Contacts of the strand formed by residues 147 - 153 (chain H) in PDB entry 1P8J
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 147 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144H GLY 2.9 14.3 + - - +
145H HIS 3.8 6.1 - - - +
146H GLY* 1.3 80.5 + - - +
148H VAL* 1.3 68.2 + - - +
149H VAL* 4.5 0.9 - - + -
219H ALA* 3.4 5.0 - - + +
220H ARG* 2.9 26.3 + - - +
248H HIS* 3.6 12.1 - - + +
249H ILE* 4.2 12.3 - - + -
379H ALA* 3.5 45.5 - - + +
382H LEU* 3.8 17.5 - - + -
383H GLU* 3.9 12.1 - - + +
386H LYS* 3.4 33.7 - - + +
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Residues in contact with VAL 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H ILE* 1.3 76.7 - - - +
149H VAL* 1.3 66.0 + - - +
168H ASP* 3.7 10.3 - - - +
171H ALA* 3.5 30.1 - - + -
220H ARG* 3.6 42.8 - - + +
246H HIS* 3.3 31.2 - - - +
247H ILE* 3.9 7.1 - - + +
248H HIS* 2.8 41.4 + - + +
249H ILE 3.2 6.9 + - - -
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Residues in contact with VAL 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H ILE* 4.5 2.5 - - + -
148H VAL* 1.3 81.4 - - - +
150H SER* 1.3 70.8 + - - +
151H ILE* 4.7 2.2 - - + -
171H ALA* 4.2 1.6 - - - +
202H VAL* 3.8 30.3 - - + -
219H ALA* 4.9 4.5 - - + -
220H ARG 3.0 9.6 + - - +
221H ILE* 3.3 18.5 - - + +
222H GLY* 2.9 24.1 + - - -
247H ILE* 4.4 0.7 - - - -
249H ILE* 3.3 35.9 - - + +
251H SER* 4.8 1.1 - - - -
375H ALA* 4.4 13.9 - - + +
379H ALA* 4.2 13.0 - - + -
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Residues in contact with SER 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149H VAL* 1.3 75.6 - - - +
151H ILE* 1.3 64.3 + - - +
152H LEU* 3.7 2.0 + - - +
171H ALA 2.8 24.6 + - - -
222H GLY 3.5 4.5 + - - -
224H VAL* 3.4 19.8 - - - +
247H ILE* 3.6 26.9 - - - +
249H ILE 2.9 7.4 + - - -
250H TYR* 3.5 10.2 - - - +
251H SER* 2.9 27.4 + - - -
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Residues in contact with ILE 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149H VAL* 4.7 0.7 - - + -
150H SER* 1.3 74.3 + - - +
152H LEU* 1.3 60.5 + - - +
153H ASP* 3.3 22.2 + - + +
155H GLY 5.8 0.5 + - - -
156H ILE* 5.9 1.1 - - + -
195H GLY* 3.9 11.4 - - - +
198H CYS* 3.8 30.1 - - + +
199H ALA* 3.8 20.6 - - + -
202H VAL* 3.9 24.0 - - + -
221H ILE* 3.9 6.7 - - + -
222H GLY 3.0 15.8 + - - +
223H GLY* 3.4 3.3 - - - -
224H VAL 2.8 26.5 + - - -
251H SER* 3.6 29.2 - - - +
253H SER* 6.2 0.7 - - - +
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Residues in contact with LEU 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150H SER* 4.2 2.9 - - - +
151H ILE* 1.3 71.1 - - - +
153H ASP* 1.3 60.7 + - - +
224H VAL* 3.4 34.1 - - + -
226H MET* 4.1 9.0 - - - -
239H SER* 3.8 26.5 - - - +
240H LEU* 3.4 34.5 - - + -
250H TYR* 4.2 26.9 - - + -
251H SER 3.0 17.9 + - - +
252H ALA* 4.1 10.0 - - + -
253H SER 4.3 0.3 + - - -
254H TRP* 2.8 39.5 + - + +
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Residues in contact with ASP 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151H ILE* 3.3 9.9 + - + +
152H LEU* 1.3 77.7 - - - +
154H ASP* 1.3 73.0 + - - +
155H GLY 3.3 4.5 - - - +
194H HIS* 2.5 48.4 + - - +
195H GLY* 3.6 22.0 + - - -
198H CYS* 4.2 6.8 - - - -
224H VAL 3.0 8.4 + - - +
226H MET* 2.8 27.9 + - - -
227H LEU* 3.1 30.1 + - - +
253H SER* 4.1 7.1 - - - +
804R LYS* 4.0 0.7 - - - +
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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