Contacts of the helix formed by residues 165 - 171 (chain K) in PDB entry 3Q2K
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 165 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163K THR* 4.5 4.2 - - + -
164K ARG* 1.3 83.9 - - - +
166K GLN* 1.3 69.2 + - - +
167K GLU* 3.0 30.4 + - + +
168K TYR* 3.0 28.0 + - + +
169K TYR* 3.5 5.7 - - - -
215K ARG* 3.7 10.1 - - - +
550K HP7 3.0 32.3 - - - +
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Residues in contact with GLN 166 (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 PRO* 1.3 72.3 - - - +
167K GLU* 1.3 70.8 + - - +
169K TYR* 3.1 21.9 + - - +
170K ASP* 3.1 41.6 + - - +
214K ALA 4.8 0.7 - - - +
215K ARG* 3.5 25.2 - - - +
216K ARG* 3.1 51.9 + - + +
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Residues in contact with GLU 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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165K PRO* 3.5 23.3 - - + +
166K GLN* 1.3 89.5 + - - +
168K TYR* 1.3 53.8 + - - +
170K ASP* 2.8 29.3 + - + +
171K ALA* 3.0 14.2 + - - +
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Residues in contact with TYR 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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20K ARG* 5.4 2.9 - - - -
164K ARG* 3.9 15.9 - - + -
165K PRO* 3.0 24.5 + - + +
167K GLU* 1.3 81.6 - - - +
169K TYR* 1.3 90.1 + + - +
171K ALA* 3.4 12.8 + - - +
175K ARG* 3.5 39.7 + - + -
181K ASP* 5.5 1.6 + - - -
187K ASN* 4.1 4.0 + - - -
188K GLN* 3.0 18.3 + - - -
550K HP7 2.5 79.7 + - - +
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Residues in contact with TYR 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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164K ARG* 3.8 38.5 - - + +
165K PRO 3.5 11.2 - - - -
166K GLN* 3.1 14.1 + - - +
168K TYR* 1.3 92.4 - + - +
170K ASP* 1.3 62.0 + - - +
171K ALA 3.5 0.2 + - - -
172K ALA 3.3 18.4 - - - +
175K ARG* 3.8 15.9 - - + +
176K GLY* 4.1 18.4 - - - -
181K ASP* 5.4 1.8 - - - -
183K GLY* 6.3 2.0 - - - -
184K ALA 5.5 1.3 + - - -
188K GLN* 4.3 10.1 + - - -
215K ARG* 3.9 20.9 - - + +
217K ILE* 3.4 46.5 - - + +
220K GLU 5.4 0.9 + - - -
221K ASP* 4.8 3.8 - - - +
241K MET* 3.8 19.1 - - - +
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Residues in contact with ASP 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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166K GLN* 3.1 46.5 + - - +
167K GLU* 2.8 15.7 + - + +
169K TYR* 1.3 76.8 - - - +
171K ALA* 1.3 63.1 + - - +
172K ALA* 3.0 7.3 + - - -
216K ARG* 3.9 21.4 + - - -
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Residues in contact with ALA 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 GLU 3.0 9.6 + - - +
168K TYR* 3.9 12.6 - - - +
169K TYR 3.2 2.2 - - - -
170K ASP* 1.3 76.3 - - - +
172K ALA* 1.3 62.2 + - - +
175K ARG* 5.1 4.7 - - - +
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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