Contacts of the helix formed by residues 167 - 178 (chain D) in PDB entry 4RZR
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 167 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118D TYR* 3.7 26.5 - - + -
165D VAL* 3.8 8.0 + - + +
166D ILE* 1.3 74.9 - - - +
168D ASP* 1.3 66.8 + - - +
169D GLU* 3.1 12.6 + - - +
170D GLU* 2.9 26.3 + - - +
171D VAL* 2.9 22.3 + - - +
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Residues in contact with ASP 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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118D TYR* 3.2 25.4 + - - -
146D LYS* 4.1 25.1 + - - +
167D ASP* 1.3 76.9 - - - +
169D GLU* 1.3 62.4 + - - +
171D VAL* 3.4 9.5 + - - +
172D LYS* 3.2 39.7 + - - +
231D ASP* 5.1 0.7 - - - +
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Residues in contact with GLU 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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167D ASP* 3.1 10.3 + - - +
168D ASP* 1.3 79.8 - - - +
170D GLU* 1.3 57.5 + - - +
172D LYS* 3.2 14.4 + - + +
173D ARG* 3.0 25.3 + - + +
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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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157D MET* 5.1 2.9 - - - +
164D LYS* 3.4 28.8 + - - -
165D VAL 4.1 7.3 - - - +
166D ILE* 4.0 12.1 - - + +
167D ASP* 2.9 23.4 + - - +
169D GLU* 1.3 70.4 - - - +
171D VAL* 1.3 57.0 + - - +
173D ARG* 2.7 45.5 + - + +
174D LEU* 2.7 51.4 + - + +
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Residues in contact with VAL 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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145D SER* 3.7 23.1 - - - +
146D LYS* 4.0 16.4 - - + -
150D PHE* 3.8 34.7 - - + -
166D ILE* 3.7 11.4 - - + +
167D ASP 2.9 18.4 + - - +
168D ASP 3.5 8.1 - - - +
169D GLU 3.3 0.2 - - - -
170D GLU* 1.3 75.4 - - - +
172D LYS* 1.3 57.9 + - - +
174D LEU* 3.2 1.7 + - - +
175D ILE* 2.9 40.9 + - + +
231D ASP* 4.0 20.4 - - - +
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Residues in contact with LYS 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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146D LYS* 5.2 1.4 - - - +
168D ASP* 3.2 26.7 + - - +
169D GLU* 3.2 15.7 + - + +
171D VAL* 1.3 77.0 - - - +
173D ARG* 1.3 65.4 + - - +
174D LEU 3.4 0.5 + - - -
175D ILE* 3.4 18.6 + - + +
176D ARG* 3.5 23.9 + - - +
231D ASP* 3.9 23.9 + - + +
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Residues in contact with ARG 173 (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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157D MET* 5.8 0.4 - - - +
169D GLU* 3.0 13.4 + - + +
170D GLU* 2.7 48.8 + - - +
172D LYS* 1.3 77.8 - - - +
174D LEU* 1.3 81.6 + - - +
176D ARG* 3.3 25.6 + - - +
177D GLU* 3.0 59.1 + - + +
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Residues in contact with LEU 174 (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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150D PHE* 4.1 19.7 - - + -
153D ILE* 4.6 2.9 - - + -
157D MET* 3.9 24.2 - - + -
166D ILE* 3.7 37.7 - - + -
170D GLU* 2.7 32.2 + - + +
171D VAL 3.2 3.1 + - - +
173D ARG* 1.3 94.9 - - - +
175D ILE* 1.3 67.5 + - - +
176D ARG 3.0 1.3 - - - -
177D GLU* 4.6 1.3 - - - -
178D LEU* 2.7 49.0 + - + +
202D LEU* 5.1 2.2 - - - +
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Residues in contact with ILE 175 (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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150D PHE* 4.2 12.3 - - + -
171D VAL* 2.9 36.5 + - + +
172D LYS* 3.6 12.6 - - + +
174D LEU* 1.3 77.4 - - - +
176D ARG* 1.3 59.4 + - + +
201D LYS* 3.9 0.3 - - - +
202D LEU* 3.3 22.1 + - + -
203D VAL* 3.1 45.9 + - + +
228D LEU 3.5 22.9 - - - +
229D ALA* 3.5 26.2 - - - +
231D ASP* 3.9 16.2 - - + -
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Residues in contact with ARG 176 (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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172D LYS* 3.5 12.4 + - - +
173D ARG* 3.3 34.6 + - - +
174D LEU 3.0 0.6 - - - -
175D ILE* 1.3 79.8 - - + +
177D GLU* 1.3 76.8 + - + +
201D LYS* 3.4 21.4 - - - +
203D VAL* 3.6 29.8 - - + +
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Residues in contact with GLU 177 (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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173D ARG* 3.0 49.2 + - + +
174D LEU* 3.0 3.2 + - - -
176D ARG* 1.3 96.3 + - + +
178D LEU* 1.3 62.5 + - - +
179D ASP 3.3 1.0 + - - -
201D LYS* 3.0 26.8 + - - +
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Residues in contact with LEU 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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150D PHE* 5.2 2.0 - - + -
153D ILE* 3.8 38.1 - - + -
157D MET* 3.9 23.6 - - + -
174D LEU* 2.7 41.4 + - + +
177D GLU* 1.3 71.8 - - - +
179D ASP* 1.3 74.6 + - - +
180D ILE* 3.1 4.5 + - - -
182D ASP* 3.7 36.8 - - + +
183D VAL* 4.6 7.5 - - + +
201D LYS* 3.7 15.8 - - - +
202D LEU* 4.3 6.4 + - + +
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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