Contacts of the strand formed by residues 188 - 195 (chain A) in PDB entry 4Y6O
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 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A ASN 3.8 7.6 - - - +
169A ILE* 3.6 8.3 - - - +
185A GLU* 3.1 30.2 + - - +
186A ALA 3.5 1.2 - - - -
187A HIS* 1.3 81.1 - - - +
189A THR* 1.3 64.5 + - - -
231A ASP 3.2 11.2 - - - -
232A ILE* 4.3 0.2 - - - -
233A VAL* 3.9 7.3 - - - +
240A PRO* 5.1 1.5 - - - +
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Residues in contact with THR 189 (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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169A ILE* 3.9 8.0 + - - +
171A THR* 3.5 13.3 + - - +
174A ARG* 3.8 25.5 + - - +
185A GLU* 4.1 7.2 + - - +
187A HIS 3.9 0.2 + - - -
188A GLY* 1.3 76.1 - - - -
190A PHE* 1.3 61.3 + - - +
191A TYR* 3.1 20.5 + - + +
192A THR* 3.7 22.9 - - - +
231A ASP* 2.9 40.6 + - + +
232A ILE* 3.4 6.7 + - - +
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Residues in contact with PHE 190 (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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131A PHE* 4.1 10.1 - + - -
135A ALA* 4.2 5.2 - - + -
139A TYR* 4.3 11.4 - + - -
143A PHE* 6.4 0.2 - - + -
169A ILE* 3.0 32.7 + - + +
170A ASP* 5.4 0.2 - - - -
171A THR* 5.5 1.3 - - + -
189A THR* 1.3 72.0 + - - +
191A TYR* 1.3 63.2 + - - +
192A THR 3.3 7.9 + - - +
193A SER* 4.5 3.1 + - - -
206A LEU* 3.6 20.9 - - + +
209A MET* 4.1 10.8 - - + -
213A ILE* 3.7 30.5 - - + -
230A PRO* 3.7 30.7 - - + +
232A ILE* 3.9 7.3 - - + +
10C MYK 3.7 55.0 - - + -
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Residues in contact with TYR 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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171A THR* 3.6 23.6 - - + +
174A ARG* 3.6 24.2 - - - +
189A THR* 3.1 18.1 + - + +
190A PHE* 1.3 77.7 - - - +
192A THR* 1.3 72.4 + - + +
205A PRO* 4.6 0.3 - - - +
206A LEU* 3.4 53.2 + - + +
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Residues in contact with THR 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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174A ARG* 5.9 0.4 - - - +
189A THR* 3.7 14.3 - - + +
190A PHE 3.8 1.0 - - - +
191A TYR* 1.3 95.0 - - + +
193A SER* 1.3 65.4 + - - +
194A HIS* 4.6 4.0 - - - -
203A GLU* 3.9 22.0 - - - +
204A TYR 4.0 5.6 - - - +
205A PRO* 5.7 3.6 - - + -
230A PRO* 3.7 1.0 - - - +
231A ASP* 2.6 51.0 + - - +
158B LYS* 4.7 9.0 - - + +
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Residues in contact with SER 193 (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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190A PHE 4.5 2.4 + - - -
191A TYR 5.4 0.2 - - - -
192A THR* 1.3 74.1 - - - +
194A HIS* 1.3 72.6 + - - +
203A GLU* 3.4 1.9 - - - +
204A TYR* 2.8 41.5 + - - +
205A PRO 5.4 0.5 - - - -
209A MET* 3.3 35.2 - - - +
228A VAL* 4.0 7.0 - - - -
229A LYS 3.3 12.3 - - - -
230A PRO* 3.3 14.6 - - - +
231A ASP* 3.5 1.3 - - - -
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Residues in contact with HIS 194 (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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192A THR* 4.6 4.3 - - - -
193A SER* 1.3 78.8 + - - +
195A CYS* 1.3 70.2 + - - +
196A VAL 3.5 0.5 + - - -
201A ARG* 3.3 53.5 + - + +
202A HIS 3.3 4.5 - - - +
203A GLU* 3.6 31.6 - - + +
228A VAL* 3.8 6.7 - - - -
229A LYS* 2.9 33.9 + - + +
231A ASP* 2.8 37.8 + - - +
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Residues in contact with CYS 195 (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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194A HIS* 1.3 74.4 - - - +
196A VAL* 1.3 64.1 + - - +
197A SER* 3.4 15.4 + - - -
200A CYS* 3.9 3.1 - - - -
201A ARG* 3.4 23.2 + - - -
202A HIS 2.9 24.2 + - - +
221A CYS* 3.8 12.6 - - + -
224A CYS* 3.4 11.7 - - - -
226A SER* 3.8 7.9 - - - -
227A LEU 3.4 7.4 - - - -
228A VAL* 3.9 7.2 - - + +
501A ZN 2.3 37.7 - - - -
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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