Contacts of the strand formed by residues 147 - 153 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144D GLY 2.9 15.2 + - - +
145D HIS 3.8 6.1 - - - +
146D GLY* 1.3 87.3 - - - +
148D VAL* 1.3 68.2 + - - +
149D VAL* 4.2 1.1 - - + -
219D ALA* 3.4 5.7 - - + +
220D ARG* 2.9 27.2 + - - +
248D HIS* 3.6 13.2 - - + +
249D ILE* 4.3 12.3 - - + -
379D ALA* 3.5 43.3 - - + +
382D LEU* 3.7 22.4 - - + -
383D GLU* 3.9 9.9 - - + +
386D LYS* 3.8 24.2 - - + +
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Residues in contact with VAL 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D GLY 4.7 2.9 - - - +
147D ILE* 1.3 76.9 - - - +
149D VAL* 1.3 65.5 + - - +
168D ASP* 3.7 18.8 - - - +
171D ALA* 3.5 30.1 - - + -
220D ARG* 3.6 16.2 - - + +
246D HIS* 3.2 38.1 - - + +
247D ILE* 3.9 5.8 - - + -
248D HIS* 2.7 41.0 + - + +
249D ILE 3.2 7.4 + - - +
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Residues in contact with VAL 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ILE* 4.5 2.7 - - + -
148D VAL* 1.3 81.6 - - - +
150D SER* 1.3 70.5 + - - +
151D ILE* 4.6 2.0 - - + -
171D ALA* 4.2 1.6 - - - +
202D VAL* 3.8 30.7 - - + -
219D ALA* 5.0 4.3 - - + -
220D ARG 2.9 9.8 + - - +
221D ILE* 3.2 17.7 - - + +
222D GLY 2.8 24.4 + - - -
247D ILE* 4.4 0.9 - - - -
249D ILE* 3.3 39.0 - - + +
251D SER* 4.7 1.3 - - - -
375D ALA* 4.4 9.4 - - + +
379D ALA* 4.2 12.6 - - + -
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Residues in contact with SER 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D VAL* 1.3 75.8 - - - +
151D ILE* 1.3 65.1 + - - +
152D LEU* 3.8 1.3 + - - +
171D ALA* 2.6 26.5 + - - -
222D GLY 3.5 3.8 + - - -
224D VAL* 3.5 19.4 - - - +
247D ILE* 3.6 27.0 - - - +
249D ILE 2.9 7.1 + - - -
250D TYR* 3.5 10.5 - - - +
251D SER* 2.9 26.7 + - - -
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Residues in contact with ILE 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D VAL* 4.6 0.7 - - + -
150D SER* 1.3 74.9 + - - +
152D LEU* 1.3 60.7 + - - +
153D ASP* 3.3 26.4 + - + +
155D GLY 5.8 0.7 + - - -
156D ILE* 6.0 0.9 - - + -
195D GLY* 3.9 9.4 - - - +
198D CYS* 3.8 28.3 - - + +
199D ALA* 3.8 21.3 - - + -
202D VAL* 4.0 22.4 - - + -
221D ILE* 4.1 7.0 - - + -
222D GLY 3.0 15.9 + - - +
223D GLY* 3.4 3.8 - - - -
224D VAL 2.8 27.0 + - - +
251D SER* 3.7 30.1 - - - +
253D SER 6.2 0.7 - - - +
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Residues in contact with LEU 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D SER* 4.3 3.4 - - - +
151D ILE* 1.3 70.2 - - - +
153D ASP* 1.3 63.6 + - - +
224D VAL* 3.4 36.3 - - + -
226D MET* 4.1 8.5 - - - -
239D SER* 3.9 26.5 - - - +
240D LEU* 3.6 32.1 - - + -
250D TYR* 4.2 26.2 - - + -
251D SER 3.0 17.5 + - - +
252D ALA* 4.1 9.2 - - + -
253D SER 4.3 0.3 + - - -
254D TRP* 2.8 39.0 + - + +
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Residues in contact with ASP 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D ILE* 3.3 9.8 + - + +
152D LEU* 1.3 76.1 - - - +
154D ASP* 1.3 72.1 + - - +
155D GLY 3.3 5.4 - - - +
194D HIS* 2.6 48.4 + - - +
195D GLY* 3.5 23.0 + - - -
198D CYS* 4.2 6.6 - - - -
224D VAL 3.0 8.4 + - - +
226D MET* 2.8 28.7 + - - +
227D LEU* 3.1 31.4 + - - +
253D SER* 4.1 7.8 + - - +
804M LYS* 4.1 0.5 - - - +
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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