Contacts of the helix formed by residues 170 - 178 (chain F) in PDB entry 5X6E
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 THR 170 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F ASN* 5.0 11.4 - - + +
169F LEU* 1.3 78.9 - - - +
171F MET* 1.3 63.0 + - - +
172F GLN* 3.0 17.6 - - + +
173F GLU* 2.4 55.4 + - + +
174F LEU* 3.1 13.7 + - - +
7G C 4.6 22.4 - - - +
8G G 3.4 13.9 - - - +
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Residues in contact with MET 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F LEU 3.7 0.2 + - - -
170F THR* 1.3 72.0 - - - +
172F GLN* 1.3 64.1 + - - +
173F GLU 3.1 1.2 + - - -
174F LEU* 3.2 20.2 + - + +
175F GLY 3.2 9.9 + - - -
183F SER* 4.9 3.6 - - - +
186F VAL* 3.3 54.4 - - + +
187F SER* 4.3 14.6 - - - +
190F ILE* 3.8 19.7 - - + -
206F PHE* 4.3 25.6 - - - -
8G G 2.8 41.1 + - + +
9G T 4.2 16.4 - - - +
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Residues in contact with GLN 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F THR* 3.0 22.4 - - + +
171F MET* 1.3 75.4 - - - +
173F GLU* 1.3 59.9 + - - +
175F GLY* 3.8 6.4 + - - -
176F TYR* 2.6 53.8 + - - -
181F ALA 5.2 5.0 - - - +
183F SER* 5.1 22.5 + - - +
186F VAL* 5.4 2.1 - - - +
7G C 5.2 13.9 - - + +
8G G 3.9 3.9 + - - +
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Residues in contact with GLU 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F LYS* 2.2 36.9 + - - -
59F ASN* 2.9 14.5 + - - +
62F TYR* 3.8 17.7 + - - +
88F ILE* 6.1 0.7 - - - -
168F ASN* 5.1 7.6 + - - +
169F LEU* 4.7 7.2 - - + -
170F THR* 2.4 46.4 + - - +
172F GLN* 1.3 67.0 - - + +
174F LEU* 1.3 61.9 + - - +
175F GLY 3.1 1.8 - - - -
176F TYR* 2.8 38.1 + - - +
177F SER* 3.5 3.8 + - - -
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Residues in contact with LEU 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F TYR* 5.8 0.4 - - - -
143F ILE* 3.7 31.2 - - + +
146F GLN* 4.0 27.8 - - + -
147F LEU* 4.0 24.2 - - + -
150F LEU* 5.1 4.5 - - + -
169F LEU* 4.8 23.5 - - + +
170F THR 3.1 8.8 + - - +
171F MET* 3.2 16.4 + - + +
173F GLU* 1.3 79.6 - - - +
175F GLY* 1.3 62.2 + - - +
177F SER* 3.0 17.3 + - - -
178F SER* 3.3 7.6 + - - -
186F VAL* 4.5 8.5 - - + -
206F PHE* 5.4 8.1 - - + -
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Residues in contact with GLY 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F MET 3.2 9.1 + - - -
172F GLN 4.1 3.6 - - - -
173F GLU 3.1 1.4 - - - -
174F LEU* 1.3 77.9 - - - +
176F TYR* 1.3 54.5 + - - +
178F SER* 3.0 9.4 + - - -
179F GLY 2.8 24.6 + - - -
180F ILE* 2.8 20.5 + - - -
186F VAL* 3.7 26.7 - - - +
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Residues in contact with TYR 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F THR* 5.9 1.6 - - - -
57F ILE* 3.5 56.8 - - + +
58F MET* 3.1 19.8 - - - +
59F ASN* 3.1 38.9 + - - +
172F GLN* 2.6 53.4 + - - -
173F GLU* 2.8 23.2 + - + +
175F GLY* 1.3 70.8 - - - -
177F SER* 1.3 62.3 + - - +
178F SER 3.2 0.2 + - - -
179F GLY 4.4 0.4 - - - +
180F ILE 4.0 11.4 - - - -
181F ALA* 5.0 13.1 + - + -
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Residues in contact with SER 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E PHE* 4.0 8.5 - - - -
58F MET* 4.3 0.2 - - - -
59F ASN* 3.2 28.6 + - - +
61F GLN* 6.2 0.2 - - - -
62F TYR* 4.0 17.3 + - - -
130F LYS* 4.2 2.1 + - - -
134F PHE* 3.6 15.4 - - - -
146F GLN* 3.4 40.2 + - - +
173F GLU 3.5 2.7 + - - -
174F LEU* 3.0 16.4 + - - -
176F TYR* 1.3 78.8 - - - +
178F SER* 1.3 56.9 + - - +
179F GLY 3.6 0.2 - - - -
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Residues in contact with SER 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E SER* 4.5 4.3 - - - -
58F MET* 4.4 2.2 - - - -
134F PHE* 4.0 8.4 - - - -
139F LYS* 3.7 13.9 + - - +
142F SER* 3.7 35.0 + - - -
143F ILE* 3.2 31.6 - - - +
146F GLN* 5.2 0.7 - - - -
174F LEU* 3.3 6.9 + - - -
175F GLY* 3.0 9.9 + - - -
177F SER* 1.3 79.8 - - - +
179F GLY* 1.3 55.6 + - - +
180F ILE* 3.2 14.7 + - - +
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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