Contacts of the helix formed by residues 161 - 172 (chain D) in PDB entry 6P19
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 THR 161 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137D ARG* 4.4 20.6 - - - +
142D GLU 5.0 1.3 - - - -
143D SER* 4.0 6.5 - - - -
144D TYR 5.0 0.9 - - - -
160D LEU* 1.3 77.3 - - - +
162D GLU* 1.3 54.7 + - - +
163D GLU* 2.7 24.6 + - - +
164D GLN* 2.7 44.0 + - - +
165D TYR* 2.6 34.5 + - - +
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Residues in contact with GLU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D GLU 4.7 11.8 + - - +
143D SER* 5.1 0.2 - - - +
144D TYR* 3.2 32.1 - - + -
161D THR* 1.3 76.7 - - - +
163D GLU* 1.3 63.1 + - + +
165D TYR* 3.2 20.3 + - - -
166D LEU* 2.9 44.5 + - + +
169D LEU* 5.7 0.2 - - - +
293D ARG* 3.8 11.8 + - - +
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Residues in contact with GLU 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D THR* 2.7 27.3 + - - +
162D GLU* 1.3 82.3 + - + +
164D GLN* 1.3 56.9 + - + +
166D LEU* 3.3 17.2 - - + +
167D ASP* 2.9 39.5 + - - +
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Residues in contact with GLN 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D ILE 4.3 2.8 - - - +
160D LEU* 3.3 23.2 - - + +
161D THR* 2.7 52.5 + - - +
163D GLU* 1.3 74.2 - - + +
165D TYR* 1.3 59.3 + - - +
167D ASP* 3.6 10.4 - - - +
168D ALA* 2.9 28.2 + - - +
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Residues in contact with TYR 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D TYR* 3.5 39.8 - + + -
160D LEU* 4.3 6.7 - - + +
161D THR 2.6 21.2 + - - +
162D GLU* 3.3 32.8 - - - +
164D GLN* 1.3 72.7 - - - +
166D LEU* 1.3 57.7 + - - +
168D ALA* 3.1 8.7 + - - +
169D LEU* 2.9 64.5 + - + +
176D PHE* 4.3 4.9 - + - -
178D ALA* 3.5 43.7 + - + -
293D ARG* 5.7 0.9 - - - -
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Residues in contact with LEU 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D GLU* 2.9 34.6 + - + +
163D GLU* 3.3 26.2 - - + +
165D TYR* 1.3 74.9 - - - +
167D ASP* 1.3 70.9 + - - +
169D LEU* 3.2 18.2 + - + +
170D GLU* 2.9 31.5 + - + +
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Residues in contact with ASP 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D GLU* 2.9 30.8 + - - +
164D GLN* 3.6 10.5 - - - +
166D LEU* 1.3 87.8 - - - +
168D ALA* 1.3 56.9 + - - +
170D GLU* 2.9 25.5 - - - +
171D GLU* 2.9 31.3 + - - +
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Residues in contact with ALA 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D LEU* 4.3 19.1 - - + -
160D LEU* 4.6 8.3 - - + -
164D GLN 2.9 14.6 + - - +
165D TYR* 3.1 10.3 + - - +
167D ASP* 1.3 73.9 - - - +
169D LEU* 1.3 60.2 - - - +
171D GLU* 4.2 9.0 - - - -
172D PHE* 2.9 27.6 + - + +
173D GLY 3.1 6.1 + - - -
176D PHE* 3.3 26.4 - - + -
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Residues in contact with LEU 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D GLU* 5.7 0.2 - - - +
165D TYR* 2.9 61.6 + - + +
166D LEU* 3.2 17.4 + - + +
168D ALA* 1.3 77.5 - - - +
170D GLU* 1.3 61.1 + - - +
172D PHE 3.8 1.6 - - - +
173D GLY* 3.3 28.7 + - - +
176D PHE* 3.7 13.5 - - + -
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Residues in contact with GLU 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D LEU* 2.9 23.3 + - + +
167D ASP* 2.9 38.2 - - - +
169D LEU* 1.3 76.1 - - - +
171D GLU* 1.3 67.7 + - - +
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Residues in contact with GLU 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ASN* 2.9 32.6 + - - +
167D ASP* 2.9 20.6 + - - +
168D ALA* 3.8 6.4 - - - +
169D LEU 3.2 0.4 - - - -
170D GLU* 1.3 86.8 - - - +
172D PHE* 1.3 89.1 + - + +
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Residues in contact with PHE 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D MET* 3.6 50.9 - - + -
153D ASN* 3.6 19.1 - - + -
154D LEU* 4.4 9.2 - - + -
168D ALA* 2.9 15.5 + - - +
169D LEU 3.8 2.5 - - - +
171D GLU* 1.3 114.8 - - + +
173D GLY* 1.3 57.4 + - - +
174D ASP* 2.9 27.2 + - - +
175D GLU* 4.7 5.6 - - + +
176D PHE* 4.0 12.6 - + + -
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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