Contacts of the helix formed by residues 187 - 192 (chain A) in PDB entry 3ZDY
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 GLY 187 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A TYR* 3.2 37.8 - - - +
167A CYS 3.2 4.6 + - - -
168A GLU* 5.1 2.9 - - - +
185A ALA 2.9 1.6 + - - -
186A PRO* 1.3 79.7 - - - +
188A GLY* 1.3 66.0 + - - +
189A TYR 3.7 0.3 + - - -
190A TYR 3.8 2.3 + - - -
191A PHE* 3.1 30.8 + - - -
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Residues in contact with GLY 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ASP 4.6 0.4 - - - -
164A LYS* 4.9 0.2 - - - -
167A CYS* 3.6 14.9 - - - +
185A ALA 3.0 14.2 + - - -
186A PRO 3.5 0.6 - - - -
187A GLY* 1.3 75.9 - - - +
189A TYR* 1.3 72.7 + - - +
192A LEU 3.1 4.0 + - - -
193A GLY* 2.8 26.2 + - - -
194A LEU* 3.8 19.7 - - - -
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Residues in contact with TYR 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A PHE 5.8 0.9 - - - -
162A TRP* 3.6 44.5 - + + -
163A ASP* 2.9 19.8 + - - +
164A LYS* 3.5 29.7 - - + +
188A GLY* 1.3 70.8 - - - +
190A TYR* 1.3 67.9 + - - +
192A LEU* 3.4 21.4 + - + +
193A GLY 4.3 5.6 - - - -
194A LEU* 3.7 31.4 - - + +
221A LEU* 4.4 6.9 - - - +
222A SER 2.7 22.3 + - - -
223A PHE 3.3 31.2 - - - -
224A ASP* 3.6 23.7 - - - +
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Residues in contact with TYR 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A PHE* 3.7 39.1 - + + +
163A ASP* 3.3 28.3 + - + +
166A TYR* 3.6 26.6 + + - -
187A GLY 3.8 1.4 + - - -
188A GLY 3.4 0.4 - - - -
189A TYR* 1.3 78.2 - - - +
191A PHE* 1.3 95.7 + + - +
192A LEU* 3.3 8.6 + - + +
232A ASP* 4.6 4.0 - - - +
166B TYR* 4.4 13.2 + - - -
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Residues in contact with PHE 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A TYR* 4.3 27.4 - + + -
168A GLU* 5.7 0.9 - - - -
186A PRO 3.9 4.0 - - - +
187A GLY* 3.1 30.0 + - - -
188A GLY 3.8 0.2 - - - -
190A TYR* 1.3 110.0 - + - +
192A LEU* 1.3 62.0 + - - +
193A GLY 3.4 0.2 - - - -
232A ASP* 3.1 38.1 - - - +
233A GLY 3.3 2.9 + - - -
234A TYR* 3.7 23.8 + + + -
163B PRO* 4.1 39.7 - - + -
164B TYR* 5.9 6.7 - + - -
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Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A PRO 4.2 0.2 - - - -
188A GLY 3.1 2.3 + - - +
189A TYR* 3.4 20.2 - - + +
190A TYR* 3.7 9.9 - - + +
191A PHE* 1.3 76.8 - - - +
193A GLY* 1.3 64.5 + - - +
223A PHE 5.8 0.7 - - - +
224A ASP* 3.4 25.1 - - - +
225A SER* 3.7 31.2 - - - +
230A TYR* 3.5 32.2 - - + +
231A PHE* 3.7 31.9 - - + -
233A GLY* 4.0 0.5 - - - -
234A TYR 3.4 4.3 + - - -
235A TRP* 3.0 26.8 + - - +
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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