Contacts of the helix formed by residues 166 - 178 (chain K) in PDB entry 3J8B
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 SER 166 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159K ALA* 5.7 0.4 - - - -
164K ASP 4.1 0.4 + - - -
165K LEU* 1.3 78.6 - - - +
167K ASP* 1.3 66.8 + - - +
168K SER* 3.1 10.8 - - - -
169K GLN* 3.2 11.7 + - - +
170K LEU* 3.0 18.0 + - - +
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Residues in contact with ASP 167 (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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159K ALA* 6.3 0.7 - - - -
166K SER* 1.3 74.3 - - - +
168K SER* 1.3 63.3 + - - +
170K LEU* 3.4 8.1 + - - +
171K LYS* 3.0 23.0 + - - +
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Residues in contact with SER 168 (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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166K SER* 3.1 7.5 - - - -
167K ASP* 1.3 79.4 - - - +
169K GLN* 1.3 60.7 + - - +
171K LYS* 3.3 20.0 - - - +
172K VAL* 3.5 6.2 + - - +
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Residues in contact with GLN 169 (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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165K LEU* 3.8 16.4 - - + -
166K SER* 3.2 17.7 + - - +
168K SER* 1.3 75.8 - - - +
170K LEU* 1.3 67.7 + - - +
172K VAL* 3.0 23.7 + - - +
173K TRP* 3.5 4.3 + - - +
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Residues in contact with LEU 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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155K ARG 5.7 1.8 - - - +
158K LEU* 6.5 0.7 - - + -
159K ALA* 4.5 20.9 - - + +
165K LEU* 4.0 5.5 - - + +
166K SER 3.0 13.6 + - - +
167K ASP* 3.5 12.1 - - - +
169K GLN* 1.3 76.0 - - - +
171K LYS* 1.3 63.8 + - - +
173K TRP* 3.0 18.0 + - - +
174K MET* 3.0 14.3 + - - +
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Residues in contact with LYS 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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167K ASP 3.0 13.0 + - - +
168K SER* 3.3 15.0 - - - +
170K LEU* 1.3 77.2 - - - +
172K VAL* 1.3 61.9 + - - +
174K MET* 3.9 7.5 - - - +
175K SER* 3.0 26.0 + - - -
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Residues in contact with VAL 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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168K SER 3.5 5.1 + - - +
169K GLN* 3.0 16.8 + - - +
171K LYS* 1.3 80.0 - - - +
173K TRP* 1.3 56.9 + - - +
175K SER* 3.5 5.5 - - - -
176K LYS* 3.0 26.5 + - - +
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Residues in contact with TRP 173 (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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139K ARG* 6.2 3.8 - - + -
143K CYS* 6.1 5.6 - - + -
162K LEU* 6.0 6.3 - - + -
169K GLN 3.5 4.2 + - - +
170K LEU* 3.0 9.4 + - - +
172K VAL* 1.3 78.6 - - - +
174K MET* 1.3 65.9 + - - +
176K LYS* 3.3 15.8 + - - +
177K TYR* 3.3 13.9 + - - +
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Residues in contact with MET 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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170K LEU 3.0 14.5 + - - +
171K LYS* 3.9 9.0 - - - +
173K TRP* 1.3 77.3 - - - +
175K SER* 1.3 58.6 + - - +
177K TYR 3.4 0.5 + - - -
178K GLY* 3.0 9.9 + - - -
179K TRP* 2.8 54.2 + - + +
187K ILE* 5.9 6.1 - - + -
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Residues in contact with SER 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 LYS 3.0 18.3 + - - -
172K VAL* 3.5 6.5 - - - -
174K MET* 1.3 78.6 - - - +
176K LYS* 1.3 60.8 + - - +
177K TYR 3.4 0.5 + - - -
178K GLY* 3.4 10.5 + - - +
179K TRP 5.2 1.1 - - - -
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Residues in contact with LYS 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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172K VAL 3.0 16.6 + - - +
173K TRP* 3.3 10.5 + - - +
175K SER* 1.3 79.3 - - - +
177K TYR* 1.3 58.2 + - + +
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Residues in contact with TYR 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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143K CYS* 5.5 11.7 - - + +
173K TRP 3.3 11.8 + - - +
174K MET 4.5 0.9 - - - +
175K SER 3.3 0.6 - - - -
176K LYS* 1.3 77.8 - - + +
178K GLY* 1.3 63.1 + - - +
179K TRP* 3.4 6.7 + - + +
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Residues in contact with GLY 178 (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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174K MET 3.0 5.8 + - - -
175K SER* 3.4 11.8 + - - -
176K LYS 3.5 0.8 + - - -
177K TYR* 1.3 78.7 - - - +
179K TRP* 1.3 61.4 + - - +
180K SER* 3.9 2.6 + - - -
189K ILE 4.9 4.0 - - - +
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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