Contacts of the strand formed by residues 289 - 295 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B HIS* 5.3 3.3 - - - -
112B SER* 3.0 17.2 + - - -
246B ILE* 3.6 12.8 - - + +
248B LEU* 4.1 17.7 - - + +
283B ILE* 4.1 22.8 + - + +
284B HIS* 5.6 2.0 - - - -
286B THR* 4.3 2.6 + - - -
287B GLY 3.7 2.0 - - - +
288B LEU* 1.3 76.5 - - - +
290B SER* 1.3 57.9 + - - +
291B ALA 3.3 29.8 - - - +
292B LEU* 4.2 5.8 - - + -
322B SER* 3.6 38.6 - - - +
323B PHE* 3.9 28.9 - - + -
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Residues in contact with SER 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B VAL* 4.4 5.0 - - - +
111B TYR 4.0 3.8 - - - +
112B SER* 3.3 11.0 - - - +
113B CYS* 3.0 21.5 + - - +
130B HIS* 3.1 29.2 + - - -
134B CYS* 5.0 4.0 - - - -
245B PRO* 3.5 21.5 - - - +
246B ILE 2.9 8.4 + - - -
288B LEU 3.2 6.3 + - - -
289B LEU* 1.3 72.8 + - - +
291B ALA* 1.3 62.7 + - - +
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B VAL* 5.5 2.0 - - + -
107B VAL* 5.1 0.9 - - + -
112B SER* 5.5 0.2 - - - -
113B CYS* 3.1 20.4 - - + +
126B THR* 6.2 0.2 - - - -
130B HIS* 3.3 15.7 - - + +
246B ILE 3.4 2.2 + - - -
247B HIS* 3.2 30.2 - - + +
248B LEU 2.9 23.6 + - - -
289B LEU* 3.3 10.0 - - - +
290B SER* 1.3 82.8 - - - +
292B LEU* 1.3 61.0 + - - +
323B PHE* 6.1 0.7 - - - -
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B CYS 2.7 11.7 + - - +
114B VAL* 3.4 18.3 - - + -
115B THR* 2.8 26.3 + - - -
248B LEU* 3.1 26.2 - - + +
250B PHE* 5.4 1.1 - - + -
289B LEU* 4.2 11.4 - - + -
291B ALA* 1.3 76.1 - - - +
293B ASP* 1.3 82.4 + - - +
294B LEU* 4.1 7.6 - - + +
318B VAL* 5.3 1.8 - - + -
319B ILE* 4.2 26.5 - - + -
322B SER* 3.5 37.0 - - - +
323B PHE* 4.3 8.5 - - + -
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Residues in contact with ASP 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B THR* 3.5 9.1 + - + +
120B HIS* 5.1 0.4 - - + +
122B LEU 6.0 0.4 - - - -
123B ALA* 4.5 6.1 - - + +
126B THR* 3.1 34.6 + - - +
247B HIS* 2.6 29.1 + - - -
248B LEU 2.7 8.9 + - - +
249B SER* 3.0 25.1 + - - +
250B PHE* 2.7 33.9 + - - +
291B ALA* 5.7 0.2 - - - +
292B LEU* 1.3 82.4 - - - +
294B LEU* 1.3 58.9 + - - +
295B VAL* 3.9 14.8 - - + -
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Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ILE* 4.1 6.0 - - + +
115B THR 3.1 10.5 + - - +
116B LEU* 3.7 7.6 - - + -
117B GLY 2.9 23.7 + - - +
250B PHE* 3.4 20.9 - - + +
252B ILE* 4.2 9.0 - - + -
292B LEU* 4.3 4.9 - - + -
293B ASP* 1.3 72.7 - - - +
295B VAL* 1.3 65.0 + - - +
297B VAL* 3.9 17.0 - - + +
315B ALA* 3.7 28.5 - - + +
318B VAL* 3.9 28.5 - - + -
319B ILE* 4.1 31.4 - - + -
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Residues in contact with VAL 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B THR* 5.1 2.0 - - + +
117B GLY* 4.1 9.4 - - - +
118B GLY 3.4 14.4 - - - +
119B ASP 4.4 5.6 - - - +
120B HIS* 3.4 50.7 - - + +
122B LEU* 5.1 6.7 - - + -
123B ALA 5.9 0.4 - - - +
250B PHE 3.1 12.8 + - - +
251B ASP* 3.9 2.7 - - - -
252B ILE* 3.2 23.6 + - - +
293B ASP* 4.2 13.2 - - + -
294B LEU* 1.3 87.4 - - - +
296B GLU* 1.3 74.5 + - + +
297B VAL* 3.3 4.7 + - - -
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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