Contacts of the helix formed by residues 169 - 177 (chain K) in PDB entry 5O6I
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 ASP 169 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146K GLY 3.7 14.6 - - - +
147K VAL* 3.7 16.5 - - + +
148K ARG* 2.7 66.7 + - - +
166K SER* 3.0 13.0 + - - +
168K ARG* 1.3 78.6 - - - +
170K ARG* 1.3 62.8 + - - +
171K ILE* 3.5 2.7 - - - -
172K LYS* 3.9 12.3 - - + +
173K PHE* 3.0 24.8 + - - +
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Residues in contact with ARG 170 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122K LEU 3.0 21.2 + - - -
123K LYS* 2.7 33.1 + - - +
125K LEU* 3.9 18.3 - - + +
167K LEU* 3.2 52.4 + - - +
168K ARG 3.4 2.0 + - - -
169K ASP* 1.3 76.8 - - - +
171K ILE* 1.3 71.0 + - + +
173K PHE* 3.2 1.2 + - - +
174K VAL* 2.9 46.8 + - + +
4L T 4.1 9.9 + - - -
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Residues in contact with ILE 171 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168K ARG 5.6 3.1 - - - +
169K ASP* 5.3 0.9 - - - -
170K ARG* 1.3 88.9 - - + +
172K LYS* 1.3 73.8 + - + +
174K VAL* 4.3 4.2 - - - +
175K HIS* 3.2 28.1 + - - +
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Residues in contact with LYS 172 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145K LEU 3.2 21.6 + - - -
146K GLY* 3.7 17.7 - - - +
147K VAL* 4.0 13.0 - - + -
169K ASP* 3.5 16.7 + - + +
170K ARG 3.2 0.6 - - - -
171K ILE* 1.3 91.3 - - + +
173K PHE* 1.3 56.1 + - - +
175K HIS* 5.2 2.9 + - - -
176K THR* 2.9 57.7 + - - +
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Residues in contact with PHE 173 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110K ILE* 4.2 7.6 - - + -
114K TYR* 3.7 23.8 - + - -
125K LEU* 3.9 20.6 - - + -
142K LEU* 4.0 13.9 - - + -
147K VAL* 4.1 19.3 - - + +
165K ILE* 3.5 36.1 - - + -
169K ASP 3.0 17.6 + - - +
170K ARG 3.8 1.8 - - - +
172K LYS* 1.3 75.7 - - - +
174K VAL* 1.3 69.6 + - - +
176K THR* 5.0 0.9 - - - -
177K ILE* 3.0 60.1 + - + +
178K LEU* 3.4 28.5 + - + -
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Residues in contact with VAL 174 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122K LEU* 4.9 12.3 - - + -
125K LEU* 4.5 10.3 - - + -
170K ARG* 2.9 34.3 + - + +
171K ILE* 4.3 3.6 - - - +
173K PHE* 1.3 81.5 - - + +
175K HIS* 1.3 54.9 + - + +
178K LEU* 3.2 27.8 + - + +
179K SER* 2.7 37.8 + - - +
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Residues in contact with HIS 175 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171K ILE 3.2 19.8 + - - +
172K LYS* 4.6 2.2 + - - -
174K VAL* 1.3 79.5 - - + +
176K THR* 1.3 77.4 + - - +
177K ILE 3.4 0.2 - - - -
179K SER* 3.0 23.5 + - - +
180K SER* 4.1 6.2 + - - -
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Residues in contact with THR 176 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K MET* 5.3 3.1 - - + -
107K ILE* 3.6 23.3 - - + +
145K LEU* 4.9 15.5 - - + +
147K VAL* 6.0 1.6 - - + -
172K LYS* 2.9 44.8 + - - +
173K PHE* 5.0 0.2 - - - -
175K HIS* 1.3 91.4 + - - +
177K ILE* 1.3 69.0 + - + +
180K SER* 3.3 17.5 - - - -
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Residues in contact with ILE 177 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107K ILE* 4.0 20.0 - - + +
110K ILE* 3.8 26.9 - - + -
111K LYS* 3.4 26.2 - - - +
142K LEU* 3.5 31.6 - - + -
145K LEU* 4.0 15.5 - - + -
147K VAL* 5.3 3.4 - - + -
173K PHE* 3.0 30.2 + - + +
176K THR* 1.3 91.2 - - + +
178K LEU* 1.3 65.4 + - + +
179K SER 3.5 0.7 - - - -
180K SER* 2.9 20.9 + - - -
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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