Contacts of the helix formed by residues 157 - 167 (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 SER 157 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151G VAL* 4.1 1.1 - - - -
155G GLY 3.9 0.6 + - - -
156G LYS* 1.3 76.2 - - - +
158G PRO* 1.3 69.9 - - - +
159G GLU* 2.9 19.7 + - - +
160G GLU* 2.6 46.3 + - - +
161G VAL* 3.1 21.0 + - - +
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Residues in contact with PRO 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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151G VAL* 4.0 19.5 - - + -
156G LYS 4.1 4.0 - - - +
157G SER* 1.3 85.1 - - - +
159G GLU* 1.3 64.8 + - - +
161G VAL* 3.3 3.1 + - + +
162G PHE* 2.9 29.5 + - - +
270G ILE* 3.5 30.6 - - + +
271G GLY* 5.7 0.2 - - - -
272G ILE* 3.6 28.1 - - + +
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Residues in contact with GLU 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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157G SER* 3.2 17.7 + - - +
158G PRO* 1.3 84.3 - - - +
160G GLU* 1.3 59.7 + - + +
162G PHE* 3.5 10.3 + - - +
163G GLU* 2.9 30.0 + - - +
272G ILE* 4.1 16.9 - - + +
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Residues in contact with GLU 160 (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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155G GLY 5.0 0.9 - - - +
156G LYS* 3.4 29.2 - - + +
157G SER* 2.6 47.3 + - - +
159G GLU* 1.3 72.9 - - - +
161G VAL* 1.3 57.2 + - - +
163G GLU* 3.3 7.3 + - - +
164G ALA* 2.9 28.6 + - - +
703G MET* 4.4 8.0 - - - +
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Residues in contact with VAL 161 (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* 4.1 26.7 - - + +
150G LEU* 4.2 19.5 - - + -
151G VAL* 4.2 11.4 - - + -
156G LYS* 4.3 3.8 - - + -
157G SER 3.1 15.5 + - - +
158G PRO* 3.3 7.8 + - + +
160G GLU* 1.3 73.1 - - - +
162G PHE* 1.3 65.2 + - - +
164G ALA* 3.2 3.6 + - - +
165G LEU* 3.0 29.1 + - + +
267G LEU* 5.1 0.7 - - + -
270G ILE* 4.4 7.6 - - + -
699G LEU* 4.2 15.9 - - + +
703G MET* 4.1 23.8 - - + -
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Residues in contact with PHE 162 (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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158G PRO 2.9 17.7 + - - +
159G GLU* 3.6 9.2 - - - +
161G VAL* 1.3 76.3 - - - +
163G GLU* 1.3 62.8 + - - +
165G LEU* 3.2 8.4 + - + +
166G LYS* 3.0 52.8 + - + +
267G LEU* 3.3 34.7 - - + +
272G ILE* 4.1 22.7 - - + -
274G GLU* 3.8 28.9 - - + -
275G ARG 4.1 5.2 - - - -
276G LEU* 4.2 9.9 - - + -
277G PRO* 3.9 27.8 - - + -
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Residues in contact with GLU 163 (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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159G GLU 2.9 18.9 + - - +
160G GLU* 3.6 8.1 - - - +
161G VAL 3.2 0.2 - - - -
162G PHE* 1.3 76.0 - - - +
164G ALA* 1.3 62.6 + - - +
166G LYS* 3.2 35.7 + - - +
167G ASN* 3.0 40.7 + - - +
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Residues in contact with ALA 164 (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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160G GLU 2.9 16.7 + - - +
161G VAL 3.2 4.5 + - - +
163G GLU* 1.3 76.3 - - - +
165G LEU* 1.3 63.2 + - - +
167G ASN* 3.1 8.1 + - - +
168G GLN* 3.1 22.7 + - - +
666G GLY* 5.5 1.2 - - - -
699G LEU* 3.7 19.0 - - + +
703G MET* 4.0 16.8 - - + -
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Residues in contact with LEU 165 (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* 5.3 2.7 - - + -
147G LEU* 4.9 4.9 - - + -
161G VAL* 3.0 20.5 + - + +
162G PHE* 3.6 6.7 - - - +
164G ALA* 1.3 75.8 - - - +
166G LYS* 1.3 63.3 + - - +
168G GLN* 3.2 15.3 + - - +
263G VAL* 4.1 18.2 - - + -
267G LEU* 3.9 29.8 - - + -
276G LEU* 4.0 12.5 - - + +
280G VAL* 3.7 4.7 - - - +
282G LEU* 3.3 45.0 - - + +
695G THR* 4.3 12.6 - - + -
699G LEU* 3.8 30.1 - - + -
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Residues in contact with LYS 166 (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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162G PHE* 3.0 47.0 + - + +
163G GLU* 3.2 30.0 + - - +
165G LEU* 1.3 76.5 - - - +
167G ASN* 1.3 63.8 + - - +
168G GLN 4.8 0.2 - - - +
274G GLU* 5.3 1.6 + - - -
276G LEU* 4.2 15.0 - - + -
277G PRO* 4.0 24.9 - - + +
280G VAL* 3.6 28.4 - - + +
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Residues in contact with ASN 167 (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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163G GLU* 3.0 39.3 + - - +
164G ALA* 3.1 9.6 + - - +
166G LYS* 1.3 83.1 + - - +
168G GLN* 1.3 60.2 + - - +
169G THR* 4.8 2.0 + - - -
634G LYS* 5.3 6.8 + - - -
665G ASN 5.1 0.9 - - - +
666G GLY* 3.7 13.0 - - - +
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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