Contacts of the helix formed by residues 182 - 187 (chain D) in PDB entry 1ZYR
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 182 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D LEU 3.6 5.2 + - - -
181D ASP* 1.3 82.6 - - - +
183D GLU* 1.3 57.8 + - - +
184D GLU 2.8 2.9 - - - -
185D VAL* 2.4 33.8 + - - -
186D VAL* 2.7 17.0 + - - -
191D LEU* 5.9 3.4 - - - -
197D SER* 4.9 2.6 + - - -
205D TYR* 5.4 10.8 - - - -
213D VAL* 5.7 0.2 - - - -
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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
----------------------------------------------------------
178D LEU 4.8 1.8 + - - -
179D VAL* 3.2 44.4 - - + +
181D ASP 4.6 0.4 - - - +
182D GLY* 1.3 72.5 - - - +
184D GLU* 1.3 64.7 + - - +
186D VAL* 2.9 24.6 + - - +
187D LYS* 4.3 5.2 + - - +
213D VAL* 4.3 25.9 - - + +
216D VAL* 3.0 35.7 - - + +
219D GLU* 3.3 18.6 - - - +
220D ARG* 5.6 2.1 + - - +
221D ALA* 5.7 3.5 - - - -
222D GLY 5.8 1.0 + - - -
389D GLU* 5.5 0.5 - - - +
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Residues in contact with GLU 184 (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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180D LYS* 2.9 40.5 - - - +
182D GLY 2.6 5.0 + - - -
183D GLU* 1.3 79.8 - - - +
185D VAL* 1.3 64.1 + - + +
186D VAL 3.4 1.6 + - - -
189D GLN* 4.2 9.2 - - - +
219D GLU* 4.2 16.3 - - - +
220D ARG* 4.7 14.4 + - - +
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Residues in contact with VAL 185 (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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181D ASP 3.4 23.6 - - - +
182D GLY* 2.4 22.0 + - - +
184D GLU* 1.3 76.2 - - + +
186D VAL* 1.3 54.9 + - - +
189D GLN* 3.2 40.8 - - + +
191D LEU* 3.3 40.7 - - + +
195D VAL* 5.8 0.2 - - + -
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Residues in contact with VAL 186 (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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182D GLY* 2.7 8.4 + - - +
183D GLU* 2.9 31.2 - - - +
184D GLU 3.4 2.4 + - - -
185D VAL* 1.3 77.2 - - - +
187D LYS* 1.3 66.8 + - + +
188D GLY 2.7 5.2 + - - -
189D GLN* 2.6 32.6 + - - +
211D VAL* 3.6 19.7 + - + +
212D ARG* 3.2 19.1 - - - +
213D VAL* 2.9 56.1 - - + +
391D ALA* 5.9 0.4 - - + -
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Residues in contact with LYS 187 (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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183D GLU 4.3 3.8 + - - +
186D VAL* 1.3 91.2 - - + +
188D GLY* 1.3 58.6 + - - +
189D GLN* 3.1 6.1 + - - +
211D VAL 5.5 1.1 - - - -
212D ARG* 4.6 13.9 - - + +
213D VAL* 3.7 32.6 + - + +
222D GLY 5.8 0.4 - - - +
223D LEU* 4.2 21.8 - - + +
224D ARG* 5.3 2.5 - - - +
225D LEU* 3.5 38.0 - - - +
438D ASP* 6.2 1.0 - - - -
440D VAL* 6.3 1.1 - - + -
445D ARG* 5.6 1.2 - - - +
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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