Contacts of the strand formed by residues 289 - 295 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A HIS* 5.0 5.4 + - - -
112A SER* 3.2 15.1 + - - -
246A ILE* 3.6 15.0 - - + +
248A LEU* 3.9 19.5 - - + +
283A ILE* 4.1 21.1 - - + +
284A HIS* 5.7 1.8 - - - -
286A THR* 4.2 3.0 + - - -
287A GLY* 3.6 3.5 - - - +
288A LEU* 1.3 74.8 - - - +
290A SER* 1.3 59.0 + - - +
291A ALA 3.2 28.5 - - - +
292A LEU* 4.2 5.8 - - + -
322A SER* 3.8 35.0 - - - +
323A PHE* 3.8 30.2 - - + -
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Residues in contact with SER 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A VAL* 5.3 4.2 - - - +
111A TYR 4.0 2.4 - - - +
112A SER* 2.8 15.4 - - - +
113A CYS 2.8 22.3 + - - -
130A HIS* 3.1 27.4 - - - -
134A CYS* 4.8 3.4 - - - -
245A PRO* 3.1 28.6 - - - +
246A ILE 2.9 7.5 + - - -
288A LEU 3.3 2.1 + - - -
289A LEU* 1.3 73.4 - - - +
291A ALA* 1.3 63.1 + - - +
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A VAL* 5.6 1.3 - - + -
107A VAL* 5.3 0.7 - - + -
112A SER* 4.8 0.4 - - - -
113A CYS* 3.0 22.4 - - + +
130A HIS* 3.5 14.4 - - + +
246A ILE 3.4 2.8 + - - -
247A HIS* 3.3 29.9 - - + +
248A LEU 3.0 22.2 + - - -
289A LEU* 3.2 11.8 - - - +
290A SER* 1.3 80.8 - - - +
292A LEU* 1.3 62.6 + - - +
293A ASP* 5.6 0.2 - - - +
323A PHE* 6.0 0.9 - - - -
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A CYS 2.7 10.8 + - - +
114A VAL* 3.4 17.5 - - + +
115A THR 2.8 31.5 + - - -
247A HIS* 5.2 0.2 - - - -
248A LEU* 3.2 27.6 - - + +
250A PHE* 5.3 1.1 - - + -
289A LEU* 4.2 11.2 - - + -
291A ALA* 1.3 76.6 - - - +
293A ASP* 1.3 77.2 + - - +
294A LEU* 4.0 7.4 - - + +
318A VAL* 5.3 2.0 - - + -
319A ILE* 3.9 29.4 - - + -
322A SER* 3.4 36.3 - - - +
323A PHE* 4.5 6.3 - - + -
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Residues in contact with ASP 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A THR* 3.5 9.9 + - - +
120A HIS* 5.1 0.4 - - + +
123A ALA* 4.4 6.1 - - - +
126A THR* 3.0 36.9 + - - +
247A HIS* 2.7 29.4 + - - -
248A LEU 2.8 7.3 + - - +
249A SER* 3.4 23.7 + - - +
250A PHE* 2.7 33.7 + - - +
292A LEU* 1.3 81.4 + - - +
294A LEU* 1.3 61.1 + - - +
295A VAL* 3.8 15.5 - - + -
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Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ILE* 3.9 10.5 - - + +
115A THR 3.0 10.1 + - - +
116A LEU* 3.6 6.3 - - + -
117A GLY* 2.9 22.9 + - - +
250A PHE* 3.4 20.0 - - + +
252A ILE* 4.4 7.4 - - + -
292A LEU* 4.0 3.5 - - + +
293A ASP* 1.3 74.5 - - - +
295A VAL* 1.3 61.8 + - - +
297A VAL* 4.0 12.6 - - + -
315A ALA* 3.6 32.3 - - + +
318A VAL* 3.8 30.7 - - + -
319A ILE* 3.8 31.0 - - + -
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Residues in contact with VAL 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A THR* 5.1 2.0 - - + +
117A GLY* 4.0 10.1 - - - +
118A GLY 3.5 14.1 - - - +
119A ASP 4.3 8.5 - - - +
120A HIS* 3.4 44.0 - - + +
122A LEU* 4.9 6.3 - - + -
123A ALA 5.8 0.4 - - - +
250A PHE 3.0 14.5 + - - +
251A ASP* 3.8 5.4 - - - -
252A ILE* 3.1 23.0 + - - +
293A ASP* 4.2 13.5 - - + +
294A LEU* 1.3 84.2 - - - +
296A GLU* 1.3 74.1 + - + +
297A VAL* 3.3 5.8 + - - +
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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