Contacts of the helix formed by residues 145 - 153 (chain G) in PDB entry 2G0B
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30G GLN* 4.9 4.5 - - - -
32G TYR* 5.5 0.2 - - - -
98G PHE* 5.4 9.8 - + - -
141G ILE* 4.2 6.7 - - + -
142G ASN* 2.7 16.3 + - + +
144G LYS* 1.3 108.4 - - + +
146G ASP* 1.3 63.7 + - - +
147G THR 3.3 1.6 - - - -
148G PHE* 3.0 23.3 + + + +
149G TYR* 3.2 48.2 + + + -
189H PHE 5.7 3.5 + - - -
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Residues in contact with ASP 146 (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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141G ILE* 3.8 10.3 - - + -
142G ASN 3.5 2.8 + - - -
143G PRO* 3.3 26.5 - - + +
144G LYS 3.3 1.4 - - - -
145G HIS* 1.3 78.5 - - - +
147G THR* 1.3 64.7 + - - +
148G PHE 3.3 0.7 + - - -
149G TYR* 3.5 0.7 + - - +
150G SER* 3.3 22.0 + - - -
156G GLN* 5.2 1.6 - - - +
171G ILE* 3.4 29.6 - - + +
173G ARG* 2.6 32.0 + - - -
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Residues in contact with THR 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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143G PRO 4.7 1.4 + - - -
144G LYS 4.6 11.2 - - - +
146G ASP* 1.3 80.6 + - - +
148G PHE* 1.3 61.3 + - + +
150G SER* 3.3 16.1 + - - -
151G LEU* 3.4 19.9 - - - +
189H PHE* 4.7 13.9 - - + -
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Residues in contact with PHE 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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118G ALA* 6.4 0.7 - - + -
122G PHE* 4.0 16.8 - + - -
144G LYS 5.9 0.2 - - - +
145G HIS* 3.0 17.3 + + + +
147G THR* 1.3 80.1 - - + +
149G TYR* 1.3 93.2 + + + +
150G SER 3.2 0.4 - - - -
151G LEU* 3.1 22.0 + - + +
152G LEU* 3.2 44.1 + - + +
186H LEU* 6.5 0.4 - - + -
189H PHE* 3.7 57.4 - + + -
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Residues in contact with TYR 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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98G PHE* 3.5 24.1 - - - -
122G PHE* 4.3 3.9 - + - -
139G ILE* 4.9 6.5 - - + -
141G ILE* 3.7 29.7 - - + +
145G HIS* 3.2 52.1 + + + +
146G ASP 4.5 0.4 - - - +
148G PHE* 1.3 104.0 - + - +
150G SER* 1.3 61.2 + - - +
151G LEU 3.2 0.2 - - - -
152G LEU* 3.2 18.1 + - + -
153G GLY 3.3 0.5 + - - -
154G PHE* 3.1 45.5 + + + +
173G ARG* 4.5 3.1 - - - -
406G NLT 3.4 48.5 - - + +
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Residues in contact with SER 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 ASP* 3.3 9.6 + - - -
147G THR* 3.3 17.2 + - - -
149G TYR* 1.3 77.3 - - - +
151G LEU* 1.3 67.3 + - - +
153G GLY* 3.7 9.8 + - - -
154G PHE 3.9 10.6 + - - +
173G ARG* 3.5 28.8 - - - +
185G LEU* 5.5 2.8 - - - +
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Residues in contact with LEU 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 THR* 3.4 17.5 - - - +
148G PHE* 3.1 10.1 + - + +
150G SER* 1.3 78.7 + - - +
152G LEU* 1.3 64.8 + - - +
153G GLY* 3.2 1.3 + - - -
184G THR* 3.3 12.1 + - - -
185G LEU* 3.7 41.0 + - + +
189H PHE* 4.3 23.8 - - + -
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Residues in contact with LEU 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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122G PHE* 4.2 16.8 - - + -
148G PHE* 3.2 46.3 + - + +
149G TYR* 3.2 16.9 + - + +
151G LEU* 1.3 78.7 - - - +
153G GLY* 1.3 55.9 + - - +
154G PHE* 3.7 26.2 - - + -
175G LEU* 5.0 6.8 - - - +
180G TRP 5.2 0.5 - - - +
184G THR* 3.1 22.5 + - - +
406G NLT 4.2 21.9 - - + +
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Residues in contact with GLY 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 TYR 3.3 0.6 + - - -
150G SER 3.7 6.4 + - - -
151G LEU 3.2 3.8 - - - -
152G LEU* 1.3 81.3 - - - +
154G PHE* 1.3 63.1 + - - +
155G THR* 3.4 2.3 + - - -
174G ALA 4.1 0.2 - - - +
175G LEU* 3.4 12.0 - - - +
183G GLN* 3.2 52.3 + - - +
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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