Contacts of the strand formed by residues 183 - 190 (chain Z) in PDB entry 3SDI
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 183 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40Z ASN* 3.2 22.5 + - - +
177Z ILE 3.5 1.6 - - - +
178Z VAL* 3.4 3.8 - - - -
179Z THR* 2.9 31.1 + - - +
180Z LYS 3.3 2.6 + - - -
182Z ASP* 1.3 79.9 - - - +
184Z VAL* 1.3 58.8 + - - -
185Z ARG* 4.1 0.8 + - - +
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Residues in contact with VAL 184 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Z ASP* 3.7 37.7 - - + +
40Z ASN* 3.7 19.1 - - - +
42Z VAL* 4.2 20.0 - - + -
176Z LEU* 4.3 13.0 - - + -
177Z ILE 3.4 6.3 - - - +
178Z VAL* 4.2 14.8 - - + -
183Z GLY* 1.3 76.6 - - - +
185Z ARG* 1.3 70.5 + - - +
186Z LYS* 5.8 0.9 - - + -
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Residues in contact with ARG 185 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148Z VAL* 4.3 16.8 - - - +
152Z ILE* 4.4 2.2 - - - +
176Z LEU* 3.4 3.8 - - - -
177Z ILE* 2.8 67.8 + - + +
179Z THR* 5.2 8.9 + - - +
183Z GLY 4.1 0.6 + - - -
184Z VAL* 1.3 75.6 - - - +
186Z LYS* 1.3 68.5 + - - +
187Z GLU* 3.4 27.2 + - + +
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Residues in contact with LYS 186 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Z TYR* 5.7 1.1 - - - -
174Z GLU* 3.8 38.1 + - + +
175Z ILE 3.4 5.8 - - - +
176Z LEU* 4.0 18.7 - - + +
184Z VAL* 5.8 1.1 - - + -
185Z ARG* 1.3 81.9 - - - +
187Z GLU* 1.3 65.2 + - - +
188Z PHE* 5.9 0.9 - - + -
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Residues in contact with GLU 187 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152Z ILE* 3.6 24.5 - - - +
173Z LEU 3.8 0.7 - - - +
174Z GLU* 3.5 4.3 - - - +
175Z ILE* 2.9 41.5 + - + +
177Z ILE* 4.3 10.1 - - + +
185Z ARG* 3.4 30.4 + - + +
186Z LYS* 1.3 78.4 - - - +
188Z PHE* 1.3 61.1 + - - +
189Z TYR* 2.8 38.8 + - + +
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Residues in contact with PHE 188 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Z THR* 4.0 7.4 - - + -
30Z TYR* 3.9 33.7 - + - -
171Z ASP 4.9 0.7 - - - -
172Z GLY* 4.1 9.2 - - - -
173Z LEU 3.3 22.7 - - - -
174Z GLU* 4.3 12.6 - - + +
186Z LYS* 4.5 1.3 + - + -
187Z GLU* 1.3 75.9 - - - +
189Z TYR* 1.3 96.0 + - - +
190Z GLU* 3.9 22.7 - - + -
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Residues in contact with TYR 189 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152Z ILE* 4.5 3.5 - - + +
156Z ARG* 3.4 54.6 + - - +
172Z GLY* 3.4 2.8 - - - -
173Z LEU* 2.7 55.9 + - + +
175Z ILE* 3.9 24.2 - - + -
187Z GLU* 2.8 39.9 + - + +
188Z PHE* 1.3 87.9 - - - +
190Z GLU* 1.3 66.0 + - - +
191Z LEU* 5.4 1.3 - - + -
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Residues in contact with GLU 190 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1521 ARG* 3.1 34.1 + - - -
198H GLU* 4.1 13.7 - - - +
171Z ASP 4.2 7.8 - - - +
188Z PHE* 3.9 20.5 - - + -
189Z TYR* 1.3 76.2 - - - +
191Z LEU* 1.3 74.5 + - - +
193Z ARG* 4.6 10.5 + - - -
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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