Contacts of the helix formed by residues 165 - 172 (chain D) in PDB entry 4OA5
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 PHE 165 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D THR* 1.3 81.9 + - - +
166D LEU* 1.3 65.8 + - - +
167D PHE 4.4 0.9 - - - +
168D GLY* 3.0 20.6 + - - +
170D VAL* 3.2 22.8 + - + +
171D PHE* 3.6 33.0 - + + -
204D ILE* 3.4 39.5 - - + -
206D PRO* 4.1 18.8 - - + -
207D THR 3.4 21.5 - - - -
208D SER 3.9 8.1 - - - +
209D GLU 3.1 9.9 + - - +
210D GLY* 3.5 17.7 - - - -
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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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139D LYS* 3.8 31.9 - - + -
163D ASN* 2.9 15.8 + - - +
164D THR 3.3 0.4 - - - -
165D PHE* 1.3 76.7 - - - +
167D PHE* 1.3 80.9 + - + +
169D SER* 2.8 39.3 + - - +
170D VAL* 4.4 3.6 - - + -
179D VAL* 4.1 8.8 - - + +
183D ALA* 3.7 11.9 - - + +
184D HIS* 3.4 40.2 - - + +
187D MET* 4.3 17.0 - - + -
209D GLU 4.2 0.2 + - - -
303D IOD 4.0 8.5 - - + -
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Residues in contact with PHE 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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139D LYS* 4.3 13.7 - - + -
163D ASN* 3.9 26.2 - - + +
165D PHE* 3.3 2.4 - - - +
166D LEU* 1.3 101.9 - - + +
168D GLY* 1.3 57.9 + - - +
169D SER* 3.3 1.3 + - - -
179D VAL* 4.3 15.0 - - + -
208D SER 5.6 4.7 - - - -
209D GLU* 5.1 6.8 + - + +
303D IOD 3.9 15.0 - - + -
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Residues in contact with GLY 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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165D PHE* 3.0 13.1 + - - +
167D PHE* 1.3 78.4 - - - +
169D SER* 1.3 58.7 + - - +
170D VAL 3.4 2.5 - - - -
171D PHE* 3.1 39.7 + - - +
172D ASP* 5.1 3.6 - - - +
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Residues in contact with SER 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D LEU* 2.8 39.5 + - - +
167D PHE 3.3 2.3 + - - -
168D GLY* 1.3 74.6 - - - +
170D VAL* 1.3 63.9 + - - +
171D PHE 3.2 4.2 + - - -
172D ASP* 3.4 15.0 + - - +
174D HIS 4.8 1.2 - - - +
176D THR* 4.5 15.3 - - - -
179D VAL* 3.6 25.7 - - - +
184D HIS* 3.0 23.3 + - - -
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Residues in contact with VAL 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D THR 3.4 20.2 - - - +
165D PHE* 3.2 23.8 + - + +
166D LEU* 4.4 4.3 - - + -
169D SER* 1.3 79.6 + - - +
171D PHE* 1.3 73.2 + - + +
172D ASP 3.3 0.2 - - - -
184D HIS* 4.1 7.0 - - + +
187D MET* 4.0 7.9 - - + -
188D ARG* 2.9 57.8 + - + +
191D ASN* 3.7 22.9 - - + +
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Residues in contact with PHE 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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165D PHE* 3.6 49.4 - + + -
168D GLY* 3.1 31.2 - - - +
169D SER 3.2 1.0 - - - -
170D VAL* 1.3 87.7 - - + +
172D ASP* 1.3 64.6 + - - +
173D GLU 4.1 0.5 + - - -
188D ARG* 3.7 8.1 + - - +
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Residues in contact with ASP 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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168D GLY 5.1 4.9 - - - +
169D SER* 3.4 9.5 + - - +
170D VAL 3.3 0.2 - - - -
171D PHE* 1.3 83.6 - - - +
173D GLU* 1.3 60.4 + - - +
174D HIS 3.6 16.8 - - - +
176D THR* 5.5 6.8 - - - +
184D HIS* 2.9 27.9 + - - -
188D ARG* 3.8 6.1 - - - -
315D IOD 4.0 11.4 - - + -
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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