Contacts of the helix formed by residues 224 - 238 (chain G) in PDB entry 5EEA
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 SER 224 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222G PRO 3.9 1.4 + - - -
223G TYR* 1.3 75.5 - - - +
225G LYS* 1.3 55.6 + - - +
226G GLY 3.8 1.7 + - - -
227G GLN* 2.6 39.7 + - - +
228G LEU* 2.8 35.8 + - - +
219J LYS* 4.8 1.6 + - - -
220J ARG 5.0 1.0 + - - -
221J ILE* 4.7 10.2 - - - +
222J PRO* 3.7 30.3 - - - -
13L A 3.9 9.0 + - - -
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Residues in contact with LYS 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224G SER* 1.3 74.3 - - - +
226G GLY* 1.3 58.1 + - - +
228G LEU* 3.7 8.0 - - - +
229G ARG* 2.9 50.4 + - - +
12L A 5.8 0.6 - - - +
13L A 3.8 45.8 + - - +
14L C 4.1 20.3 - - - +
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Residues in contact with GLY 226 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224G SER 3.3 0.2 - - - -
225G LYS* 1.3 71.9 - - - +
227G GLN* 1.3 65.5 + - - +
229G ARG* 3.4 21.4 + - - +
230G GLU* 3.3 22.5 + - - +
253G THR* 4.9 0.2 - - - +
219J LYS* 3.9 20.0 + - - -
12L A 5.1 0.2 - - - -
13L A 2.6 24.2 + - - -
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Residues in contact with GLN 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222G PRO 4.8 0.3 - - - +
223G TYR* 3.3 15.5 - - + +
224G SER* 2.6 43.8 + - - +
226G GLY* 1.3 73.9 - - - +
228G LEU* 1.3 68.1 + - - +
230G GLU* 3.1 4.7 + - - +
231G LEU* 3.1 26.8 + - - +
253G THR* 2.9 44.0 + - + +
254G SER* 4.9 1.6 - - - -
255G LEU* 3.6 26.9 - - + +
219J LYS* 4.0 7.2 - - - +
221J ILE* 4.2 22.9 - - + +
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Residues in contact with LEU 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223G TYR* 3.8 33.4 - - + +
224G SER 2.8 21.2 + - - +
225G LYS* 3.7 7.4 - - - +
227G GLN* 1.3 73.5 - - - +
229G ARG* 1.4 54.3 + - - +
231G LEU* 3.0 5.6 + - + +
232G GLU* 2.8 43.9 + - + +
263G TRP* 3.9 28.3 - - + +
8H T 5.4 2.7 - - - +
9H T 4.0 13.5 - - - +
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Residues in contact with ARG 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225G LYS* 2.9 39.1 + - - +
226G GLY* 3.4 26.7 + - - +
227G GLN 3.2 0.4 - - - -
228G LEU* 1.4 76.3 - - - +
230G GLU* 1.3 61.7 + - - +
232G GLU* 4.2 4.3 - - - +
233G ARG* 3.0 31.5 + - + +
12L A 5.5 0.8 - - - -
13L A 3.4 15.8 + - - -
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Residues in contact with GLU 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226G GLY 3.3 11.2 + - - +
227G GLN 3.1 7.8 + - - +
229G ARG* 1.3 82.7 - - + +
231G LEU* 1.4 63.1 + - - +
233G ARG* 3.2 50.8 + - - +
234G GLU* 3.1 23.7 + - - +
248G LYS 6.0 0.2 - - - -
249G ILE* 4.4 14.2 - - + +
252G ALA* 4.2 24.7 - - + +
253G THR* 4.0 15.9 - - + -
219J LYS* 6.3 2.0 - - - +
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Residues in contact with LEU 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223G TYR* 3.9 18.6 - - + -
227G GLN 3.1 18.7 + - - +
228G LEU* 3.0 7.5 + - - +
230G GLU* 1.4 73.7 - - - +
232G GLU* 1.3 60.3 + - - +
234G GLU* 3.1 4.5 + - - +
235G TYR* 2.9 28.1 + - - +
249G ILE* 3.7 28.9 - - + -
253G THR* 4.8 0.7 - - + -
255G LEU* 3.6 22.9 - - + -
260G ILE* 3.9 16.2 - - + -
263G TRP* 3.7 43.7 - - + +
264G PHE* 4.2 11.5 - - + -
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Residues in contact with GLU 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228G LEU* 2.8 30.8 + - + +
229G ARG* 4.2 4.5 - - - +
231G LEU* 1.3 70.5 - - - +
233G ARG* 1.3 64.0 + - - +
235G TYR* 3.7 6.6 - - - +
236G ALA* 3.1 24.4 + - - +
263G TRP* 3.6 19.1 - - + -
267G ARG* 3.0 41.1 + - - -
270G LYS* 4.9 5.7 + - - -
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Residues in contact with ARG 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229G ARG* 3.0 22.4 + - + +
230G GLU* 3.2 38.2 + - - +
231G LEU 3.2 0.2 - - - -
232G GLU* 1.3 77.9 - - - +
234G GLU* 1.3 88.8 + - - +
236G ALA* 3.5 5.5 + - - +
237G ALA* 3.4 17.7 + - - +
249G ILE* 6.0 0.2 - - - +
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Residues in contact with GLU 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230G GLU 3.1 7.5 + - - +
231G LEU 3.1 3.9 + - - +
233G ARG* 1.3 103.6 + - - +
235G TYR* 1.4 57.4 + - - +
237G ALA* 3.0 22.4 + - - +
238G ASN* 2.9 29.3 + - + +
241G ILE* 4.1 14.1 - - + -
245G LYS* 3.4 37.6 + - + +
249G ILE* 3.5 35.2 - - + +
264G PHE* 4.2 4.0 - - + -
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Residues in contact with TYR 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231G LEU 2.9 16.2 + - - +
232G GLU* 3.7 8.7 - - - +
234G GLU* 1.4 76.0 - - - +
236G ALA* 1.3 66.3 + - - +
238G ASN 3.0 24.0 - - - -
239G LYS* 3.4 35.5 + - + +
263G TRP* 3.9 10.5 - + + -
264G PHE* 3.9 23.9 - + + -
267G ARG* 3.4 49.1 - - + -
268G ARG* 3.6 27.8 - - + +
271G GLU* 3.1 36.6 + - - +
272G LYS* 5.6 0.2 + - - -
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Residues in contact with ALA 236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232G GLU 3.1 15.0 + - - +
233G ARG* 3.9 6.3 - - - +
234G GLU 3.3 0.2 - - - -
235G TYR* 1.3 83.0 - - + +
237G ALA* 1.3 60.8 + - - +
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Residues in contact with ALA 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233G ARG 3.4 8.8 + - - +
234G GLU* 3.0 26.2 + - - +
236G ALA* 1.3 80.9 - - - +
238G ASN* 1.3 62.7 + - + +
245G LYS* 6.0 1.1 - - - -
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Residues in contact with ASN 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234G GLU* 2.9 15.5 + - + +
235G TYR* 3.0 14.7 + - - +
237G ALA* 1.3 81.4 - - + +
239G LYS* 1.3 73.6 + - - +
240G PHE* 3.0 38.1 + - - +
242G THR* 6.0 2.8 - - - -
245G LYS* 6.0 7.8 - - + +
264G PHE* 3.6 7.1 - - - -
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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