Contacts of the helix formed by residues 293 - 302 (chain E) in PDB entry 2CNW
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 293 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280E VAL* 5.6 1.4 - - - +
291E PRO 3.4 5.7 + - - +
292E PHE* 1.3 76.3 - - - +
294E PRO* 1.3 59.2 - - - +
295E GLU* 3.5 15.8 + - - +
296E ALA* 3.3 33.3 + - + +
297E PHE* 2.8 37.8 + - - +
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Residues in contact with PRO 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E VAL* 3.9 29.2 - - + +
76E LEU* 4.4 6.1 - - + -
77E GLU* 4.0 28.3 - - + +
292E PHE* 3.7 36.7 - - + +
293E ASP* 1.3 87.3 - - - +
295E GLU* 1.3 57.6 + - - +
297E PHE* 3.7 0.9 - - - +
298E VAL* 3.0 35.2 + - - +
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Residues in contact with GLU 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E VAL* 3.8 26.8 - - + +
77E GLU* 6.0 0.2 - - - +
82E ARG* 4.1 22.5 + - - +
86E ARG* 4.3 18.3 + - - +
92E PRO* 5.9 1.9 - - - +
293E ASP* 3.3 10.6 + - - +
294E PRO* 1.3 79.9 - - + +
296E ALA* 1.3 56.9 + - - +
298E VAL* 3.3 2.9 + - - +
299E GLU* 3.1 29.3 + - - +
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Residues in contact with ALA 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293E ASP* 3.3 29.6 + - + +
295E GLU* 1.3 79.1 - - - +
297E PHE* 1.3 58.2 + - - +
299E GLU* 4.0 9.1 - - - +
300E ALA* 3.1 29.5 + - - +
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Residues in contact with PHE 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E LEU* 3.7 28.9 - - + -
257E LEU* 4.1 25.6 - - + -
262E LYS 3.0 29.4 - - - -
263E GLY* 3.6 18.2 - - - -
266E LEU* 3.8 17.0 - - + -
267E ILE* 4.3 9.9 - - + -
280E VAL* 5.4 0.7 - - + -
292E PHE* 3.6 22.0 - + + -
293E ASP 2.8 18.1 + - - +
294E PRO 3.7 3.1 - - - +
296E ALA* 1.3 77.7 - - - +
298E VAL* 1.3 58.8 + - + +
300E ALA* 3.5 7.1 + - + +
301E LEU* 2.9 44.2 + - + +
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Residues in contact with VAL 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E LYS* 3.9 39.3 - - + -
72E LEU* 3.7 35.7 - - + -
73E VAL* 3.8 17.3 - - + +
76E LEU* 3.9 18.2 - - + -
267E ILE* 5.8 0.7 - - + -
294E PRO 3.0 19.3 + - - +
295E GLU 3.3 1.5 + - - +
297E PHE* 1.3 76.3 - - + +
299E GLU* 1.3 67.0 + - - +
301E LEU* 3.1 17.4 + - + +
302E LEU* 3.1 15.5 + - + +
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Residues in contact with GLU 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E LYS* 4.2 27.5 - - + +
295E GLU 3.1 16.0 + - - +
296E ALA* 4.0 9.1 - - - +
298E VAL* 1.3 75.2 - - - +
300E ALA* 1.3 57.7 + - - +
302E LEU* 2.9 20.4 + - - +
303E GLU* 2.9 45.1 + - + +
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Residues in contact with ALA 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E LYS* 2.7 34.2 + - + +
296E ALA 3.1 17.7 + - - +
297E PHE* 3.6 8.5 - - + +
299E GLU* 1.3 79.4 + - - +
301E LEU* 1.3 58.0 + - - +
302E LEU 3.3 0.7 + - - -
303E GLU* 3.3 19.5 + - - +
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Residues in contact with LEU 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ALA* 4.8 6.6 - - - +
39E LEU* 3.9 21.8 - - + -
42E ALA* 3.8 20.3 - - + +
44E VAL* 4.2 6.1 - - + -
72E LEU* 4.8 9.2 - - + -
262E LYS* 3.6 27.5 - - + +
264E GLY* 3.9 28.3 - - - -
267E ILE* 4.7 6.5 - - + -
297E PHE* 2.9 38.1 + - + +
298E VAL* 3.1 8.2 + - - +
300E ALA* 1.3 76.5 - - - +
302E LEU* 1.3 76.6 + - + +
303E GLU 3.5 0.7 - - - +
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Residues in contact with LEU 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E TRP* 4.4 24.6 + - + +
35E LEU* 4.4 20.4 - - + -
38E ALA* 4.8 13.9 - - + -
39E LEU* 4.5 6.1 - - + -
68E VAL* 3.9 17.5 - - + -
69E LYS* 3.8 39.0 - - + -
72E LEU* 5.0 1.3 - - + -
298E VAL* 3.6 13.7 - - + +
299E GLU 2.9 11.1 + - - +
301E LEU* 1.3 98.9 - - + +
303E GLU* 1.3 60.4 + - - +
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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