Contacts of the helix formed by residues 222 - 243 (chain E) in PDB entry 4P9U
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 ASN 222 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E TYR 3.8 2.9 - - - +
220E PHE 3.1 0.6 - - - -
221E SER* 1.3 81.5 - - - +
223E PRO* 1.3 70.7 - - - +
224E GLN* 3.0 33.7 + - - +
225E ALA* 3.0 17.5 + - + +
226E ARG* 3.3 14.9 + - - +
262E ILE* 4.4 4.0 - - - +
265E GLN* 3.5 27.3 + - - +
266E MET* 3.6 33.7 - - + +
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Residues in contact with PRO 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E LEU* 5.3 2.2 - - + +
221E SER 3.7 7.6 - - - +
222E ASN* 1.3 90.3 - - - +
224E GLN* 1.3 58.9 + - - +
226E ARG* 3.1 36.4 + - + +
227E GLU* 3.0 26.0 + - - +
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Residues in contact with GLN 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222E ASN* 3.0 21.8 + - - +
223E PRO* 1.3 78.7 - - - +
225E ALA* 1.3 59.2 + - - +
227E GLU* 4.1 6.5 + - - +
228E LEU* 3.6 27.4 + - - +
262E ILE* 3.7 13.8 - - + +
265E GLN* 4.0 19.7 + - - +
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Residues in contact with ALA 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219E TYR* 3.4 50.9 + - + +
220E PHE* 4.4 2.9 - - + -
222E ASN* 3.0 12.7 + - + +
224E GLN* 1.3 77.6 - - - +
226E ARG* 1.3 59.9 + - - +
227E GLU 3.2 2.0 - - - -
228E LEU* 3.3 4.0 + - - +
229E ALA* 2.9 29.4 + - - +
262E ILE* 3.7 17.2 - - + +
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Residues in contact with ARG 226 (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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138E LEU* 3.8 25.5 - - + +
174E GLU* 5.0 11.3 + - - -
177E ILE* 3.7 30.9 - - - +
178E ALA 4.8 0.4 - - - +
181E PHE* 3.2 45.1 - - + -
220E PHE* 2.8 48.1 + - + +
221E SER* 3.8 16.6 + - - +
222E ASN 3.5 8.7 - - - +
223E PRO* 3.1 38.5 + - - +
225E ALA* 1.3 77.0 - - - +
227E GLU* 1.3 57.0 + - - +
229E ALA 3.3 0.2 + - - -
230E MET* 3.0 25.8 + - - +
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Residues in contact with GLU 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E LEU* 4.6 3.5 - - + +
223E PRO 3.0 14.5 + - - +
224E GLN* 4.4 6.5 - - - +
225E ALA 3.2 0.2 - - - -
226E ARG* 1.3 76.1 - - - +
228E LEU* 1.3 73.1 + - + +
230E MET* 3.4 17.5 + - + +
231E GLU* 3.0 27.3 + - + +
234E ARG* 4.7 2.6 + - - +
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Residues in contact with LEU 228 (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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219E TYR* 5.6 1.1 - - - +
224E GLN 3.6 14.5 + - - +
225E ALA* 3.3 9.0 + - - +
227E GLU* 1.3 89.8 - - + +
229E ALA* 1.3 61.1 + - - +
231E GLU* 3.7 8.5 - - + +
232E PHE* 2.9 29.8 + - - +
255E TYR* 3.8 12.7 - - + -
258E ALA* 3.7 32.1 - - + -
259E SER* 4.7 1.3 - - - +
262E ILE* 3.9 20.2 - - + -
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Residues in contact with ALA 229 (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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181E PHE* 3.3 28.9 - - + -
220E PHE* 4.0 6.1 - - + -
225E ALA 2.9 16.1 + - - +
226E ARG 3.5 0.7 - - - +
227E GLU 3.2 0.2 - - - -
228E LEU* 1.3 78.0 - - - +
230E MET* 1.3 57.6 + - - +
232E PHE* 3.2 2.3 + - - +
233E TYR* 2.9 45.6 + - - +
255E TYR* 3.9 23.3 - - - +
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Residues in contact with MET 230 (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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132E ILE* 5.0 4.7 - - + +
135E CYS* 3.4 32.5 - - + +
136E GLU* 3.8 15.9 - - - +
138E LEU* 3.7 26.2 - - + -
139E VAL* 6.2 2.2 - - + -
181E PHE* 3.6 14.1 - - + -
226E ARG 3.0 16.7 + - - +
227E GLU* 3.8 14.6 - - + +
228E LEU 3.3 0.2 - - - -
229E ALA* 1.3 76.4 - - - +
231E GLU* 1.3 56.6 + - - +
233E TYR* 3.1 12.7 + - + +
234E ARG* 3.0 61.6 + - - +
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Residues in contact with GLU 231 (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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227E GLU* 3.0 18.8 + - + +
228E LEU* 3.7 9.9 - - + +
230E MET* 1.3 74.9 - - - +
232E PHE* 1.3 58.0 + - - +
234E ARG* 3.3 21.6 + - - +
235E GLN* 2.9 62.5 + - - +
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Residues in contact with PHE 232 (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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113E MET* 5.0 1.6 - - + -
189E PHE* 3.7 28.7 - + - -
228E LEU 2.9 17.7 + - - +
229E ALA 3.3 4.0 - - - +
231E GLU* 1.3 77.0 - - - +
233E TYR* 1.3 69.7 + + - +
235E GLN* 3.2 9.1 + - - +
236E LEU* 2.9 58.7 + - + +
251E VAL* 3.6 27.4 - - + -
252E ILE* 4.0 20.2 - - + -
255E TYR* 3.4 54.7 - + + -
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Residues in contact with TYR 233 (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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128E MET* 3.6 6.9 - - - +
