Contacts of the helix formed by residues 175 - 183 (chain D) in PDB entry 2PK9
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 HIS 175 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174D ASP* 1.3 73.8 - - + +
176D ASN* 1.3 65.1 + - - +
177D ILE 3.4 1.1 - - - -
178D THR* 3.2 19.2 + - + -
179D LEU* 3.0 34.7 + - + +
204D TYR 6.0 1.6 + - - -
205D SER 4.2 19.6 + - - -
206D TYR* 3.0 35.3 + + + +
209D ARG* 3.8 33.7 + - + -
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Residues in contact with ASN 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLU* 4.0 4.0 - - - +
100D TYR* 3.1 21.9 + - - +
104D LEU* 4.3 4.4 - - - +
169D ARG* 2.8 69.4 + - - +
171D ILE 3.3 24.9 + - - +
173D ARG* 3.1 20.3 + - + +
174D ASP 3.1 3.8 + - - -
175D HIS* 1.3 76.0 - - - +
177D ILE* 1.3 55.1 + - - +
179D LEU* 3.3 1.2 + - - +
180D CYS* 2.9 28.9 + - - +
206D TYR* 3.4 3.7 + - - -
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Residues in contact with ILE 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D TYR* 3.6 30.9 + - + +
103D ASP* 3.8 30.3 - - + +
104D LEU* 3.7 24.5 - - + -
107D THR* 4.0 29.6 - - + +
108D VAL* 4.3 0.8 - - + +
174D ASP 4.4 4.9 + - - +
175D HIS 3.4 0.4 - - - -
176D ASN* 1.3 74.5 - - - +
178D THR* 1.3 59.1 + - - +
180D CYS* 3.2 2.6 + - - +
181D SER* 2.9 29.7 + - - +
220D TYR* 4.4 4.0 - - - +
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Residues in contact with THR 178 (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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174D ASP 5.4 0.4 + - - -
175D HIS* 3.2 22.1 + - + +
177D ILE* 1.3 79.9 - - - +
179D LEU* 1.3 63.0 + - + +
181D SER* 3.4 7.1 + - - -
182D ILE* 3.1 44.9 + - + +
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Residues in contact with LEU 179 (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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59C GLU* 5.3 0.9 - - - +
169D ARG* 3.6 32.3 + - - +
175D HIS* 3.0 32.5 + - + +
178D THR* 1.3 80.1 - - + +
180D CYS* 1.3 66.7 + - - +
182D ILE* 4.2 11.3 - - + +
183D GLU* 3.1 28.2 + - - +
204D TYR* 3.8 50.5 - - + +
206D TYR* 4.3 13.5 - - + +
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Residues in contact with CYS 180 (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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104D LEU* 4.0 9.4 - - + -
108D VAL* 3.5 25.4 - - + -
166D VAL* 3.3 45.1 - - - -
167D ASN* 5.5 0.9 - - - -
169D ARG* 4.0 14.7 - - + +
176D ASN 2.9 17.5 + - - +
177D ILE 3.5 5.2 - - - +
179D LEU* 1.3 78.0 - - - +
181D SER* 1.3 61.9 + - - +
183D GLU* 3.7 4.2 + - - +
184D GLN* 3.4 23.4 + - - +
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Residues in contact with SER 181 (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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107D THR* 3.7 18.7 + - - +
108D VAL* 3.6 20.6 - - - +
177D ILE* 2.9 12.1 + - - +
178D THR* 3.4 11.9 - - - -
180D CYS* 1.3 74.5 - - - +
182D ILE* 1.3 68.3 + - - +
184D GLN* 3.1 21.5 + - - +
186D GLN* 4.5 5.2 + - - -
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Residues in contact with ILE 182 (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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178D THR* 3.1 33.0 + - + +
179D LEU* 3.7 13.9 + - + +
181D SER* 1.3 80.6 - - - +
183D GLU* 1.3 61.4 + - - +
184D GLN 3.3 9.0 + - - +
186D GLN* 3.5 20.4 - - - +
194D ASN* 6.1 1.1 - - - +
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Residues in contact with GLU 183 (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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58C LYS* 3.7 20.0 + - - +
167D ASN* 3.1 46.5 + - - +
169D ARG* 3.5 25.5 + - - -
179D LEU 3.1 18.5 + - - +
180D CYS* 4.0 4.9 - - - +
181D SER 3.2 0.4 - - - -
182D ILE* 1.3 74.1 - - - +
184D GLN* 1.3 63.9 + - - +
204D TYR* 4.2 10.3 + - - +
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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
------------------------------------------------------------
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