Contacts of the helix formed by residues 294 - 306 (chain R) in PDB entry 6DDE
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 THR 294 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241R PHE* 3.9 16.8 - - - -
290R ILE* 3.0 25.8 + - - -
291R VAL* 5.1 1.1 - - - -
293R TRP* 1.3 77.3 - - - +
295R PRO* 1.4 68.2 - - - +
297R HIS* 3.1 6.1 + - - +
298R ILE* 2.9 35.3 + - - +
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Residues in contact with PRO 295 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291R VAL 4.0 7.6 - - - +
292R CYS 3.7 13.2 - - - +
294R THR* 1.4 92.8 - - - +
296R ILE* 1.3 58.4 + - - +
298R ILE* 4.2 7.6 - - + +
299R TYR* 2.9 33.7 + - + +
321R CYS* 4.8 13.2 - - + +
324R LEU* 3.7 22.7 - - + -
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Residues in contact with ILE 296 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D TYR* 3.8 31.4 - - + +
2D DAL 4.2 8.3 - - + -
151R MET* 6.0 0.4 - - + -
292R CYS 4.6 0.7 - - - +
293R TRP* 3.6 34.8 - - + +
295R PRO* 1.3 79.8 - - - +
297R HIS* 1.3 73.7 + - + +
299R TYR* 5.1 0.8 - - - +
300R VAL* 3.4 23.0 + - - +
318R TRP* 4.4 11.8 + - - +
321R CYS* 3.9 16.0 + - + +
322R ILE* 3.7 39.9 - - + +
325R GLY* 4.3 6.3 - - - -
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Residues in contact with HIS 297 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D TYR* 4.0 19.0 + + - -
151R MET* 3.6 31.1 - - + +
236R VAL* 4.3 14.1 - - + -
237R PHE* 3.4 32.5 - - + -
240R ALA* 4.4 6.1 + - + -
241R PHE* 3.7 28.3 - + + +
293R TRP* 3.1 32.4 - - + +
294R THR 3.1 6.9 + - - +
296R ILE* 1.3 88.0 - - + +
298R ILE* 1.3 62.3 + - - +
299R TYR 3.5 0.2 - - - -
300R VAL* 3.4 6.5 - - - +
301R ILE* 3.3 23.7 - - - +
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Residues in contact with ILE 298 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237R PHE* 4.4 19.3 - - + -
241R PHE* 5.4 6.3 - - + -
294R THR* 2.9 29.3 + - - +
295R PRO* 3.4 6.7 + - + +
297R HIS* 1.3 77.3 - - - +
299R TYR* 1.3 60.4 + - - +
301R ILE* 3.2 6.5 + - + +
302R ILE* 3.0 47.6 + - + +
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Residues in contact with TYR 299 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295R PRO* 2.9 17.5 + - + +
296R ILE* 5.1 0.9 - - - +
298R ILE* 1.3 79.1 - - - +
300R VAL* 1.3 58.4 + - - +
302R ILE* 4.2 21.3 - - + -
303R LYS* 2.9 43.7 + - + +
308R ILE* 3.6 16.6 - - + +
314R GLN* 2.3 38.5 + - + -
318R TRP* 3.3 55.3 - + + +
321R CYS* 5.8 1.8 - - + -
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Residues in contact with VAL 300 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D TYR* 3.6 25.8 - - + +
2D DAL 4.1 22.7 - - + -
233R LYS* 4.0 23.8 + - + +
237R PHE* 5.4 1.3 - - + -
296R ILE 3.4 19.9 + - - +
297R HIS* 3.4 23.6 - - + +
299R TYR* 1.3 80.2 - - - +
301R ILE* 1.3 70.3 + - + +
303R LYS* 4.3 7.6 - - + +
304R ALA* 3.9 16.3 + - - +
318R TRP* 5.6 3.5 - - + +
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Residues in contact with ILE 301 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233R LYS* 4.1 29.6 - - + +
234R ILE* 4.7 12.6 - - + +
237R PHE* 4.0 24.9 - - + -
297R HIS 3.3 17.5 - - - +
298R ILE* 3.2 8.1 + - + +
299R TYR 3.1 0.2 - - - -
300R VAL* 1.3 85.6 - - + +
302R ILE* 1.3 62.1 + - + +
303R LYS 3.3 0.4 - - - -
304R ALA* 3.2 7.6 + - + +
305R LEU* 2.9 31.8 + - + +
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Residues in contact with ILE 302 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298R ILE* 3.0 42.3 + - + +
299R TYR* 3.3 22.4 + - + +
301R ILE* 1.3 79.0 - - + +
303R LYS* 1.3 58.4 + - - +
305R LEU* 4.4 4.7 - - - +
306R ILE* 3.0 50.9 + - + +
308R ILE* 6.4 0.9 - - + -
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Residues in contact with LYS 303 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ETA 2.9 32.8 + - - -
233R LYS* 5.2 3.4 - - - +
299R TYR* 2.9 38.9 + - + +
300R VAL* 4.6 8.3 - - + +
302R ILE* 1.3 78.8 - - - +
304R ALA* 1.3 58.4 + - - +
306R ILE* 3.1 17.3 - - - +
307R THR* 4.8 3.1 + - - -
308R ILE* 4.9 17.5 - - + -
318R TRP* 3.7 19.8 - - + -
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Residues in contact with ALA 304 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230R ASN* 5.0 10.8 - - - +
233R LYS* 3.2 34.9 - - + +
300R VAL 3.9 6.8 + - - +
301R ILE* 3.2 14.9 + - + +
303R LYS* 1.3 78.7 - - - +
305R LEU* 1.3 64.3 + - - +
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Residues in contact with LEU 305 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301R ILE* 2.9 20.7 + - + +
302R ILE* 4.0 4.5 - - - +
304R ALA* 1.3 80.2 - - - +
306R ILE* 1.3 69.8 + - + +
307R THR* 4.3 0.5 + - - -
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Residues in contact with ILE 306 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302R ILE* 3.0 42.3 + - + +
303R LYS* 3.1 12.7 - - - +
305R LEU* 1.3 85.3 - - + +
307R THR* 1.3 63.5 + - - +
308R ILE* 3.4 26.2 + - + +
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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