Contacts of the helix formed by residues 187 - 195 (chain B) in PDB entry 4AY1
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B SER* 3.1 9.7 + - - -
186B ALA* 1.3 77.9 - - - +
188B ARG* 1.3 66.0 + - - -
189B GLN 3.3 2.7 - - - -
190B MET* 3.1 7.7 + - - -
191B ILE* 2.9 22.0 + - - +
214B PHE* 5.2 4.3 - - - -
242B TYR 5.6 0.4 - - - -
243B TYR* 5.3 11.9 - - - -
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Residues in contact with ARG 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ALA 3.8 3.2 + - - -
187B GLY* 1.3 71.0 - - - -
189B GLN* 1.3 57.5 + - - +
191B ILE* 3.3 11.9 + - - +
192B ASP* 2.9 38.4 + - - +
242B TYR* 3.5 56.5 + - + +
243B TYR* 5.4 2.6 - - - -
247B TYR* 2.7 45.4 + - + -
251B TYR* 3.3 37.8 + - + -
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Residues in contact with GLN 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLN* 5.9 0.8 - - - +
187B GLY 3.1 0.8 + - - -
188B ARG* 1.3 79.9 - - - +
190B MET* 1.3 58.4 + - + +
192B ASP* 3.4 11.0 + - - +
193B ASN* 2.9 56.0 + - - +
242B TYR* 5.4 2.4 - - + -
243B TYR* 6.0 4.6 - - + +
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Residues in contact with MET 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B TYR* 3.7 51.1 - - + -
148B ASP* 3.8 31.4 - - - +
185B SER* 3.5 18.6 - - - +
187B GLY* 3.1 4.9 + - - +
189B GLN* 1.3 81.3 - - + +
191B ILE* 1.3 56.9 + - - +
193B ASN* 3.3 5.8 + - - +
194B SER* 2.8 57.2 + - - +
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Residues in contact with ILE 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B SER 3.3 22.7 - - - +
186B ALA 3.7 14.8 - - - +
187B GLY 2.9 21.9 + - - +
188B ARG* 3.5 10.8 - - - +
190B MET* 1.3 73.6 - - - +
192B ASP* 1.3 66.2 + - - +
195B TYR* 3.1 42.2 + - + +
197B VAL* 4.7 13.0 - - + -
248B ALA* 5.1 1.6 - - + +
251B TYR* 3.9 26.2 - - + -
252B TRP* 3.3 37.7 - - + +
255B LYS* 4.9 4.7 + - + -
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Residues in contact with ASP 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ASN* 4.5 5.5 + - - -
188B ARG* 2.9 34.8 + - - +
189B GLN* 3.6 12.1 - - - +
191B ILE* 1.3 76.1 - - - +
193B ASN* 1.3 65.5 + - - +
195B TYR 4.5 3.6 + - - +
251B TYR* 2.4 31.6 + - - -
255B LYS* 3.1 21.4 + - - +
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Residues in contact with ASN 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ASP* 3.1 42.7 + - - +
149B GLN* 3.4 35.8 + - + +
152B ASN* 3.1 15.1 + - - -
189B GLN* 2.9 48.4 + - - +
190B MET* 3.6 13.1 - - - +
192B ASP* 1.3 79.9 - - - +
194B SER* 1.3 57.2 + - - +
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Residues in contact with SER 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B PRO* 3.9 9.0 - - - +
148B ASP* 2.8 34.2 + - - -
152B ASN* 3.3 32.6 - - - +
155B PHE* 4.6 1.0 - - - -
190B MET* 2.8 31.6 + - - +
193B ASN* 1.3 76.1 - - - +
195B TYR* 1.3 86.1 + - - +
196B GLN 4.1 0.2 + - - -
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Residues in contact with TYR 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B TRP 4.3 4.6 + - - -
145B ILE* 5.6 0.2 - - - +
146B TYR* 4.2 6.1 - - - -
147B PRO* 4.1 14.3 - - + +
152B ASN* 3.5 4.9 + - - +
155B PHE* 3.7 32.8 - + - -
183B GLY 4.4 0.5 + - - -
184B VAL* 3.4 15.7 - - + -
185B SER* 3.0 36.4 + - - -
191B ILE* 3.1 28.3 + - - +
192B ASP 4.8 3.1 - - - +
193B ASN 3.8 0.2 - - - -
194B SER* 1.3 96.9 - - - +
196B GLN* 1.3 63.8 + - - +
197B VAL* 3.3 21.0 + - + +
200B LEU* 3.7 12.6 - - + -
252B TRP* 3.4 30.5 - + + -
255B LYS* 5.1 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