131E VAL* 4.1 20.2 - - + -
132E ILE* 3.6 23.1 - - + +
135E CYS* 4.3 7.4 - - - -
181E PHE* 3.9 22.6 - + - -
185E ASP* 2.4 47.3 + - - +
188E LEU* 3.5 33.0 - - + -
189E PHE* 4.7 1.8 - + - -
229E ALA* 2.9 35.2 + - + +
230E MET* 3.3 15.7 - - + +
232E PHE* 1.3 94.2 - + - +
234E ARG* 1.3 57.4 + - - +
236E LEU* 3.3 6.0 + - + -
237E LEU* 2.9 26.9 + - - +
255E TYR* 5.5 0.2 - - - -
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Residues in contact with ARG 234 (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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132E ILE* 3.9 29.6 - - + +
136E GLU* 4.6 9.1 + - - -
227E GLU* 4.7 3.2 + - - +
230E MET* 3.0 66.4 + - - +
231E GLU* 3.6 21.8 + - - +
232E PHE 3.3 0.2 - - - -
233E TYR* 1.3 72.6 - - - +
235E GLN* 1.3 62.0 + - - +
237E LEU* 3.3 5.6 + - + +
238E ALA* 2.9 27.5 + - - +
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Residues in contact with GLN 235 (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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231E GLU* 2.9 52.8 + - - +
232E PHE* 3.2 9.7 + - - +
234E ARG* 1.3 74.1 - - + +
236E LEU* 1.3 60.3 + - - +
238E ALA* 3.2 8.7 + - - +
239E VAL* 2.9 33.3 + - - +
251E VAL* 3.6 32.1 - - + +
254E GLN* 5.0 7.2 + - - +
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Residues in contact with LEU 236 (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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113E MET* 4.0 26.9 - - + -
117E PHE* 3.9 6.3 - - + -
128E MET* 3.4 18.6 - - + -
188E LEU* 4.4 13.5 - - + -
192E LEU* 4.9 1.6 - - + -
232E PHE* 2.9 60.2 + - + +
233E TYR* 3.3 6.3 + - - +
235E GLN* 1.3 76.2 - - - +
237E LEU* 1.3 58.8 + - - +
239E VAL* 3.1 7.2 + - - +
240E CYS* 2.9 29.6 + - - +
248E LEU* 3.7 28.3 - - + -
251E VAL* 4.1 5.8 - - + -
252E ILE* 4.4 1.8 - - + -
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Residues in contact with LEU 237 (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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125E GLU* 4.0 26.7 - - + +
128E MET* 3.2 17.0 - - + +
129E ILE* 3.6 33.2 - - + -
132E ILE* 4.0 15.9 - - + -
233E TYR 2.9 14.9 + - - +
234E ARG* 3.5 11.2 - - + +
236E LEU* 1.3 77.0 - - - +
238E ALA* 1.3 58.2 + - - +
240E CYS* 3.3 1.4 + - + -
241E GLN* 2.9 61.2 + - - +
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Residues in contact with ALA 238 (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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234E ARG 2.9 13.6 + - - +
235E GLN* 3.2 12.5 + - - +
237E LEU* 1.3 75.4 - - - +
239E VAL* 1.3 57.9 + - + +
241E GLN* 3.9 10.8 - - - +
242E SER* 2.9 32.6 + - - -
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Residues in contact with VAL 239 (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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117E PHE* 4.1 9.6 - - + -
235E GLN 2.9 21.9 + - - +
236E LEU* 3.1 11.2 + - - +
238E ALA* 1.3 77.1 - - + +
240E CYS* 1.3 58.0 + - - +
242E SER* 3.3 4.5 + - - -
243E GLY* 2.8 28.6 + - - -
244E GLU 3.8 18.6 + - - +
245E ARG* 4.4 5.3 - - + +
247E HIS* 4.9 8.3 - - + +
248E LEU* 4.0 34.5 - - + +
251E VAL* 4.3 20.6 - - + -
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Residues in contact with CYS 240 (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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117E PHE* 3.5 45.7 - - + +
121E LYS* 3.1 43.9 - - - +
124E ALA* 4.0 3.6 - - - -
125E GLU* 3.4 18.4 - - + +
128E MET* 4.6 4.9 - - - -
236E LEU 2.9 15.2 + - - +
237E LEU* 3.9 4.0 - - + +
239E VAL* 1.3 77.9 - - - +
241E GLN* 1.3 63.1 + - - +
243E GLY* 3.5 9.8 + - - -
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Residues in contact with GLN 241 (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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121E LYS* 4.2 12.5 + - - -
125E GLU* 3.1 27.1 + - - +
129E ILE* 4.5 10.1 - - - +
237E LEU* 2.9 49.6 + - + +
238E ALA* 3.9 9.4 - - - +
240E CYS* 1.3 74.3 - - - +
242E SER* 1.3 66.1 + - - +
243E GLY* 3.4 0.3 + - - -
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Residues in contact with SER 242 (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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238E ALA 2.9 20.1 + - - -
239E VAL* 3.8 4.5 - - - -
241E GLN* 1.3 78.3 - - - +
243E GLY* 1.3 61.8 + - - +
244E GLU* 3.6 17.4 + - - +
247E HIS* 5.4 3.9 - - - -
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Residues in contact with GLY 243 (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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117E PHE 6.1 0.7 - - - -
121E LYS* 6.1 2.0 - - - -
239E VAL 2.8 11.6 + - - -
240E CYS* 3.5 9.2 + - - -
241E GLN 3.2 2.3 - - - -
242E SER* 1.3 78.5 - - - +
244E GLU* 1.3 60.8 + - - +
245E ARG* 3.7 19.3 + - - +
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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