Contacts of the helix formed by residues 142 - 153 (chain G) in PDB entry 6V3O
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 ASP 142 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122G ARG* 5.6 7.0 - - - +
140G GLU 3.9 1.4 + - - -
141G SER* 1.3 72.4 - - - +
143G ILE* 1.3 60.6 + - + +
144G GLU* 3.1 10.9 + - - +
145G GLU* 2.7 53.6 + - - +
146G THR* 2.7 30.9 + - - -
692G GLN* 3.2 25.4 - - - +
696G ALA* 4.9 0.7 - - - -
208H ASP* 5.4 3.6 - - - +
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Residues in contact with ILE 143 (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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142G ASP* 1.3 74.1 - - + +
144G GLU* 1.3 66.7 + - + +
146G THR* 3.3 4.5 + - - -
147G LEU* 3.0 52.8 + - + +
165G LEU* 5.3 2.9 - - + -
259G PHE* 4.6 5.4 - - + -
262G ARG* 3.8 28.5 - - + +
263G VAL* 4.3 15.5 - - + -
266G ALA* 4.2 14.1 - - + -
692G GLN* 3.1 26.5 + - + +
695G THR* 4.2 19.5 - - + -
696G ALA* 4.1 26.0 - - + +
699G LEU* 4.8 5.4 - - + -
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Residues in contact with GLU 144 (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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142G ASP* 3.1 9.2 + - - +
143G ILE* 1.3 84.0 - - + +
145G GLU* 1.3 58.3 + - + +
147G LEU* 3.1 5.2 + - + +
148G LYS* 2.8 60.8 + - + +
262G ARG* 6.2 0.2 - - - -
266G ALA* 4.0 26.8 + - + +
269G ASN* 3.6 30.3 + - + +
270G ILE* 5.7 0.2 - - + -
208H ASP* 2.9 41.7 - - - +
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Residues in contact with GLU 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127G LYS* 3.1 31.6 + - - -
140G GLU 3.9 0.7 - - - +
141G SER* 3.3 10.4 - - - -
142G ASP* 2.7 49.8 + - - +
144G GLU* 1.3 72.3 - - + +
146G THR* 1.3 58.1 + - - +
148G LYS* 3.3 8.5 + - - +
149G ARG* 2.9 34.6 + - - +
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Residues in contact with THR 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 SER* 3.6 12.0 - - - -
142G ASP 2.7 20.3 + - - -
143G ILE* 3.5 7.9 - - - -
144G GLU 3.2 0.2 - - - -
145G GLU* 1.3 76.7 - - - +
147G LEU* 1.3 66.5 + - + +
149G ARG* 3.3 12.1 + - - +
150G LEU* 3.0 29.8 + - + +
653G HIS* 4.8 1.1 - - - +
696G ALA* 3.5 30.5 - - + +
699G LEU* 5.2 1.6 - - + -
700G GLU* 3.7 37.6 + - + +
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Residues in contact with LEU 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 ILE* 3.0 43.5 + - + +
144G GLU* 3.1 7.8 + - - +
146G THR* 1.3 76.8 - - - +
148G LYS* 1.3 63.1 + - - +
150G LEU* 3.2 8.7 + - - +
151G VAL* 3.2 27.5 + - - +
161G VAL* 4.1 13.9 - - + -
165G LEU* 4.9 3.6 - - + -
263G VAL* 5.0 1.1 - - + +
266G ALA* 3.6 36.8 - - + +
267G LEU* 3.8 23.3 - - + -
270G ILE* 4.1 16.8 - - + +
699G LEU* 3.8 21.3 - - + -
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Residues in contact with LYS 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 GLU* 2.8 50.2 + - + +
145G GLU* 3.7 7.9 - - - +
147G LEU* 1.3 77.9 - - - +
149G ARG* 1.3 57.5 + - - +
151G VAL* 3.4 9.0 + - + +
152G SER* 2.4 39.0 + - - +
269G ASN* 3.7 23.1 - - - +
270G ILE* 4.5 9.9 - - + -
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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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134G GLU* 3.0 14.1 + - - -
141G SER* 2.5 34.9 + - - -
145G GLU* 2.9 20.2 + - - +
146G THR* 3.7 12.5 - - - +
148G LYS* 1.3 77.5 - - - +
150G LEU* 1.3 63.9 + - + +
152G SER* 4.2 0.2 - - - -
153G GLU* 3.0 54.4 + - + +
154G VAL* 3.0 14.6 + - + +
653G HIS* 5.6 0.2 + - - -
657G LEU* 5.7 0.2 - - - +
700G GLU* 2.6 46.0 + - - -
704G HIS* 4.6 10.8 - - + -
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Residues in contact with LEU 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 THR* 3.0 24.5 + - + +
147G LEU* 3.5 11.4 - - - +
148G LYS 3.2 0.4 - - - -
149G ARG* 1.3 79.5 - - + +
151G VAL* 1.3 58.6 + - - +
154G VAL* 3.3 22.2 - - + +
155G GLY 3.1 10.2 + - - -
156G LYS* 3.0 22.9 + - + +
161G VAL* 4.2 15.5 - - + -
699G LEU* 4.0 20.9 - - + -
700G GLU* 4.3 20.2 - - + +
703G MET* 3.6 48.5 - - + -
704G HIS* 4.5 3.4 - - + -
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Residues in contact with VAL 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 LEU 3.2 12.5 + - - +
148G LYS* 3.5 16.4 - - + +
150G LEU* 1.3 77.5 - - - +
152G SER* 1.3 66.1 + - - +
153G GLU 3.6 0.2 - - - -
155G GLY* 3.3 21.3 - - - -
156G LYS 3.2 21.0 - - - +
157G SER 4.1 2.0 - - - -
158G PRO* 4.0 30.7 - - + -
161G VAL* 4.2 10.3 - - + -
270G ILE* 4.4 16.6 - - + -
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Residues in contact with SER 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 LYS* 2.4 31.3 + - - +
149G ARG* 4.2 0.2 - - - -
151G VAL* 1.3 82.5 - - - +
153G GLU* 1.3 68.4 + - - +
155G GLY* 4.4 1.7 + - - -
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Residues in contact with GLU 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* 3.0 40.4 + - + +
152G SER* 1.3 90.2 + - - +
154G VAL* 1.3 65.3 + - + +
155G GLY* 3.3 1.4 + - - -
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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