Contacts of the helix formed by residues 177 - 188 (chain V) in PDB entry 5Z58
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 ASN 177 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172V LYS 5.4 4.5 - - - +
173V VAL* 5.8 0.7 - - - -
174V ASN* 3.7 14.4 + - + +
175V ILE 3.2 0.4 - - - -
176V SER* 1.3 81.0 - - - +
178V ILE* 1.3 64.9 + - - +
179V SER* 3.1 4.3 + - - -
180V ILE* 3.1 12.1 + - + +
181V ILE* 3.1 21.3 + - + +
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Residues in contact with ILE 178 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173V VAL* 5.5 3.8 - - + -
174V ASN 3.4 18.4 + - - +
175V ILE* 3.7 10.0 + - - +
176V SER 3.7 0.6 - - - -
177V ASN* 1.3 76.5 - - - +
179V SER* 1.3 57.5 + - - +
181V ILE* 3.2 9.6 + - - +
182V ILE* 2.9 28.6 + - - +
214V VAL* 5.9 4.0 - - + +
217V ALA* 5.9 6.5 - - + -
218V LEU* 6.1 7.2 - - + +
356V GLY 5.5 4.5 - - - +
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Residues in contact with SER 179 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177V ASN 3.2 1.0 - - - -
178V ILE* 1.3 78.5 - - - +
180V ILE* 1.3 62.5 + - - +
182V ILE* 3.3 8.4 + - - +
183V GLN* 3.0 22.1 + - - +
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Residues in contact with ILE 180 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177V ASN* 3.1 14.0 + - + +
179V SER* 1.3 78.4 - - - +
181V ILE* 1.3 58.6 + - - +
183V GLN* 3.2 8.1 + - - +
184V GLU* 2.9 30.0 + - - +
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Residues in contact with ILE 181 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169V LEU* 4.9 15.1 - - + +
172V LYS* 5.9 2.2 - - + -
173V VAL* 4.4 22.7 - - + -
177V ASN* 3.1 12.8 + - + +
178V ILE* 3.2 12.8 + - - +
180V ILE* 1.3 77.0 - - - +
182V ILE* 1.3 52.0 + - - +
184V GLU* 3.2 7.2 + - - +
185V LEU* 2.8 36.4 + - - +
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Residues in contact with ILE 182 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178V ILE 2.9 12.9 + - - +
179V SER* 3.5 11.0 - - - +
180V ILE 3.3 0.2 - - - -
181V ILE* 1.3 74.7 - - - +
183V GLN* 1.3 57.9 + - - +
185V LEU* 3.2 7.4 + - - +
186V LEU* 2.9 31.8 + - - +
221V ILE* 5.2 15.3 - - + -
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Residues in contact with GLN 183 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179V SER 3.0 13.2 + - - +
180V ILE* 3.5 11.4 - - - +
182V ILE* 1.3 78.5 - - - +
184V GLU* 1.3 61.6 + - - +
186V LEU* 3.5 10.8 + - - +
187V GLN* 3.5 12.1 + - - +
406V LEU 5.1 5.3 - - - +
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Residues in contact with GLU 184 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169V LEU* 5.8 5.8 - - + -
180V ILE 2.9 16.3 + - - +
181V ILE* 3.7 6.3 - - - +
183V GLN* 1.3 74.7 - - - +
185V LEU* 1.3 66.5 + - - +
187V GLN* 3.3 19.9 + - - +
188V GLU* 3.9 4.2 + - - +
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Residues in contact with LEU 185 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169V LEU* 5.3 12.7 - - + +
181V ILE 2.8 17.7 + - - +
182V ILE* 3.5 8.3 - - - +
184V GLU* 1.3 77.2 - - - +
186V LEU* 1.3 56.8 + - - +
188V GLU* 3.0 31.4 + - - +
190V ILE* 4.7 8.5 - - + +
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Residues in contact with LEU 186 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182V ILE 2.9 17.0 + - - +
183V GLN* 3.9 7.4 - - - +
184V GLU 3.3 0.4 - - - -
185V LEU* 1.3 74.1 - - - +
187V GLN* 1.3 63.1 + - - +
188V GLU 3.3 9.1 + - - +
190V ILE* 6.0 1.6 - - - -
402V LYS* 4.3 16.8 - - + +
406V LEU 4.3 20.0 - - - +
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Residues in contact with GLN 187 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183V GLN 3.5 9.3 + - - +
184V GLU* 3.3 14.5 + - - +
185V LEU 3.2 0.6 - - - -
186V LEU* 1.3 77.8 - - - +
188V GLU* 1.3 59.3 + - - +
189V ASN 4.1 0.3 + - - -
402V LYS* 5.6 3.4 - - - -
406V LEU 5.4 0.2 + - - -
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Residues in contact with GLU 188 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162V LEU* 5.8 10.1 - - + +
165V SER* 5.6 10.5 - - - -
166V ILE* 6.2 1.3 - - + +
184V GLU 3.9 3.7 + - - +
185V LEU* 3.0 18.6 + - - +
186V LEU 3.3 12.0 - - - +
187V GLN* 1.3 80.6 - - - +
189V ASN* 1.3 62.5 + - - +
190V ILE* 2.8 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