Contacts of the strand formed by residues 290 - 301 (chain A) in PDB entry 3PIK
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 SER 290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A ASP* 6.6 0.2 - - - -
119A PHE* 6.3 1.8 - - - +
288A PHE 3.6 3.7 + - - -
289A PRO* 1.3 75.4 - - - +
291A ILE* 1.3 63.6 + - - +
292A SER* 4.1 1.3 + - - -
320A LYS 3.8 0.3 - - - +
321A ILE* 3.4 1.6 - - - -
322A GLU* 2.9 49.2 + - - +
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Residues in contact with ILE 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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116A ASP* 4.0 2.3 - - - +
117A LEU* 3.0 59.3 + - + +
118A ASP 4.4 3.0 + - - +
119A PHE* 5.1 21.4 - - + +
289A PRO* 5.3 1.6 - - + -
290A SER* 1.3 77.6 - - - +
292A SER* 1.3 68.7 + - - +
293A LEU* 6.0 0.4 - - + -
319A PRO* 5.6 5.4 - - + -
320A LYS 3.2 10.5 - - - +
321A ILE* 3.9 28.0 - - + -
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Residues in contact with SER 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PHE 3.5 5.4 - - - -
116A ASP* 3.6 20.4 - - - -
290A SER 4.1 1.7 + - - -
291A ILE* 1.3 81.3 - - - +
293A LEU* 1.3 65.9 + - - +
294A THR* 5.4 6.8 - - - +
318A ILE 4.9 0.2 - - - -
319A PRO* 3.5 2.9 - - - +
320A LYS* 2.8 51.0 + - - +
322A GLU* 5.5 3.5 + - - +
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Residues in contact with LEU 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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114A SER* 3.4 1.6 - - - -
115A PHE* 2.8 52.7 + - + +
117A LEU* 4.7 17.0 - - + -
291A ILE* 6.0 0.2 - - + -
292A SER* 1.3 79.3 - - - +
294A THR* 1.3 78.4 + - - +
295A SER* 4.8 1.6 - - - +
317A PHE* 3.4 44.4 - - + -
318A ILE 3.9 9.0 - - - +
319A PRO* 4.4 5.8 - - + -
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Residues in contact with THR 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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112A ASN* 6.0 2.2 - - - -
113A ALA 3.3 9.0 - - - -
114A SER* 3.7 18.4 - - - +
292A SER* 5.4 6.1 - - - +
293A LEU* 1.3 85.7 - - - +
295A SER* 1.3 57.9 + - - +
316A ASN* 4.3 1.9 + - - +
317A PHE* 3.8 0.2 - - - -
318A ILE* 2.7 59.4 + - - +
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Residues in contact with SER 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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112A ASN* 3.5 3.1 - - - +
113A ALA* 2.8 40.8 + - - +
293A LEU* 5.0 1.3 - - - -
294A THR* 1.3 76.0 - - - +
296A GLY* 1.3 58.0 + - - +
316A ASN* 2.7 22.1 + - - -
317A PHE* 3.7 22.9 - - - +
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Residues in contact with GLY 296 (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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111A LEU 3.2 10.8 - - - -
112A ASN* 4.2 5.8 - - - -
295A SER* 1.3 76.7 + - - +
297A ILE* 1.3 65.6 + - - +
298A SER* 5.2 1.3 - - - -
314A MET 3.7 0.6 - - - +
315A TRP* 3.3 4.3 - - - -
316A ASN* 2.8 49.5 + - - +
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Residues in contact with ILE 297 (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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109A THR 4.0 0.7 - - - +
110A GLY* 3.6 0.5 - - - -
111A LEU* 2.8 52.7 + - + +
296A GLY* 1.3 73.9 - - - +
298A SER* 1.3 69.9 + - - +
299A THR* 5.5 4.7 - - + -
313A GLY* 6.1 0.4 - - - -
314A MET 3.4 4.5 - - - +
315A TRP* 3.7 28.0 - - + +
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Residues in contact with SER 298 (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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108A SER* 5.6 1.6 - - - -
109A THR 3.3 10.0 + - - -
110A GLY* 4.6 5.9 - - - -
296A GLY 5.2 2.5 - - - -
297A ILE* 1.3 79.1 - - - +
299A THR* 1.3 75.1 + - - +
312A SER 4.6 0.2 - - - -
313A GLY* 3.1 0.5 - - - -
314A MET* 2.6 47.5 + - - -
316A ASN* 6.1 2.9 - - - -
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Residues in contact with THR 299 (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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108A SER* 3.3 5.0 - - - -
109A THR* 3.0 39.2 + - - +
297A ILE* 5.5 5.6 - - + -
298A SER* 1.3 87.5 + - - +
300A ALA* 1.3 66.0 + - - +
307A LEU* 3.1 33.9 - - - +
308A PHE* 5.0 13.2 - - + -
309A ASN 5.2 1.6 - - - +
312A SER 3.2 11.0 - - - -
313A GLY* 4.0 9.6 - - - +
314A MET* 5.9 0.2 - - - -
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Residues in contact with ALA 300 (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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106A GLU* 3.3 17.0 - - + +
107A PHE 3.0 12.3 - - - +
108A SER* 4.2 6.7 - - - -
299A THR* 1.3 81.8 - - - +
301A SER* 1.3 66.3 + - - +
307A LEU* 4.2 2.9 - - - -
312A SER* 3.1 25.1 + - - +
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Residues in contact with SER 301 (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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106A GLU* 3.1 12.0 + - - -
107A PHE* 2.7 40.9 + - - +
300A ALA* 1.3 77.6 - - - +
302A SER* 1.3 61.6 + - - +
303A ASP* 3.1 21.2 + - - -
306A SER* 2.9 38.4 + - - -
307A LEU* 4.0 4.7 - - - +
312A SER* 4.1 2.0 - - - -
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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