Contacts of the helix formed by residues 176 - 185 (chain R) in PDB entry 5IY8
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 PRO 176 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171R ILE* 4.0 20.8 - - + +
174R ALA 4.8 1.1 - - - +
175R LEU* 1.3 101.7 - - + +
177R ASN* 1.3 64.4 + - - +
178R SER* 3.4 7.8 + - - +
179R GLN* 4.1 18.9 + - + +
180R LYS* 4.4 1.6 + - - +
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Residues in contact with ASN 177 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167R LEU* 4.0 16.8 - - + +
170R ASP* 2.6 33.2 + - - +
171R ILE* 3.6 25.3 - - + +
175R LEU 3.5 2.0 + - - -
176R PRO* 1.3 72.3 - - - +
178R SER* 1.3 62.5 + - - +
179R GLN 3.1 0.2 + - - -
180R LYS* 3.0 24.1 - - - +
181R ALA* 2.9 52.9 + - - +
189R ILE* 5.2 9.9 - - - +
191R PHE* 3.5 17.1 - - - -
202R PHE* 5.3 2.4 - - - +
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Residues in contact with SER 178 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171R ILE* 5.4 5.0 - - - +
176R PRO* 3.4 5.8 - - - +
177R ASN* 1.3 79.6 + - - +
179R GLN* 1.3 57.6 - - - +
181R ALA* 3.5 7.0 - - - +
182R VAL* 3.1 36.6 + - - +
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Residues in contact with GLN 179 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175R LEU* 6.2 0.4 - - + -
176R PRO* 4.1 17.6 + - + +
177R ASN 3.1 1.2 + - - -
178R SER* 1.3 79.0 - - - +
180R LYS* 1.3 65.1 + - - +
181R ALA 3.5 0.2 + - - -
182R VAL* 3.7 11.6 + - - +
183R LYS* 4.0 7.4 + - - +
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Residues in contact with LYS 180 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148R LYS 5.9 1.4 + - - -
149R LYS* 6.1 2.8 - - - +
150R ALA 5.9 2.8 - - - +
170R ASP* 3.8 32.6 + - - -
175R LEU* 3.8 31.2 - - + +
176R PRO 4.6 0.2 + - - -
177R ASN* 3.0 31.6 + - - +
179R GLN* 1.3 78.4 - - - +
181R ALA* 1.3 51.4 + - - +
183R LYS* 3.3 9.1 + - - +
184R ALA* 2.8 35.4 + - + +
188R GLN* 6.0 4.3 - - - +
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Residues in contact with ALA 181 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177R ASN* 2.9 36.6 + - - +
178R SER* 3.5 9.2 - - - +
179R GLN 3.2 0.2 - - - -
180R LYS* 1.3 76.0 - - - +
182R VAL* 1.3 57.9 + - - +
184R ALA* 2.9 10.0 + - - -
185R LEU* 2.5 38.1 + - - +
189R ILE* 4.6 2.2 - - + -
191R PHE* 4.0 19.3 - - + -
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Residues in contact with VAL 182 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178R SER* 3.1 24.2 + - - +
179R GLN* 4.1 7.6 - - - +
180R LYS 3.4 0.2 - - - -
181R ALA* 1.3 75.2 - - - +
183R LYS* 1.3 62.3 + - - +
185R LEU* 4.0 14.4 + - - +
186R GLY 5.1 0.5 + - - -
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Residues in contact with LYS 183 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179R GLN 4.0 4.1 + - - +
180R LYS* 3.3 11.2 + - - +
181R ALA 3.1 0.4 - - - -
182R VAL* 1.3 79.8 - - - +
184R ALA* 1.3 63.7 + - - +
185R LEU 3.4 0.7 + - - -
186R GLY 3.7 7.8 + - - -
187R ASP* 4.0 23.2 + - + +
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Residues in contact with ALA 184 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180R LYS* 2.8 22.5 + - + +
181R ALA* 2.9 11.6 + - - +
183R LYS* 1.3 74.0 - - - +
185R LEU* 1.3 53.1 + - - +
186R GLY 3.0 4.9 - - - -
187R ASP* 2.8 29.3 + - - -
188R GLN* 3.0 30.2 + - + +
189R ILE* 3.2 22.2 + - + -
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Residues in contact with LEU 185 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181R ALA* 2.5 19.9 + - + +
182R VAL* 4.0 13.5 - - - +
183R LYS 3.3 1.0 - - - -
184R ALA* 1.3 71.2 - - - +
186R GLY* 1.3 55.4 + - - +
187R ASP 3.5 0.4 - - - -
189R ILE* 3.9 29.4 - - + +
190R LEU* 5.5 1.1 - - + -
191R PHE* 4.3 27.6 - - + +
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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