Contacts of the helix formed by residues 292 - 304 (chain B) in PDB entry 2CUY
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 ASP 292 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ARG* 4.9 6.4 + - - -
292A ASP* 5.6 2.3 - - - +
19B ALA* 3.8 11.9 - - + -
20B LEU* 3.5 12.6 - - - +
290B VAL 3.9 0.4 - - - -
291B GLN* 1.3 91.3 + - + +
293B PRO* 1.3 71.6 - - + +
294B ASP* 3.4 9.8 + - - +
295B SER* 2.7 35.1 + - - -
296B LEU* 2.9 28.6 + - - +
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Residues in contact with PRO 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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294A ASP* 4.2 18.2 - - - +
19B ALA* 3.8 24.9 - - + +
20B LEU* 3.7 5.6 - - + -
23B ALA* 4.2 19.7 - - + -
292B ASP* 1.3 89.4 - - + +
294B ASP* 1.3 63.9 + - - +
296B LEU* 3.3 11.4 - - + +
297B ARG* 2.8 30.5 + - - +
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Residues in contact with ASP 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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19A ALA* 5.1 10.9 - - - +
292A ASP* 6.0 0.5 - - - +
293A PRO* 5.2 9.5 - - - +
294A ASP* 5.6 5.9 - - - +
292B ASP* 3.3 9.7 + - - +
293B PRO* 1.3 83.3 - - - +
295B SER* 1.3 63.3 + - - +
297B ARG* 3.2 19.6 + - - +
298B LYS* 3.1 30.5 + - + +
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Residues in contact with SER 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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288B LEU* 5.1 3.9 - - - +
289B SER 3.0 23.3 + - - -
290B VAL* 4.1 4.1 - - - +
291B GLN* 3.1 20.0 + - - +
292B ASP* 2.7 32.7 + - - -
294B ASP* 1.3 73.9 - - - +
296B LEU* 1.3 63.2 + - - +
298B LYS* 3.5 13.6 + - - +
299B ALA* 3.0 23.9 + - - +
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Residues in contact with LEU 296 (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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20B LEU* 4.0 18.8 - - + -
23B ALA* 6.5 0.4 - - + -
24B SER* 4.9 7.4 - - - -
73B ALA* 4.2 15.0 - - + +
74B PHE* 3.7 38.8 - - + +
77B ALA* 5.3 2.2 - - + -
290B VAL* 4.0 19.3 - - + +
292B ASP 2.9 18.2 + - - +
293B PRO* 3.3 9.6 - - + +
295B SER* 1.3 78.6 + - - +
297B ARG* 1.3 64.4 + - - +
299B ALA* 3.1 3.9 + - - +
300B LEU* 3.0 43.2 + - + +
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Residues in contact with ARG 297 (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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293B PRO 2.8 13.5 + - - +
294B ASP* 3.4 19.5 + - - +
296B LEU* 1.3 78.0 - - - +
298B LYS* 1.3 86.5 + - - +
300B LEU* 3.2 11.0 + - - +
301B GLU* 2.7 77.7 + - + +
304B ARG* 5.3 0.8 + - - +
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Residues in contact with LYS 298 (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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18A ARG* 6.0 4.6 - - - +
22A GLU* 5.4 8.3 + - - -
288B LEU* 4.2 16.1 - - + +
294B ASP* 3.1 18.9 + - + +
295B SER* 3.9 12.6 - - - +
297B ARG* 1.3 104.2 - - - +
299B ALA* 1.3 62.4 + - - +
301B GLU* 3.4 15.9 + - - +
302B VAL* 3.4 18.7 + - - +
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Residues in contact with ALA 299 (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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74B PHE* 4.1 13.5 - - + -
266B LEU* 4.0 14.1 - - + -
288B LEU* 4.1 7.5 - - + +
290B VAL* 3.5 24.9 - - + -
295B SER 3.0 18.3 + - - +
296B LEU 3.1 4.9 + - - +
298B LYS* 1.3 75.5 - - - +
300B LEU* 1.3 57.9 + - - +
302B VAL* 3.2 10.0 - - - +
303B GLU* 2.8 31.4 + - - +
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Residues in contact with LEU 300 (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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74B PHE* 3.5 43.1 - - + +
77B ALA* 3.6 27.1 - - + +
79B GLY* 3.8 13.2 - - - +
296B LEU* 3.0 33.0 + - + +
297B ARG* 3.5 10.1 - - - +
299B ALA* 1.3 75.8 - - - +
301B GLU* 1.3 63.6 + - - +
304B ARG* 2.8 62.4 + - + +
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Residues in contact with GLU 301 (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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297B ARG* 2.7 52.6 + - + +
298B LYS* 3.7 12.1 - - - +
299B ALA 3.3 0.4 - - - -
300B LEU* 1.3 76.8 - - - +
302B VAL* 1.3 63.6 + - + +
304B ARG* 4.5 14.3 + - - +
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Residues in contact with VAL 302 (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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264B ARG* 3.8 40.9 + - - +
266B LEU* 5.5 0.9 - - + -
286B GLU* 4.6 11.2 - - - +
288B LEU* 4.5 10.5 - - + -
298B LYS 3.5 13.0 - - - +
299B ALA* 3.2 17.7 - - - +
301B GLU* 1.3 83.3 - - + +
303B GLU* 1.3 68.3 + - + +
304B ARG 3.9 0.7 - - - -
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Residues in contact with GLU 303 (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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1B MET 4.1 15.4 + - - -
2B TYR* 3.2 44.4 + - + +
74B PHE* 3.6 12.7 - - + -
80B LYS* 3.0 48.7 + - + +
263B LYS* 5.6 0.3 + - - -
264B ARG* 3.0 29.4 + - - +
266B LEU* 4.4 6.1 - - + -
299B ALA 2.8 16.4 + - - +
300B LEU 3.7 0.4 - - - -
302B VAL* 1.3 84.4 - - + +
304B ARG* 1.3 58.4 + - - +
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Residues in contact with ARG 304 (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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77B ALA* 3.2 21.5 + - - +
78B GLY* 3.5 17.3 - - - +
79B GLY* 4.1 1.8 - - - -
80B LYS* 2.8 16.1 + - - -
297B ARG* 5.3 0.6 + - - +
300B LEU* 2.8 62.7 + - + +
301B GLU* 4.4 13.1 - - - +
302B VAL 3.9 0.6 - - - -
303B GLU* 1.3 72.6 - - - +
305B ALA* 1.3 81.4 + - - +
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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