Contacts of the helix formed by residues 227 - 239 (chain A) in PDB entry 5DQZ
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 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A ILE 4.4 2.7 + - - -
224A LYS 4.2 1.2 + - - -
225A PHE 3.4 0.2 - - - -
226A ASP* 1.3 90.1 + - - +
228A VAL* 1.3 67.5 + - - +
229A VAL 3.4 2.0 - - - -
230A PRO* 3.1 18.0 - - - +
231A LYS* 3.2 14.0 + - - +
254A ILE* 3.5 42.6 - - + +
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Residues in contact with VAL 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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183A ALA* 3.7 20.9 - - + +
184A THR 4.9 0.4 - - - +
187A LEU* 4.1 24.0 - - + -
223A ILE 5.6 0.2 - - - +
224A LYS* 3.5 13.9 + - - +
227A THR* 1.3 85.0 - - + +
229A VAL* 1.3 68.5 + - + +
231A LYS* 3.3 7.9 + - - +
232A ALA* 2.9 25.3 + - - +
247A VAL* 5.3 0.2 - - - +
251A CYS* 4.0 22.1 - - - -
254A ILE* 4.6 7.4 - - + -
255A PHE* 4.1 28.3 - - + -
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Residues in contact with VAL 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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149A TYR* 4.5 9.2 - - + +
152A LEU* 4.0 9.9 - - + -
180A ILE* 4.6 11.2 - - + -
183A ALA* 5.0 1.8 - - + -
184A THR* 4.6 10.8 - - + -
224A LYS* 3.4 39.7 + - + +
225A PHE* 4.2 18.2 - - + -
228A VAL* 1.3 78.8 - - + +
230A PRO* 1.4 73.4 - - + +
232A ALA* 3.0 9.6 + - - +
233A PHE* 3.0 47.9 + - + -
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Residues in contact with PRO 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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152A LEU* 4.0 20.6 - - + -
156A TYR* 3.6 36.3 - - + +
225A PHE 3.4 26.2 - - - +
226A ASP 4.1 6.7 - - - +
227A THR* 3.1 17.0 - - - +
229A VAL* 1.4 94.1 - - + +
231A LYS* 1.3 57.5 + - - +
233A PHE* 3.1 7.0 + - + +
234A GLU 2.9 22.3 + - - -
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Residues in contact with LYS 231 (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 THR 3.2 10.9 + - - +
228A VAL* 3.8 7.2 - - - +
229A VAL 3.2 0.4 - - - -
230A PRO* 1.3 76.2 - - - +
232A ALA* 1.3 61.4 + - - +
234A GLU* 3.4 31.2 - - - +
235A ILE* 2.9 39.8 + - + +
238A ARG* 4.6 7.4 - - - +
247A VAL* 5.7 1.3 - - + -
250A ALA* 3.8 30.4 + - + +
251A CYS* 6.0 2.5 - - - -
253A ASP* 5.5 4.2 - - - +
254A ILE* 3.5 34.4 - - + +
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Residues in contact with ALA 232 (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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176A ILE* 4.1 1.6 - - - -
179A CYS* 3.5 40.8 - - - +
180A ILE* 3.8 13.9 - - + +
183A ALA* 4.1 3.8 - - + -
228A VAL 2.9 14.4 + - - +
229A VAL* 3.2 13.5 - - - +
231A LYS* 1.3 76.9 - - - +
233A PHE* 1.3 56.6 + - - +
235A ILE* 4.1 0.2 - - - +
236A ALA* 2.9 28.4 + - - +
247A VAL* 4.5 8.4 - - - +
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Residues in contact with PHE 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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149A TYR* 3.8 23.1 - + - -
152A LEU* 3.9 20.4 - - + -
153A ALA* 3.6 33.9 - - + -
156A TYR* 3.9 16.8 - - + -
158A VAL* 3.7 21.7 - - + +
160A TRP* 4.3 14.8 - + - -
176A ILE* 3.7 31.6 - - + -
180A ILE* 4.2 7.9 - - + -
229A VAL* 3.0 45.0 + - + -
230A PRO 3.1 8.5 + - - +
232A ALA* 1.3 75.8 - - - +
234A GLU* 1.3 59.4 + - - +
236A ALA* 3.2 3.5 + - - +
237A ARG* 2.9 26.0 + - - +
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Residues in contact with GLU 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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156A TYR* 3.5 34.2 + - + -
230A PRO 2.9 8.4 + - - +
231A LYS* 3.4 32.2 - - - +
233A PHE* 1.3 76.9 - - - +
235A ILE* 1.3 57.6 + - - +
237A ARG* 3.2 7.8 + - - +
238A ARG* 3.0 62.7 + - + +
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Residues in contact with ILE 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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179A CYS* 4.5 3.4 - - - -
231A LYS* 2.9 22.0 + - + +
232A ALA 4.1 2.5 - - - +
234A GLU* 1.3 73.7 - - - +
236A ALA* 1.3 65.8 + - - +
238A ARG* 3.1 31.6 + - - +
239A ASN 3.1 17.7 + - - -
240A PRO* 3.4 26.6 - - + +
243A PRO* 4.1 3.1 - - + +
246A GLU* 3.4 35.7 - - + +
247A VAL* 3.6 31.0 - - + -
250A ALA* 3.7 16.2 - - + -
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Residues in contact with ALA 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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158A VAL* 4.4 8.7 - - + -
175A THR* 4.7 10.7 - - + +
176A ILE* 3.6 37.5 - - + +
179A CYS* 4.2 9.8 - - - -
232A ALA 2.9 20.5 + - - +
233A PHE 3.2 7.2 - - - +
235A ILE* 1.3 75.6 - - - +
237A ARG* 1.3 60.3 + - - +
239A ASN* 3.2 18.4 + - - +
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Residues in contact with ARG 237 (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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154A LYS 5.2 0.4 + - - -
155A GLN 4.5 4.9 + - - -
156A TYR* 2.4 47.1 + - + +
157A GLY* 3.2 18.3 + - - +
158A VAL* 4.0 9.1 - - + +
233A PHE 2.9 13.2 + - - +
234A GLU* 3.2 9.6 + - - +
236A ALA* 1.3 71.3 - - - +
238A ARG* 1.3 67.0 + - + +
239A ASN* 3.0 7.2 + - - +
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Residues in contact with ARG 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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231A LYS* 4.6 8.1 - - - +
234A GLU* 3.0 49.4 + - + +
235A ILE* 3.1 39.5 + - - +
237A ARG* 1.3 78.0 - - + +
239A ASN* 1.3 69.7 + - - +
240A PRO* 4.5 8.3 - - + +
246A GLU* 5.9 1.4 + - - -
250A ALA* 5.9 0.2 - - - +
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Residues in contact with ASN 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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175A THR* 5.0 13.0 + - - +
235A ILE 3.1 8.7 + - - -
236A ALA 3.2 12.9 + - - +
237A ARG 3.0 6.8 - - - +
238A ARG* 1.3 80.4 - - - +
240A PRO* 1.3 70.0 - - - +
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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