Contacts of the helix formed by residues 292 - 304 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ALA* 4.1 10.8 - - + -
20A LEU* 3.6 11.5 - - - +
291A GLN* 1.3 90.9 + - - +
293A PRO* 1.3 71.8 - - + +
294A ASP* 3.4 9.2 + - - +
295A SER* 2.8 43.0 + - - -
296A LEU* 2.8 27.5 + - - +
292B ASP* 5.6 2.4 - - - +
294B ASP* 6.0 0.7 - - - +
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Residues in contact with PRO 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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19A ALA* 3.5 23.8 - - + +
20A LEU* 3.7 9.6 - - + -
23A ALA* 3.8 29.4 - - + -
292A ASP* 1.3 87.6 - - + +
294A ASP* 1.3 65.8 + - - +
296A LEU* 3.0 10.8 + - + +
297A ARG* 2.8 35.7 + - + +
294B ASP* 5.2 8.7 - - - +
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Residues in contact with ASP 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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292A ASP* 3.3 8.3 + - - +
293A PRO* 1.3 82.4 - - - +
295A SER* 1.3 63.8 + - - +
297A ARG* 3.4 7.6 + - - +
298A LYS* 3.1 25.8 + - - +
293B PRO* 4.2 20.3 - - - +
294B ASP* 5.6 6.1 - - - +
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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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288A LEU* 5.2 1.9 - - - +
289A SER 2.8 25.5 - - - +
290A VAL* 4.4 2.8 - - - +
291A GLN* 2.8 27.3 + - - +
292A ASP* 2.8 34.6 + - - -
294A ASP* 1.3 72.6 - - - +
296A LEU* 1.3 62.4 + - - +
298A LYS* 3.2 9.5 + - - +
299A ALA* 3.0 22.3 + - - +
18B ARG* 5.6 7.0 - - - -
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Residues in contact with LEU 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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20A LEU* 4.0 18.8 - - + -
24A SER* 5.5 3.4 - - - -
73A ALA* 4.2 19.7 - - + +
74A PHE* 3.4 46.7 - - + +
77A ALA* 4.6 7.4 - - + -
290A VAL* 3.8 19.5 - - + +
292A ASP 2.8 13.8 + - - +
293A PRO* 3.0 12.1 + - + +
295A SER* 1.3 75.8 + - - +
297A ARG* 1.3 77.7 + - - +
299A ALA* 3.0 15.0 + - - +
300A LEU* 3.0 19.2 + - + +
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Residues in contact with ARG 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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77A ALA* 4.0 21.6 + - - +
293A PRO* 2.8 32.9 + - + +
294A ASP* 3.8 7.6 - - - +
296A LEU* 1.3 83.8 - - - +
298A LYS* 1.3 64.2 + - - +
300A LEU* 3.1 24.8 + - - +
301A GLU* 3.0 35.3 + - + +
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Residues in contact with LYS 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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286A GLU* 4.9 3.4 + - - -
288A LEU* 3.5 24.6 - - + +
294A ASP 3.1 14.8 + - - +
295A SER* 3.2 13.0 + - - +
297A ARG* 1.3 76.4 - - - +
299A ALA* 1.3 63.6 + - - +
301A GLU* 3.3 23.3 + - + +
302A VAL* 3.2 45.9 + - + +
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A PHE* 3.7 15.0 - - + -
266A LEU* 3.9 12.6 - - + -
288A LEU* 4.0 7.1 - - + +
290A VAL* 3.6 29.2 - - + -
295A SER 3.0 7.6 + - - +
296A LEU 3.0 9.4 + - - +
298A LYS* 1.3 77.2 - - - +
300A LEU* 1.3 60.3 + - - +
302A VAL* 2.9 28.8 - - - +
303A GLU* 3.1 10.7 + - - +
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Residues in contact with LEU 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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74A PHE* 3.7 22.2 - - + +
77A ALA* 3.5 32.3 - - + +
78A GLY 4.2 1.6 - - - -
79A GLY* 3.6 31.0 - - - +
296A LEU* 3.0 20.7 + - + +
297A ARG* 3.1 35.9 + - - +
299A ALA* 1.3 77.0 - - - +
301A GLU* 1.3 52.5 + - + +
303A GLU* 3.1 4.3 + - + +
304A ARG* 2.6 44.6 + - + +
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Residues in contact with GLU 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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297A ARG* 3.0 30.5 + - + +
298A LYS* 3.4 29.8 + - + +
299A ALA 3.3 0.2 - - - -
300A LEU* 1.3 78.7 - - + +
302A VAL* 1.3 64.2 + - + +
304A ARG* 3.3 12.0 + - - -
305A ALA* 3.6 22.5 + - + +
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Residues in contact with VAL 302 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A ARG* 3.7 38.3 + - - +
266A LEU* 5.0 1.8 - - + -
286A GLU* 3.7 27.4 - - - +
288A LEU* 4.1 10.5 - - + -
298A LYS* 3.3 31.2 - - - +
299A ALA* 2.9 27.1 - - - +
301A GLU* 1.3 77.3 - - + +
303A GLU* 1.3 61.1 + - + +
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Residues in contact with GLU 303 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 3.4 22.7 + - - +
2A TYR* 3.5 28.6 - - + -
74A PHE* 4.4 13.5 - - + -
80A LYS* 5.0 11.0 + - - +
264A ARG* 2.8 39.3 + - - +
266A LEU* 4.6 3.4 - - + -
299A ALA 3.5 13.5 - - - +
300A LEU* 3.1 7.2 + - + +
302A VAL* 1.3 81.3 - - + +
304A ARG* 1.3 68.3 + - + +
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Residues in contact with ARG 304 (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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78A GLY 4.2 14.3 + - - +
80A LYS* 3.1 49.6 - - - +
300A LEU* 2.6 30.5 + - - +
301A GLU 3.3 3.5 + - - -
303A GLU* 1.3 81.2 + - + +
305A ALA* 1.3 69.7 + - - +
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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