Contacts of the strand formed by residues 289 - 295 (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 LEU 289 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24D HIS* 5.0 5.2 + - - -
112D SER* 3.2 15.6 + - - -
246D ILE* 3.6 14.6 - - + +
248D LEU* 3.9 19.5 - - + +
283D ILE* 4.1 20.9 - - + +
284D HIS* 5.7 2.0 - - - -
286D THR* 4.2 2.4 + - - -
287D GLY 3.6 2.4 - - - +
288D LEU* 1.3 75.6 - - - +
290D SER* 1.3 58.2 + - - +
291D ALA 3.2 28.7 - - - +
292D LEU* 4.2 5.8 - - + -
322D SER* 3.8 35.0 - - - +
323D PHE* 3.8 30.1 - - + -
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Residues in contact with SER 290 (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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107D VAL* 5.3 4.2 - - - +
111D TYR 4.0 2.5 - - - +
112D SER* 2.8 34.0 - - - +
113D CYS 2.8 3.8 + - - -
130D HIS* 3.1 28.0 + - - -
134D CYS* 4.8 3.4 - - - -
245D PRO* 3.1 27.9 - - - +
246D ILE 2.9 7.9 + - - -
288D LEU 3.3 2.6 + - - -
289D LEU* 1.3 74.4 - - - +
291D ALA* 1.3 61.2 + - - +
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Residues in contact with ALA 291 (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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103D VAL* 5.7 1.6 - - + -
107D VAL* 5.3 0.4 - - + -
112D SER 4.8 0.2 - - - -
113D CYS* 3.0 23.1 - - + +
126D THR* 6.2 0.2 - - - -
130D HIS* 3.5 14.4 - - + +
246D ILE 3.4 2.6 + - - -
247D HIS* 3.3 29.5 - - + +
248D LEU 3.0 22.6 + - - -
289D LEU* 3.2 12.2 - - - +
290D SER* 1.3 80.8 - - - +
292D LEU* 1.3 61.0 + - - +
293D ASP* 5.6 0.2 - - - +
323D PHE* 6.0 0.7 - - - -
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Residues in contact with LEU 292 (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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113D CYS 2.7 10.9 + - - +
114D VAL* 3.4 18.0 - - + +
115D THR 2.8 31.4 + - - -
248D LEU* 3.2 25.8 - - + +
250D PHE* 5.3 0.7 - - + -
289D LEU* 4.2 11.2 - - + -
291D ALA* 1.3 77.9 - - - +
293D ASP* 1.3 77.6 + - - +
294D LEU* 4.0 7.9 - - + +
318D VAL* 4.9 1.6 - - + +
319D ILE* 3.9 27.6 - - + -
322D SER* 3.3 37.2 - - - +
323D PHE* 4.5 6.1 - - + -
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Residues in contact with ASP 293 (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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113D CYS 5.5 0.2 - - - +
115D THR* 3.5 10.5 + - - +
120D HIS* 5.2 0.4 - - + +
123D ALA* 4.4 5.5 - - - +
126D THR* 3.0 36.9 + - - +
247D HIS* 2.7 28.5 + - - -
248D LEU 2.8 8.5 + - - -
249D SER* 3.4 23.8 + - - +
250D PHE* 2.7 34.8 + - - +
292D LEU* 1.3 81.7 + - - +
294D LEU* 1.3 58.5 + - - +
295D VAL* 3.8 16.2 - - + -
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Residues in contact with LEU 294 (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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49D ILE* 3.9 11.1 - - + +
115D THR 3.0 10.5 + - - +
116D LEU* 3.6 6.7 - - + -
117D GLY 2.9 23.2 + - - +
250D PHE* 3.4 20.9 - - + +
252D ILE* 4.4 6.7 - - + -
292D LEU* 4.0 3.1 - - + +
293D ASP* 1.3 74.3 - - - +
295D VAL* 1.3 63.0 + - - +
297D VAL* 4.0 12.5 - - + +
315D ALA* 3.6 31.6 - - + +
318D VAL* 3.8 30.7 - - + -
319D ILE* 3.8 31.4 - - + -
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Residues in contact with VAL 295 (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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115D THR* 5.1 2.2 - - + +
117D GLY* 4.0 10.3 - - - +
118D GLY 3.5 13.9 - - - +
119D ASP 4.3 7.9 - - - +
120D HIS* 3.5 44.6 - - + +
122D LEU* 4.9 6.7 - - + -
123D ALA 5.8 0.2 - - - +
250D PHE 3.0 14.3 + - - +
251D ASP* 3.8 5.4 - - - -
252D ILE* 3.1 23.7 + - - +
293D ASP* 4.2 12.8 - - + -
294D LEU* 1.3 84.3 - - - +
296D GLU* 1.3 74.6 + - + +
297D VAL* 3.3 5.0 + - - +
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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