Contacts of the strand formed by residues 246 - 251 (chain D) in PDB entry 1PQ3
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 246 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D HIS* 4.5 2.5 - - - -
138D CYS* 3.6 22.4 - - - +
140D VAL* 4.2 18.4 - - + -
235D PHE* 4.3 17.9 - - + -
238D LEU* 6.0 0.4 - - + -
239D ILE* 4.4 12.3 - - + -
244D ARG 3.7 6.3 - - - +
245D PRO* 1.3 74.9 - - - +
247D HIS* 1.3 71.9 + - - +
248D LEU 4.3 1.6 - - - +
283D ILE* 4.7 11.7 - - + -
286D THR* 3.7 18.8 - - + +
288D LEU* 3.0 34.1 + - + +
289D LEU* 3.6 12.8 - - + +
290D SER* 2.9 24.5 + - - -
291D ALA 3.4 4.7 + - - -
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Residues in contact with HIS 247 (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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126D THR* 3.8 20.2 - - - -
127D ILE* 3.3 33.7 - - + +
130D HIS* 2.9 29.3 + - + +
137D LEU* 4.3 4.7 - - + -
138D CYS 2.9 14.8 + - - +
139D VAL* 3.4 10.9 - - + +
140D VAL 2.9 26.2 + - - +
245D PRO 4.1 0.2 + - - -
246D ILE* 1.3 74.7 - - - +
248D LEU* 1.3 60.4 + - - +
249D SER* 3.7 8.9 + - - -
291D ALA* 3.3 24.0 - - + +
293D ASP* 2.7 35.3 + - - -
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Residues in contact with LEU 248 (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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140D VAL* 3.5 24.0 - - + +
142D VAL* 4.0 16.6 - - + -
246D ILE* 4.0 1.4 - - + -
247D HIS* 1.3 73.8 - - - +
249D SER* 1.3 58.3 + - - +
250D PHE* 3.6 20.9 + - + -
279D ILE* 5.1 1.3 - - + -
280D ALA* 5.3 3.4 - - - -
283D ILE* 3.3 35.2 - - + -
289D LEU* 3.9 15.5 - - + -
291D ALA 3.0 9.0 + - - +
292D LEU* 3.2 17.6 - - + -
293D ASP 2.8 24.9 + - - +
318D VAL* 5.3 0.2 - - + -
322D SER* 3.6 25.6 - - - +
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Residues in contact with SER 249 (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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120D HIS* 2.6 31.4 + - - -
123D ALA* 4.2 0.7 - - - +
139D VAL* 4.8 1.1 - - - -
140D VAL 3.0 8.4 + - - +
141D TRP* 3.5 29.7 - - - -
142D VAL 3.0 26.7 + - - +
247D HIS* 3.7 9.6 + - - -
248D LEU* 1.3 72.5 - - - +
250D PHE* 1.3 58.1 + - - +
251D ASP 4.1 0.4 - - - -
293D ASP* 3.4 23.2 + - - +
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Residues in contact with PHE 250 (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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142D VAL* 3.6 40.2 - - + -
248D LEU* 4.4 18.4 - - + -
249D SER* 1.3 72.8 + - - +
251D ASP* 1.3 79.8 + - - +
252D ILE* 3.7 3.6 + - + -
254D ALA* 4.4 2.0 - - + -
255D PHE* 3.5 41.5 - + - -
271D LEU* 4.5 5.8 - - + -
276D GLY* 4.6 11.0 - - - -
279D ILE* 4.8 7.4 - - + -
280D ALA* 5.6 1.6 - - + -
292D LEU* 5.3 1.1 - - + -
293D ASP 2.7 17.7 + - - +
294D LEU* 3.4 18.1 - - + +
295D VAL* 3.0 28.2 + - - +
318D VAL* 3.9 23.1 - - + -
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Residues in contact with ASP 251 (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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120D HIS* 3.4 6.2 + - + +
142D VAL 2.9 8.1 + - - +
143D ASP* 3.2 22.0 - - - +
249D SER 4.0 0.8 + - - -
250D PHE* 1.3 75.0 - - - +
252D ILE* 1.3 66.0 + - - +
253D ASP* 2.7 34.1 + - - +
254D ALA* 2.9 22.5 + - - +
295D VAL* 3.8 5.8 - - - -
296D GLU* 3.4 19.1 - - - +
506D MN 2.2 31.7 + - - +
507D MN 2.6 7.4 + - - -
554D S2C 2.8 6.8 + - - -
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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