Contacts of the strand formed by residues 256 - 263 (chain A) in PDB entry 3PU3
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 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A PHE* 3.7 6.3 - - - -
254A GLY 3.7 0.4 + - - -
255A ALA* 1.3 74.6 - - - +
257A ALA* 1.3 63.2 + - - +
315A ILE 3.3 11.4 - - - -
316A PRO 3.6 0.5 - - - -
317A SER* 3.1 20.2 + - - +
335A HIS* 3.3 5.5 + - - -
336A PHE* 2.8 59.4 + - - -
338A HIS* 3.1 23.1 + - - -
345A GLN* 5.3 0.2 + - - -
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Residues in contact with ALA 257 (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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251A ASP* 3.8 13.0 - - - +
256A SER* 1.3 78.0 - - - +
258A TRP* 1.3 60.1 + - - +
259A TYR* 4.0 19.5 - - + -
313A LEU 3.7 0.4 - - - +
314A PHE* 3.1 5.7 - - - +
315A ILE* 2.7 43.5 + - + +
334A GLY 3.4 6.3 - - - +
335A HIS* 3.6 21.3 - - + +
336A PHE* 4.0 7.4 - - - -
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Residues in contact with TRP 258 (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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11A EDO 2.4 33.3 + - - -
137A LEU* 3.9 22.2 - - + -
139A VAL* 5.7 0.2 - - + -
206A VAL* 4.3 12.3 - - + -
208A PRO* 3.9 15.7 - - + +
209A PRO* 3.7 19.1 - - + -
212A VAL* 3.6 19.7 - - + -
234A THR 3.9 6.7 - - - -
235A LYS* 5.2 0.9 - - - -
257A ALA* 1.3 76.2 - - - +
259A TYR* 1.3 64.6 + - - +
260A HIS* 4.0 14.4 - - + -
312A THR* 4.6 3.4 - - + -
313A LEU 3.2 5.8 - - - +
314A PHE* 3.8 26.9 - - + -
332A PHE* 3.6 25.1 - - + -
333A ALA* 3.2 47.7 - - - +
334A GLY* 3.2 18.9 + - - +
336A PHE* 4.3 2.5 - + - -
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Residues in contact with TYR 259 (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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1A OGA 2.6 48.1 + - - -
238A LEU* 3.8 23.6 - - + -
257A ALA* 4.0 13.0 - - + -
258A TRP* 1.3 78.2 - - - +
260A HIS* 1.3 61.5 + - - +
261A VAL* 4.1 4.4 + - + -
266A LYS* 5.8 3.8 - - + -
268A PHE* 3.8 38.8 - + + -
307A VAL* 5.0 2.2 - - + +
311A GLN 3.9 0.9 - - - +
312A THR* 3.2 5.1 - - - -
313A LEU* 2.8 42.3 + - + +
315A ILE* 4.0 14.1 - - + -
321A TYR* 2.6 29.5 + + - -
331A ALA* 5.4 6.1 - - + -
332A PHE 3.4 4.7 - - - -
333A ALA* 3.7 9.9 - - + -
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Residues in contact with HIS 260 (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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132A LYS* 4.5 11.1 - - + -
137A LEU* 3.3 19.3 - - + +
139A VAL* 4.1 22.2 - - + +
258A TRP* 4.0 16.9 - - + -
259A TYR* 1.3 73.9 - - - +
261A VAL* 1.3 74.6 + - - +
262A LEU* 3.4 20.3 + - + +
310A GLY* 3.3 33.8 - - - -
311A GLN 3.4 2.7 + - - -
312A THR* 2.8 24.4 + - - +
331A ALA* 3.2 5.8 - - - +
332A PHE* 2.8 41.5 + + + +
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Residues in contact with VAL 261 (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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259A TYR* 4.1 3.6 - - + +
260A HIS* 1.3 73.7 + - - +
262A LEU* 1.3 57.0 + - - +
263A LYS 3.6 14.8 - - - +
264A GLY 3.4 29.2 - - - +
265A GLU* 4.2 0.7 - - - -
266A LYS* 4.4 15.7 - - + -
268A PHE* 5.7 2.0 - - + -
307A VAL* 3.7 31.4 - - + +
308A LYS 3.7 11.0 - - - +
309A GLN* 3.9 4.0 - - - +
310A GLY* 2.6 34.5 + - - -
311A GLN 3.1 8.3 + - - +
329A CYS* 3.9 10.3 - - - -
330A LEU 4.0 2.2 - - - -
331A ALA* 4.1 6.1 - - + -
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Residues in contact with LEU 262 (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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139A VAL* 4.1 14.6 - - + -
140A PRO* 3.4 22.9 - - + +
141A ALA 4.1 15.7 - - - +
142A PRO* 4.0 19.6 - - + +
144A PHE* 4.1 23.1 - - + +
260A HIS* 3.4 12.0 + - + +
261A VAL* 1.3 74.0 - - - +
263A LYS* 1.3 62.8 + - + +
309A GLN* 3.3 17.6 - - - +
310A GLY* 4.6 1.1 + - - -
330A LEU* 2.9 26.6 + - + +
332A PHE* 3.8 35.4 - - + -
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Residues in contact with LYS 263 (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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142A PRO* 4.4 20.9 - - + +
144A PHE 5.3 3.1 - - - +
145A TYR* 4.2 24.6 - - + +
181A TYR* 5.0 9.4 + - - -
261A VAL* 3.5 1.1 - - - -
262A LEU* 1.3 85.2 - - + +
264A GLY* 1.3 67.7 + - - +
309A GLN* 3.4 13.5 - - - +
328A ASP* 5.3 6.5 - - - +
329A CYS* 3.4 8.3 - - - -
330A LEU* 3.0 39.5 + - + +
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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