Contacts of the helix formed by residues 146 - 153 (chain G) in PDB entry 3A2C
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 LEU 146 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144G GLY 3.5 1.8 + - - -
145G GLU* 1.3 69.8 - - - +
147G PHE* 1.3 93.8 + - + +
149G ARG* 3.5 12.6 + - - +
150G ILE* 3.5 17.2 + - + +
166G ILE* 3.8 35.0 - - + -
170G ILE* 4.6 6.3 - - + -
189G PRO* 4.5 4.4 + - + +
192G LEU* 2.8 41.5 + - + +
194G TYR* 3.8 25.5 - - + +
203G LEU* 4.0 10.5 - - + -
252G ILE* 4.6 7.0 - - + -
256G LEU* 4.5 6.1 - - + -
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Residues in contact with PHE 147 (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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2G PDY 4.8 13.7 - - - -
145G GLU* 2.8 4.1 + - + +
146G LEU* 1.3 90.7 - - + +
148G SER* 1.3 68.3 + - - +
149G ARG 3.0 2.2 - - - -
150G ILE* 2.9 9.0 + - + +
151G GLN* 2.9 26.3 + - - +
189G PRO* 3.3 38.5 + - + +
252G ILE* 4.3 10.3 - - + -
255G ILE* 3.3 42.4 - - + -
256G LEU* 3.7 31.4 - - + -
338G THR* 5.2 0.2 - - + -
342G LEU* 3.7 27.9 - - + +
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Residues in contact with SER 148 (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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144G GLY* 4.6 3.8 - - - -
145G GLU* 2.7 42.1 + - - +
147G PHE* 1.3 72.4 - - - +
149G ARG* 1.3 59.4 - - - +
151G GLN* 3.5 22.3 - - - +
152G ASP* 3.7 12.3 + - - +
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Residues in contact with ARG 149 (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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143G GLY 3.2 22.4 + - - +
144G GLY 4.8 0.4 - - - -
145G GLU 3.3 6.3 + - - +
146G LEU 3.7 4.5 - - - +
147G PHE 3.0 0.8 - - - -
148G SER* 1.3 75.3 - - - +
150G ILE* 1.3 63.3 + - + +
151G GLN 3.1 1.8 - - - -
152G ASP* 2.8 27.7 + - - +
153G ARG* 3.3 9.7 + - - +
194G TYR* 3.7 45.4 - - + -
196G SER 3.6 8.7 + - - -
197G LYS* 3.6 36.9 + - - +
198G ARG 3.8 5.5 + - - -
199G PRO* 3.8 21.8 + - - +
201G ALA* 4.3 1.0 - - - +
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Residues in contact with ILE 150 (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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146G LEU* 3.5 24.0 + - + +
147G PHE* 2.9 13.1 + - + +
149G ARG* 1.3 76.8 - - + +
151G GLN* 1.3 63.2 + - - +
153G ARG* 3.1 12.2 - - - +
158G PHE* 3.4 44.0 - - + -
166G ILE* 4.2 1.6 - - + -
194G TYR* 6.0 0.7 - - + +
256G LEU* 3.4 22.0 - - + -
338G THR* 3.8 15.5 - - + -
339G SER* 3.0 33.1 + - - +
342G LEU* 3.7 18.6 - - + -
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Residues in contact with GLN 151 (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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147G PHE 2.9 10.4 + - - +
148G SER* 3.5 17.9 - - - +
150G ILE* 1.3 78.5 - - - +
152G ASP* 1.3 62.5 + - - +
153G ARG 2.9 14.4 + - - +
339G SER* 4.2 9.7 - - - +
342G LEU* 4.2 41.8 + - + +
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Residues in contact with ASP 152 (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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148G SER* 4.0 12.9 + - - +
149G ARG* 2.8 17.4 + - - +
151G GLN* 1.3 77.5 - - - +
153G ARG* 1.3 66.6 + - - +
154G GLY 3.7 0.3 + - - -
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Residues in contact with ARG 153 (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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149G ARG 3.3 5.9 + - - -
150G ILE* 3.1 12.6 + - - +
151G GLN 2.9 10.0 + - - +
152G ASP* 1.3 83.7 - - - +
154G GLY* 1.3 65.5 + - - +
155G ASP* 3.7 3.3 + - - +
157G ALA* 3.3 32.0 + - + +
158G PHE* 3.8 12.3 - - + +
162G GLU* 2.6 44.8 + - - -
339G SER* 3.0 28.9 - - - +
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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