Contacts of the helix formed by residues 153 - 160 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G LEU* 5.7 3.4 - - + -
129G THR* 6.4 0.2 - - + -
150G CYS* 5.3 3.4 - - - -
152G VAL* 1.3 85.5 - - + +
154G GLN* 1.4 64.9 + - - +
155G ALA* 3.9 11.0 - - + -
156G LEU* 3.3 31.1 + - + +
157G ASP* 3.2 17.4 - - - +
177G TYR 3.7 5.2 - - - +
178G CYS* 3.4 33.9 - - - +
179G TYR* 3.6 35.7 - - + +
194G LEU* 4.8 2.5 - - + -
196G LEU* 3.8 28.7 - - + -
231G HIS* 5.3 0.7 - - - -
234G ARG* 4.6 1.6 - - - +
239G LEU* 5.4 3.8 - - - -
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Residues in contact with GLN 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150G CYS* 4.3 20.2 - - - -
153G ILE* 1.4 71.2 - - - +
155G ALA* 1.4 61.5 + - - +
157G ASP* 3.2 9.7 + - + +
158G LEU* 3.0 41.7 + - + +
176G LYS 4.3 8.7 - - - +
177G TYR* 3.2 40.3 + - + +
178G CYS 5.3 0.4 + - - -
236G ASP* 5.6 1.2 - - - +
239G LEU* 5.0 20.8 - - + +
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Residues in contact with ALA 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G LEU* 4.2 8.6 - - + +
153G ILE* 3.2 16.4 - - + -
154G GLN* 1.4 70.5 - - - +
156G LEU* 1.4 52.9 + - - +
158G LEU* 3.5 3.2 + - - +
159G SER* 2.7 39.0 + - - -
171G VAL* 5.3 0.4 - - + -
173G ALA* 3.8 29.2 - - + -
177G TYR* 2.8 26.0 + - + +
178G CYS* 4.1 1.3 - - - -
196G LEU* 4.0 9.0 - - + -
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Residues in contact with LEU 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G VAL* 5.2 1.3 - - + -
127G LEU* 4.4 20.9 - - + -
143G LEU* 3.8 28.0 - - + -
145G PHE* 3.9 24.0 - - + -
152G VAL* 4.1 13.5 - - + -
153G ILE* 3.3 31.1 + - + +
154G GLN 3.2 0.8 - - - -
155G ALA* 1.4 73.7 - - - +
157G ASP* 1.3 60.3 + - - +
159G SER* 3.8 4.9 - - - +
160G VAL* 3.0 49.9 + - + +
196G LEU* 4.3 15.3 - - + -
198G VAL* 4.8 10.3 - - + -
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Residues in contact with ASP 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145G PHE* 4.7 9.6 - - - -
146G THR 3.9 3.6 - - - +
147G LEU* 3.9 8.5 - - - +
148G GLY* 2.8 32.8 + - - +
149G ASP 3.3 0.3 + - - -
150G CYS* 3.1 44.6 + - - -
151G ASP 4.4 2.0 + - - -
152G VAL 5.0 1.0 + - - -
153G ILE 3.2 14.7 + - - +
154G GLN* 3.2 8.8 + - + +
156G LEU* 1.3 77.8 - - - +
158G LEU* 1.3 60.6 + - + +
161G PRO* 3.2 23.4 - - - +
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Residues in contact with LEU 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G ILE* 4.1 7.1 - - + +
97G LEU* 4.3 18.6 - - + -
102G LEU* 3.6 26.0 - - + -
154G GLN* 3.0 33.5 + - + +
155G ALA 4.0 0.7 - - - +
157G ASP* 1.3 81.9 - - + +
159G SER* 1.3 58.8 + - - +
161G PRO* 3.8 6.1 - - - +
162G LEU* 3.9 15.4 - - - +
177G TYR* 3.9 31.0 - - + -
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Residues in contact with SER 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G ILE* 4.1 16.4 - - - -
102G LEU* 4.8 1.8 - - - -
104G LYS* 4.3 2.4 - - - +
155G ALA 2.7 23.5 + - - -
156G LEU* 3.7 6.8 + - - +
158G LEU* 1.3 77.2 - - - +
160G VAL* 1.3 68.1 + - - +
161G PRO* 3.4 2.7 - - - -
162G LEU* 3.1 20.8 + - - +
163G MET* 3.7 9.6 - - - +
171G VAL* 3.8 37.7 - - - +
196G LEU* 5.7 0.5 - - - +
198G VAL* 5.3 2.1 - - - +
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Residues in contact with VAL 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G PRO* 3.7 7.4 - - + +
123G VAL* 4.4 6.1 - - + -
125G VAL* 4.6 1.6 - - + -
145G PHE* 4.1 15.5 - - + -
147G LEU* 3.6 21.5 - - + -
156G LEU* 3.0 34.5 + - + +
159G SER* 1.3 72.3 - - - +
161G PRO* 1.4 58.6 - - + +
162G LEU 3.0 4.5 - - - -
163G MET* 3.0 43.8 + - - +
198G VAL* 4.5 10.8 - - + -
200G LEU* 4.2 26.5 - - + -
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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