Contacts of the helix formed by residues 181 - 192 (chain D) in PDB entry 1Z1G
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 THR 181 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179D ARG* 5.0 4.0 - - + +
180D LEU* 1.3 76.0 - - - +
182D ALA* 1.3 66.2 + - - +
183D ASP* 3.4 15.1 + - - +
184D GLU* 3.1 39.6 + - + +
185D TYR* 3.3 12.0 + - - +
313D LEU* 4.3 2.7 - - - -
316D ARG* 4.6 4.3 - - - +
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Residues in contact with ALA 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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181D THR* 1.3 72.6 - - - +
183D ASP* 1.3 62.8 + - - +
185D TYR* 3.5 2.2 + - - +
186D LEU* 3.3 18.5 + - - +
250D ALA* 5.2 9.2 - - + +
251D LEU* 3.6 24.0 - - + +
313D LEU* 4.0 12.0 - - + +
316D ARG* 5.0 0.8 - - - +
317D LEU* 4.5 23.3 - - + +
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Residues in contact with ASP 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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181D THR* 3.2 10.7 + - - +
182D ALA* 1.3 76.5 - - - +
184D GLU* 1.3 59.8 + - + +
186D LEU* 3.2 11.0 - - - +
187D LYS* 3.0 29.8 + - - +
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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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179D ARG 3.7 12.8 - - - +
180D LEU* 4.0 11.4 - - + -
181D THR* 3.1 43.3 + - + +
183D ASP* 1.3 74.6 - - + +
185D TYR* 1.3 55.7 + - - +
187D LYS* 2.8 5.2 + - - +
188D ILE* 2.7 43.2 + - + +
298D LEU* 3.4 34.4 - - + +
299D SER 4.8 2.6 - - - +
300D PHE* 3.5 27.1 - - + -
305D PRO* 5.0 0.2 - - - +
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Residues in contact with TYR 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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180D LEU* 4.0 12.4 - - + +
181D THR 3.3 5.3 + - - +
182D ALA 3.8 6.7 - - - +
183D ASP 3.4 0.4 - - - -
184D GLU* 1.3 75.6 - - - +
186D LEU* 1.3 60.3 + - + +
188D ILE* 3.0 7.0 + - - +
189D TYR* 2.7 57.8 + + + -
203D MSE 3.8 23.9 - - + +
204D GLU* 3.4 32.2 + - - +
207D VAL* 3.8 23.1 - - + -
251D LEU* 3.5 25.6 - - + -
253D ILE* 3.5 16.6 - - + +
289D PHE* 5.6 0.2 - + - -
310D LEU* 3.6 22.2 - - + -
313D LEU* 3.8 21.1 - - + -
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Residues in contact with LEU 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 ALA 3.3 8.1 + - - +
183D ASP* 3.2 15.0 + - - +
184D GLU 3.2 0.2 - - - -
185D TYR* 1.3 85.8 - - + +
187D LYS* 1.3 65.9 + - + +
189D TYR* 3.2 17.7 + - + +
190D GLN* 3.1 39.4 + - + +
251D LEU* 4.4 19.3 - - + +
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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 ASP* 3.0 15.4 + - - +
184D GLU* 2.8 16.0 + - - +
186D LEU* 1.3 76.1 - - + +
188D ILE* 1.3 59.2 + - - +
190D GLN* 3.7 18.0 + - + +
191D ALA* 3.3 19.2 + - - +
296D SER* 4.0 15.4 - - - +
298D LEU* 3.6 39.9 - - + +
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Residues in contact with ILE 188 (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 LEU* 3.9 25.6 - - + -
184D GLU* 2.7 25.8 + - + +
185D TYR* 3.5 6.5 - - - +
187D LYS* 1.3 71.0 - - - +
189D TYR* 1.3 66.6 + - - +
190D GLN 3.0 2.0 - - - -
191D ALA* 2.9 4.3 + - - +
192D ALA* 2.9 21.3 + - - +
203D MSE 3.7 17.5 - - + -
289D PHE* 3.7 21.5 - - + +
292D ALA* 4.0 21.8 - - + -
293D ARG* 4.6 20.2 - - + +
296D SER* 4.3 19.1 - - - +
298D LEU* 6.3 0.7 - - + -
300D PHE* 5.6 8.3 - - + -
305D PRO* 6.4 1.1 - - + -
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Residues in contact with TYR 189 (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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185D TYR* 2.7 47.1 + + + +
186D LEU* 3.5 18.6 - - + +
188D ILE* 1.3 71.7 - - - +
190D GLN* 1.3 63.1 + - + +
192D ALA* 3.4 14.3 - - - +
200D ARG* 3.7 61.5 + - + -
203D MSE 3.7 13.6 - - + +
204D GLU* 3.6 23.6 + - - -
253D ILE* 6.2 2.2 - - + -
261D LYS* 5.4 2.1 + - - -
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Residues in contact with GLN 190 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186D LEU* 3.1 33.3 + - + +
187D LYS* 3.7 17.4 - - + +
188D ILE 3.0 0.6 - - - -
189D TYR* 1.3 76.9 - - + +
191D ALA* 1.3 58.7 + - - +
192D ALA 3.1 1.9 + - - -
193D GLU* 2.5 49.6 + - - +
200D ARG* 4.8 3.1 - - - +
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Residues in contact with ALA 191 (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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187D LYS 3.3 11.2 + - - +
188D ILE 2.9 7.9 + - - +
190D GLN* 1.3 73.1 - - - +
192D ALA* 1.3 56.4 + - - +
193D GLU* 2.9 16.3 + - - +
194D SER* 3.3 19.1 + - - -
195D SER* 4.1 0.7 + - - -
292D ALA* 3.7 26.5 - - - +
295D ALA* 4.2 11.0 - - + +
296D SER* 4.0 15.9 - - - +
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Residues in contact with ALA 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D ILE 2.9 10.5 + - - +
189D TYR* 3.4 15.3 - - - +
190D GLN 3.1 0.4 - - - -
191D ALA* 1.3 74.3 - - - +
193D GLU* 1.3 60.9 + - - +
195D SER* 3.1 31.6 + - - +
199D LEU* 3.7 22.2 - - + -
200D ARG* 3.7 18.0 + - + +
203D MSE 4.1 14.6 - - - -
292D ALA* 4.2 6.0 - - + +
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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