Contacts of the helix formed by residues 191 - 197 (chain Z) in PDB entry 5L4K
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 ILE 191 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131Z MET* 4.0 33.7 - - + +
135Z GLY* 6.6 0.4 - - - -
171Z GLN* 6.1 2.0 - - + -
175Z ASP* 3.4 32.3 - - - +
187Z LEU* 2.9 44.2 + - + +
188Z VAL* 3.9 13.9 - - + +
189Z LYS 3.3 1.6 - - - -
190Z GLU* 1.3 77.3 - - - +
192Z VAL* 1.3 66.5 + - - +
193Z PRO 3.4 0.2 - - - -
194Z TYR* 3.1 18.0 + - + +
195Z ASN* 3.2 27.2 + - - +
207Z LEU* 5.1 0.4 - - + -
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Residues in contact with VAL 192 (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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175Z ASP* 4.8 9.2 - - - +
188Z VAL 5.5 2.0 - - - +
189Z LYS 4.1 4.4 + - - +
191Z ILE* 1.3 76.6 - - - +
193Z PRO* 1.3 63.9 - - + +
194Z TYR 3.3 0.2 + - - -
195Z ASN* 3.4 5.9 + - - +
196Z MET* 2.9 22.7 + - - +
204Z ALA* 2.9 46.4 - - + +
207Z LEU* 3.5 31.4 - - + -
208Z LEU* 4.3 12.8 - - + +
211Z ILE* 6.3 0.4 - - + -
232Z TYR* 3.9 21.8 - - + +
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Residues in contact with PRO 193 (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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189Z LYS* 3.3 23.1 - - + +
190Z GLU* 3.7 24.5 - - + +
192Z VAL* 1.3 93.6 - - + +
194Z TYR* 1.3 57.1 + - - +
196Z MET* 3.5 17.5 - - + +
197Z ALA* 3.0 29.1 + - - +
232Z TYR* 3.9 11.0 - - + +
235Z SER* 5.6 3.1 - - - -
236Z CYS* 3.9 29.4 - - - -
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Residues in contact with TYR 194 (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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132Z THR* 6.6 0.2 - - - -
135Z GLY* 3.7 28.0 - - - -
136Z GLU* 3.7 25.6 - - + +
143Z ARG* 5.3 4.5 + - - -
187Z LEU* 5.8 1.6 - - + -
190Z GLU* 3.7 17.2 + - + +
191Z ILE* 3.1 18.5 + - + +
193Z PRO* 1.3 78.8 - - - +
195Z ASN* 1.3 69.8 + - - +
197Z ALA* 3.6 7.3 + - + +
198Z HIS* 3.0 56.9 + + - -
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Residues in contact with ASN 195 (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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135Z GLY* 4.3 11.6 - - - +
138Z GLU* 5.4 2.4 - - - +
171Z GLN* 3.7 28.7 + - - +
191Z ILE* 3.2 26.7 + - - +
192Z VAL* 4.0 3.3 - - - +
194Z TYR* 1.3 84.7 - - - +
196Z MET* 1.3 62.4 + - - +
198Z HIS* 3.3 12.1 + - - -
200Z ALA* 2.7 48.7 - - + +
203Z GLU 4.8 0.9 - - - -
204Z ALA* 4.3 6.7 - - + +
207Z LEU* 3.9 19.6 - - - +
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Residues in contact with MET 196 (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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192Z VAL 2.9 18.8 + - - +
193Z PRO* 3.3 26.4 + - + +
195Z ASN* 1.3 78.3 - - - +
197Z ALA* 1.3 65.3 + - + +
198Z HIS 3.2 11.4 + - - +
200Z ALA 3.9 2.9 - - - -
201Z GLU* 3.6 12.0 - - - +
204Z ALA* 3.5 13.9 - - + +
232Z TYR* 5.4 1.3 - - - +
236Z CYS* 4.9 2.5 - - - -
240Z VAL* 3.8 29.6 - - + -
244Z GLU* 4.0 22.0 - - + +
248Z LEU* 3.8 45.5 - - + -
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Residues in contact with ALA 197 (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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193Z PRO 3.0 15.7 + - - +
194Z TYR* 3.9 7.2 - - + +
195Z ASN 3.3 0.6 - - - -
196Z MET* 1.3 85.1 - - + +
198Z HIS* 1.3 71.5 + - + +
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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