - +
158N GLU* 4.1 3.3 - - - +
159N GLU* 2.9 32.6 + - - +
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Residues in contact with HIS 156 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866 U 5.5 6.7 - - - +
152N LEU 2.9 20.3 + - - +
153N ARG* 4.0 5.4 - - - +
155N LYS* 1.3 77.0 - - - +
157N GLY* 1.3 58.0 + - - +
159N GLU* 4.4 3.9 - - - +
160N PHE* 2.8 31.2 + - - +
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Residues in contact with GLY 157 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153N ARG 2.9 18.3 + - - -
154N GLU* 3.9 1.6 - - - -
156N HIS* 1.3 75.9 - - - +
158N GLU* 1.3 62.9 + - - +
160N PHE* 3.4 4.9 + - - +
161N PHE* 3.1 25.8 + - - +
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Residues in contact with GLU 158 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154N GLU 2.9 18.8 + - - +
155N LYS* 4.1 4.7 - - - +
157N GLY* 1.3 76.9 - - - +
159N GLU* 1.3 57.1 + - - +
161N PHE* 2.8 27.0 - - - +
352O PHE* 5.6 10.3 - - + -
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Residues in contact with GLU 159 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135N TYR* 5.8 9.0 - - + -
155N LYS 2.9 19.7 + - - +
156N HIS* 4.4 3.4 - - - +
158N GLU* 1.3 77.6 - - - +
160N PHE* 1.3 59.6 + - - +
161N PHE 3.3 2.8 + - - -
162N PRO* 4.8 4.9 - - - +
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Residues in contact with PHE 160 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156N HIS 2.8 22.9 + - - +
157N GLY* 3.7 7.0 - - - +
158N GLU 3.2 0.2 - - - -
159N GLU* 1.3 78.2 - - - +
161N PHE* 1.3 57.5 + - - +
162N PRO* 3.4 10.2 - - - +
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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