Contacts of the helix formed by residues 153 - 160 (chain E) in PDB entry 5MGX
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 ILE 153 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E LEU* 5.9 1.3 - - + -
150E CYS* 5.4 3.6 - - - -
152E VAL* 1.3 89.2 - - + +
154E GLN* 1.3 64.2 + - - +
155E ALA* 3.2 20.9 - - + -
156E LEU* 3.3 30.7 + - + +
157E ASP* 3.2 16.8 + - - +
177E TYR 3.7 5.6 - - - +
178E CYS* 3.5 35.0 - - + +
179E TYR* 3.6 34.8 - - + +
194E LEU* 4.7 0.4 - - + -
196E LEU* 3.9 24.9 - - + -
231E HIS* 5.4 1.1 - - - -
234E ARG* 5.0 1.3 - - - +
239E LEU* 5.4 2.7 - - - -
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Residues in contact with GLN 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E CYS* 4.4 19.3 - - - -
153E ILE* 1.3 70.8 - - - +
155E ALA* 1.4 62.5 + - - +
157E ASP* 3.2 9.9 + - + +
158E LEU* 3.0 40.9 + - + +
176E LYS 4.3 8.8 - - - +
177E TYR* 3.2 41.7 + - + +
178E CYS 5.2 0.4 + - - -
239E LEU* 5.0 20.5 - - + +
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Residues in contact with ALA 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E LEU* 4.2 9.4 - - + +
153E ILE* 3.2 16.1 - - + -
154E GLN* 1.4 71.6 - - - +
156E LEU* 1.3 51.0 + - - +
158E LEU* 3.5 3.0 + - - +
159E SER* 2.7 38.7 + - - -
171E VAL* 5.3 0.2 - - + -
173E ALA* 3.8 29.2 - - + -
177E TYR* 2.8 26.2 + - + +
178E CYS* 4.1 1.1 - - - -
196E LEU* 4.0 8.3 - - + -
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Residues in contact with LEU 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E VAL* 5.2 1.1 - - + -
127E LEU* 4.1 28.7 - - + -
143E LEU* 3.8 27.8 - - + -
145E PHE* 3.9 23.1 - - + -
147E LEU* 4.5 0.2 - - - +
152E VAL* 4.1 12.8 - - + -
153E ILE* 3.3 31.2 + - + +
154E GLN 3.2 0.4 - - - -
155E ALA* 1.3 77.7 - - - +
157E ASP* 1.3 57.7 + - - +
159E SER* 3.8 2.9 - - - +
160E VAL* 3.0 49.7 + - + +
196E LEU* 4.3 10.3 - - + -
198E VAL* 4.5 9.6 - - + -
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Residues in contact with ASP 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E PHE* 4.7 8.5 - - - -
146E THR 3.9 4.0 - - - +
147E LEU* 3.9 9.1 - - - +
148E GLY* 2.8 34.2 + - - +
149E ASP 3.3 0.5 + - - -
150E CYS* 3.1 42.3 + - - -
151E ASP 4.4 1.4 + - - -
152E VAL 5.0 0.9 + - - -
153E ILE 3.2 15.3 + - - +
154E GLN* 3.2 8.1 + - + +
156E LEU* 1.3 78.1 - - - +
158E LEU* 1.3 60.7 + - + +
161E PRO* 3.2 22.3 - - - +
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Residues in contact with LEU 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E ILE* 4.2 7.4 - - + +
97E LEU* 4.3 18.2 - - + -
102E LEU* 3.6 29.2 - - + -
154E GLN* 3.0 33.9 + - + +
155E ALA 3.9 0.9 - - - +
157E ASP* 1.3 81.5 - - + +
159E SER* 1.3 58.9 + - - +
161E PRO* 3.8 6.4 - - - +
162E LEU* 4.0 15.9 - - - +
177E TYR* 3.9 27.6 - - + -
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Residues in contact with SER 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E ILE* 4.1 17.0 - - - -
102E LEU* 4.8 1.6 - - - -
104E LYS* 4.3 2.9 - - - +
155E ALA 2.7 24.1 + - - -
156E LEU* 3.7 6.8 + - - +
158E LEU* 1.3 76.1 - - - +
160E VAL* 1.3 68.6 + - - +
161E PRO* 3.4 2.7 - - - -
162E LEU* 3.1 22.8 + - - +
163E MET* 3.9 7.1 + - - +
171E VAL* 3.8 37.0 - - - +
196E LEU* 5.6 0.5 - - - +
198E VAL* 5.4 2.1 - - - +
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Residues in contact with VAL 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E PRO* 3.7 13.7 - - + +
123E VAL* 4.3 8.3 - - + -
125E VAL* 4.6 1.3 - - + -
145E PHE* 4.0 16.6 - - + -
147E LEU* 3.9 18.8 - - + -
156E LEU* 3.0 33.8 + - + +
159E SER* 1.3 73.1 - - - +
161E PRO* 1.4 59.4 - - + +
162E LEU 3.0 4.7 - - - -
163E MET* 3.0 42.8 + - - +
198E VAL* 4.4 9.9 - - + -
200E LEU* 4.3 20.2 - - + -
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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