Contacts of the helix formed by residues 227 - 239 (chain A) in PDB entry 4DAJ
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 GLU 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A PHE 4.5 1.0 + - - +
225A LEU 3.2 1.0 - - - -
226A SER* 1.3 80.5 - - - +
228A PRO* 1.3 82.4 - - - +
229A THR* 3.2 18.5 + - - +
230A ILE* 3.4 22.2 - - + +
231A THR* 2.9 26.5 + - - -
163B PHE* 5.7 0.2 - - + -
166B TYR* 4.0 21.2 + - - -
167B PHE* 3.5 36.0 - - + -
170B THR* 4.7 5.2 + - - +
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Residues in contact with PRO 228 (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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226A SER 3.5 6.9 - - - +
227A GLU* 1.3 99.4 - - - +
229A THR* 1.3 60.3 + - + +
231A THR* 3.6 7.4 - - - +
232A PHE* 2.9 26.6 + - - +
510A VAL* 4.9 2.0 - - + +
513A ASN* 3.3 39.9 - - - +
514A THR* 3.5 18.6 + - - +
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Residues in contact with THR 229 (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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227A GLU* 3.6 17.0 + - - +
228A PRO* 1.3 77.3 - - + +
230A ILE* 1.3 65.3 + - - +
231A THR 2.9 1.1 - - - -
232A PHE* 2.6 29.2 + - - +
233A GLY* 2.9 12.0 + - - -
514A THR* 4.6 15.0 - - + +
163B PHE* 3.2 25.1 - - - -
166B TYR* 5.4 4.4 - - + +
245B ILE* 4.2 9.9 - - - +
248B ILE* 5.5 9.0 - - + -
249B LEU* 4.0 21.7 - - + +
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Residues in contact with ILE 230 (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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224A PHE* 3.4 46.7 - - + +
225A LEU* 4.3 4.9 - - + -
227A GLU* 3.4 31.6 - - + +
229A THR* 1.3 77.0 + - - +
231A THR* 1.3 58.6 + - - +
233A GLY* 4.0 0.8 - - - +
234A THR* 3.0 37.9 + - - +
163B PHE* 4.2 19.6 - - + -
167B PHE* 5.8 2.5 - - + -
245B ILE* 4.7 5.3 - - - +
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Residues in contact with THR 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 2.9 43.6 + - + +
227A GLU 2.9 12.4 + - - -
228A PRO* 3.6 7.2 - - + +
229A THR 2.9 0.6 - - - -
230A ILE* 1.3 77.0 - - - +
232A PHE* 1.3 66.5 + - - +
234A THR* 3.8 1.1 - - - -
235A ALA* 2.9 23.0 + - - +
510A VAL* 3.6 22.7 - - + -
2000A 0HK 4.0 22.1 - - + +
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Residues in contact with PHE 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A PRO 2.9 8.3 + - - +
229A THR* 2.6 17.5 + - - +
231A THR* 1.3 68.9 - - - +
233A GLY* 1.3 66.1 + - - +
235A ALA* 2.9 5.7 + - - +
236A ILE* 2.9 54.7 + - + +
240A TYR* 5.0 6.1 - + - -
510A VAL* 4.2 8.3 - - + -
511A LEU* 3.6 44.4 - - + -
514A THR* 3.2 31.4 - - + +
515A PHE* 5.5 1.1 - + - -
244B THR* 4.9 7.4 - - - -
245B ILE* 5.1 7.9 - - + -
248B ILE* 4.1 25.6 - - + -
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Residues in contact with GLY 233 (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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229A THR 2.9 12.5 + - - -
230A ILE 4.0 0.2 - - - -
232A PHE* 1.3 76.2 - - - +
234A THR* 1.3 56.5 + - - +
236A ILE* 3.3 4.9 + - - +
237A ALA* 2.9 30.1 + - - +
241B MET* 3.5 21.0 - - - +
245B ILE* 3.6 26.9 - - - +
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Residues in contact with THR 234 (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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199A TRP* 3.5 35.0 - - + -
224A PHE* 5.6 3.3 - - + -
225A LEU* 5.0 7.4 - - + +
230A ILE* 3.0 27.5 + - - +
231A THR* 4.0 4.3 - - - -
233A GLY* 1.3 73.2 - - - +
235A ALA* 1.3 60.7 + - - +
237A ALA* 4.0 5.1 - - + +
238A ALA* 2.9 28.9 + - + +
2000A 0HK 4.2 6.3 - - + -
241B MET* 5.0 2.0 - - - +
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Residues in contact with ALA 235 (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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231A THR 2.9 17.8 + - - +
232A PHE* 3.4 5.4 - - + +
234A THR* 1.3 73.1 - - - +
236A ILE* 1.3 57.2 + - - +
239A PHE* 2.5 40.0 + - - +
240A TYR* 3.8 9.6 - - + -
507A ASN* 3.6 17.7 - - - +
510A VAL* 4.4 15.9 - - + -
2000A 0HK 3.8 21.5 - - + -
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Residues in contact with ILE 236 (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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232A PHE* 2.9 53.0 + - + +
233A GLY* 3.6 8.3 - - - +
235A ALA* 1.3 75.8 - - - +
237A ALA* 1.3 60.8 + - - +
240A TYR* 2.7 36.8 + - + -
241A MET 2.7 32.4 + - - +
236B ILE* 4.7 13.0 - - + -
241B MET* 4.5 19.7 - - + -
244B THR* 4.9 8.5 - - - +
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Residues in contact with ALA 237 (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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233A GLY 2.9 17.6 + - - +
234A THR* 4.0 5.6 - - - +
236A ILE* 1.3 79.0 - - - +
238A ALA* 1.3 57.5 + - + +
241A MET* 3.5 17.6 - - + +
242A PRO* 3.0 23.6 - - - +
236B ILE* 6.0 0.4 - - - -
237B ALA* 5.0 15.0 - - + +
241B MET* 3.7 20.4 - - + -
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Residues in contact with ALA 238 (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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152A ASN* 4.8 4.5 - - - +
155A VAL* 4.2 13.9 - - - +
199A TRP* 4.4 15.9 - - + -
234A THR* 2.9 21.8 + - + +
235A ALA 4.3 0.4 - - - +
237A ALA* 1.3 76.5 - - + +
239A PHE* 1.3 57.8 + - - +
242A PRO* 3.8 12.7 - - - +
2000A 0HK 3.7 32.6 - - + -
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Residues in contact with PHE 239 (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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235A ALA 2.5 19.6 + - - +
236A ILE 3.3 0.4 + - - -
238A ALA* 1.3 76.5 - - - +
240A TYR* 1.3 93.5 + + - +
242A PRO* 3.0 5.0 - - - +
243A VAL* 2.9 52.5 + - + +
499A PHE* 3.9 9.2 - + - -
500A ILE* 4.7 1.8 - - + -
503A TRP* 3.3 31.9 - + + -
504A THR* 3.3 35.9 - - + -
507A ASN* 3.1 51.8 - - + +
2000A 0HK 3.5 5.6 - - - +
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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