Contacts of the helix formed by residues 167 - 174 (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 LEU 167 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165R GLY 3.6 1.0 + - - -
166R ILE* 1.3 73.8 - - - +
168R LEU* 1.3 64.2 + - + +
170R ASP* 3.3 3.9 + - - +
171R ILE* 3.1 45.4 + - + +
177R ASN* 4.0 31.6 - - + +
191R PHE* 4.5 16.4 - - + -
200R ILE* 3.2 57.8 + - + +
202R PHE* 4.5 15.5 - - + -
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Residues in contact with LEU 168 (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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166R ILE* 3.2 13.6 - - + +
167R LEU* 1.3 86.3 - - + +
169R GLU* 1.3 60.1 + - - +
171R ILE* 4.0 11.5 - - + +
172R GLU* 3.0 33.6 + - - +
199R LYS* 5.3 20.0 - - + +
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Residues in contact with GLU 169 (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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53Q LYS* 6.4 0.4 - - - +
142R LYS* 2.6 32.1 + - - -
144R ASN* 5.4 7.5 + - - +
145R VAL* 5.0 3.8 - - - +
165R GLY* 5.5 0.7 - - - -
166R ILE* 3.0 29.7 + - + +
168R LEU* 1.3 79.9 - - - +
170R ASP* 1.3 56.6 + - - +
172R GLU* 4.0 14.4 - - - +
173R GLU* 3.2 23.6 + - - +
202R PHE* 5.8 1.1 - - + -
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Residues in contact with ASP 170 (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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166R ILE 3.2 2.8 + - - -
167R LEU* 3.3 8.5 + - - +
169R GLU* 1.3 78.3 - - - +
171R ILE* 1.3 62.0 + - - +
173R GLU* 3.6 24.5 + - - +
174R ALA* 4.2 2.1 + - - +
175R LEU 3.7 8.0 + - - +
177R ASN* 2.6 37.6 + - - +
180R LYS* 3.8 19.8 + - - -
202R PHE* 3.9 32.8 - - + -
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Residues in contact with ILE 171 (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* 3.1 37.9 + - + +
168R LEU* 4.0 12.8 - - + +
170R ASP* 1.3 74.4 - - - +
172R GLU* 1.3 63.5 + - - +
174R ALA 4.0 4.0 + - - +
175R LEU 3.5 21.1 + - - +
176R PRO* 4.0 16.5 - - + -
177R ASN* 3.6 27.4 - - + +
178R SER* 5.4 5.4 - - - +
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Residues in contact with GLU 172 (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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86R LYS* 3.0 40.2 + - - +
89R HIS* 3.6 19.8 + - + +
90R GLN* 3.8 28.8 + - + +
141R PRO* 5.2 7.1 - - - +
142R LYS* 4.8 7.6 + - - +
168R LEU* 3.0 21.2 + - - +
169R GLU* 4.0 18.0 - - - +
171R ILE* 1.3 76.8 - - - +
173R GLU* 1.3 66.2 + - - +
174R ALA* 3.2 3.7 + - - +
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Residues in contact with GLU 173 (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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89R HIS* 3.7 9.0 + - - -
142R LYS* 4.1 25.6 - - + +
145R VAL* 3.5 28.9 - - + +
148R LYS* 3.3 59.2 + - + +
149R LYS 4.5 2.8 + - - +
169R GLU* 3.2 19.0 + - - +
170R ASP* 3.8 18.4 - - - +
171R ILE 3.4 1.4 - - - -
172R GLU* 1.3 77.6 - - - +
174R ALA* 1.3 60.5 + - + +
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Residues in contact with ALA 174 (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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89R HIS 5.8 0.2 - - - +
90R GLN* 4.7 10.2 - - - +
92R GLY* 5.8 2.8 - - - -
148R LYS* 3.8 31.9 - - + +
170R ASP 4.2 2.1 + - - +
171R ILE 4.0 4.8 + - - +
172R GLU 3.2 3.9 + - - +
173R GLU* 1.3 84.1 - - + +
175R LEU* 1.3 71.8 + - + +
176R PRO* 4.8 0.9 - - - +
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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