Contacts of the helix formed by residues 181 - 189 (chain K) in PDB entry 4PHZ
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 LEU 181 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245J THR* 4.0 20.4 - - + +
247J LYS* 3.1 34.3 + - + +
249J ILE* 4.5 22.0 - - + -
179K TYR 3.2 3.6 + - - -
180K SER* 1.3 69.4 + - - +
182K ALA* 1.3 67.3 + - - +
184K LEU* 3.0 18.1 + - + +
185K ILE* 2.9 43.4 + - + +
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Residues in contact with ALA 182 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243J TYR 4.4 4.3 - - - +
245J THR* 3.6 28.5 + - + +
247J LYS 4.6 0.6 + - - -
180K SER* 4.1 4.3 - - - +
181K LEU* 1.3 80.1 - - - +
183K PHE* 1.3 56.1 + - - +
185K ILE* 3.5 10.1 + - - +
186K VAL* 3.0 30.5 + - - +
230K GLY* 3.3 24.0 - - - +
233K GLY* 3.7 3.6 - - - +
234K VAL* 3.6 15.5 - - + +
237K GLN* 4.5 0.7 - - - +
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Residues in contact with PHE 183 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107K LEU* 4.2 10.1 - - + -
111K LEU* 4.2 10.5 - - + -
161K ALA 4.2 5.8 - - - -
164K ALA* 3.4 29.2 - - + -
165K PHE* 3.3 41.0 - + + -
168K ALA* 3.9 19.3 - - + -
175K PHE* 4.0 18.2 - + + -
180K SER* 3.2 20.6 + - - +
181K LEU 3.1 0.8 - - - -
182K ALA* 1.3 75.1 - - - +
184K LEU* 1.3 64.6 + - - +
186K VAL* 3.2 14.0 + - + -
187K ALA* 3.0 22.6 + - + +
234K VAL* 3.5 33.6 - - + +
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Residues in contact with LEU 184 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B VAL* 5.8 6.7 - - + -
249J ILE* 3.9 22.9 - - + -
252J ILE* 4.2 21.3 - - + -
165K PHE* 3.8 26.9 - - + -
179K TYR* 3.7 27.6 - - + -
180K SER 2.9 10.3 + - - +
181K LEU* 3.2 18.6 - - + +
183K PHE* 1.3 76.2 - - - +
185K ILE* 1.3 58.8 + - + +
187K ALA* 3.4 1.0 + - - -
188K ILE* 3.0 49.3 + - + +
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Residues in contact with ILE 185 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243J TYR* 4.8 22.2 - - + -
245J THR* 5.7 3.1 - - + -
181K LEU* 2.9 42.5 + - + +
182K ALA* 3.6 8.5 - - - +
184K LEU* 1.3 78.4 - - + +
186K VAL* 1.3 58.1 + - - +
188K ILE* 5.2 1.1 - - - -
189K GLY* 2.7 33.4 + - - +
190K PRO* 4.2 0.2 - - - +
227K MET 5.1 0.9 - - - +
228K ALA* 4.5 10.6 - - + +
230K GLY* 4.7 11.9 - - - -
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Residues in contact with VAL 186 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111K LEU* 6.0 2.2 - - + -
114K TYR* 3.6 35.3 + - + +
161K ALA* 4.1 5.5 - - + +
182K ALA 3.0 13.0 + - - +
183K PHE* 3.2 24.0 + - + +
185K ILE* 1.3 80.2 - - - +
187K ALA* 1.3 59.4 + - - +
190K PRO* 3.1 22.9 - - - +
228K ALA* 4.7 7.4 - - + +
230K GLY* 3.3 39.5 - - - +
231K VAL* 3.6 15.3 - - + +
234K VAL* 4.5 2.9 - - + -
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Residues in contact with ALA 187 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158K SER* 5.0 1.0 + - - +
161K ALA* 4.1 18.5 - - - +
162K VAL* 4.4 11.5 - - + +
165K PHE* 4.0 28.5 - - + -
183K PHE 3.0 16.3 + - - +
186K VAL* 1.3 76.9 - - + +
188K ILE* 1.3 74.3 + - + +
190K PRO* 3.7 8.2 - - - +
191K PHE* 3.6 19.4 - - - -
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Residues in contact with ILE 188 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B VAL* 3.8 31.6 - - + -
151B VAL* 5.2 8.7 - - + -
234B PHE* 5.0 16.8 - - + -
162K VAL* 5.7 3.4 - - + -
165K PHE* 6.0 2.9 - - + -
184K LEU* 3.0 33.0 + - + +
185K ILE* 5.8 0.7 - - - -
187K ALA* 1.3 90.0 - - + +
189K GLY* 1.3 72.5 + - - +
190K PRO 3.2 1.8 - - - -
191K PHE* 2.9 31.3 + - + +
192K MET* 3.9 10.7 + - + +
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Residues in contact with GLY 189 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185K ILE* 2.7 27.4 + - - +
188K ILE* 1.3 70.0 - - - +
190K PRO* 1.4 56.8 - - - -
192K MET* 2.7 39.7 + - - +
193K ILE* 3.5 4.4 + - - +
228K ALA* 4.9 7.4 - - - -
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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