Contacts of the strand formed by residues 183 - 188 (chain Z) in PDB entry 5A0Q
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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39Z PRO 4.5 1.3 - - - -
40Z TYR* 4.3 12.1 - - - -
104Z TRP* 6.0 0.2 - - - -
178Z HIS 3.4 2.6 - - - +
179Z VAL* 3.9 11.0 - - - -
180Z ARG* 3.2 37.5 + - - +
181Z GLU 4.7 0.2 - - - -
182Z ASP* 1.4 79.6 - - - +
184Z TRP* 1.3 66.5 + - - -
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Residues in contact with TRP 184 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36Z GLU* 3.0 34.7 + - + -
38Z ASN 3.0 8.9 + - - -
39Z PRO* 2.1 45.3 + - + +
40Z TYR* 3.8 4.5 - - - -
42Z LEU* 3.1 23.3 - - + -
177Z TYR* 3.5 33.9 - + + -
178Z HIS 2.9 13.2 - - - +
179Z VAL* 3.8 16.5 - - + +
183Z GLY* 1.3 74.0 - - - -
185Z ILE* 1.3 73.7 + - - +
186Z ARG* 4.1 18.4 - - + -
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Residues in contact with ILE 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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153Z TYR* 4.5 7.9 - - - +
177Z TYR* 3.3 4.0 - - - -
178Z HIS* 3.1 29.6 + - + +
180Z ARG* 3.4 44.2 - - - +
184Z TRP* 1.3 88.4 - - - +
186Z ARG* 1.3 58.8 + - - +
187Z VAL* 3.0 32.6 + - + +
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Residues in contact with ARG 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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32Z LYS* 3.5 30.3 - - - +
175Z ASN* 3.7 27.1 + - - +
176Z LEU 2.9 32.3 + - - -
177Z TYR* 3.3 39.3 + - - -
184Z TRP* 4.1 12.0 - - + -
185Z ILE* 1.3 67.7 - - - +
187Z VAL* 1.3 63.1 + - - +
188Z SER* 2.9 21.9 + - - -
189Z SER* 3.1 26.1 + - - +
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Residues in contact with VAL 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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153Z TYR* 2.7 48.7 - - + +
176Z LEU* 3.3 18.1 + - + -
178Z HIS* 3.0 35.9 - - + +
185Z ILE* 3.0 30.6 + - + +
186Z ARG* 1.3 71.7 - - - +
188Z SER* 1.3 66.6 + - - +
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Residues in contact with SER 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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153Z TYR* 5.1 0.5 - - - -
157Z ARG* 3.1 30.0 + - - -
174Z VAL 5.3 0.2 - - - -
176Z LEU* 3.0 31.6 + - - +
186Z ARG* 2.9 20.3 + - - -
187Z VAL* 1.3 87.3 + - - +
189Z SER* 1.3 62.7 + - - +
190Z ASP* 4.1 21.1 + - - -
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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