Contacts of the helix formed by residues 224 - 238 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220G ARG 5.2 0.7 + - - -
221G ILE* 4.6 9.7 - - - +
222G PRO* 3.7 30.5 - - - -
13I A 3.8 7.5 + - - -
222J PRO 3.9 1.6 + - - -
223J TYR* 1.3 75.7 - - - +
225J LYS* 1.3 65.8 + - - +
226J GLY* 3.6 1.9 + - - -
227J GLN* 2.8 35.5 + - - +
228J LEU* 3.0 20.7 + - - +
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Residues in contact with LYS 225 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I A 6.0 0.2 - - - +
13I A 3.7 51.4 + - - +
14I C 4.3 16.0 + - - +
224J SER* 1.3 74.6 - - - +
226J GLY* 1.3 58.9 + - - +
228J LEU* 3.5 6.8 + - - +
229J ARG* 3.0 39.5 + - + +
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Residues in contact with GLY 226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G LYS* 4.3 14.3 + - - -
13I A 2.6 29.2 + - - -
224J SER* 4.3 0.2 - - - -
225J LYS* 1.3 71.5 - - - +
227J GLN* 1.3 64.5 + - - +
229J ARG* 3.4 22.4 + - - +
230J GLU* 3.2 25.5 + - - +
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Residues in contact with GLN 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221G ILE* 4.0 28.2 - - + +
222J PRO 4.8 0.3 - - - +
223J TYR* 3.4 15.9 - - + +
224J SER* 2.8 43.0 + - - +
226J GLY* 1.3 74.9 - - - +
228J LEU* 1.3 63.9 + - - +
230J GLU* 3.4 5.2 + - - +
231J LEU* 3.1 27.4 + - - +
253J THR* 3.0 44.2 + - + +
254J SER 4.9 1.0 - - - -
255J LEU* 3.4 27.4 - - + +
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Residues in contact with LEU 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223J TYR* 3.4 41.3 - - + +
224J SER 3.0 13.1 + - - +
225J LYS* 4.0 6.5 - - - +
227J GLN* 1.3 72.1 - - - +
229J ARG* 1.3 58.7 + - - +
231J LEU* 3.0 6.1 + - + +
232J GLU* 2.7 46.5 + - + +
263J TRP* 3.8 29.4 - - + +
8K T 5.5 1.3 - - - +
9K T 4.1 14.1 - - - +
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Residues in contact with ARG 229 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219G LYS* 4.3 11.9 - - - +
13I A 5.7 0.6 + - - -
225J LYS* 3.0 28.2 + - + +
226J GLY* 3.4 23.6 + - - +
228J LEU* 1.3 74.8 - - - +
230J GLU* 1.3 78.8 + - - +
232J GLU* 3.7 5.1 - - - +
233J ARG* 2.8 38.4 + - - +
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Residues in contact with GLU 230 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E A 4.5 8.1 + - - -
219G LYS* 5.9 3.8 - - - +
226J GLY 3.2 12.7 + - - +
227J GLN 3.6 7.6 - - - +
228J LEU 3.3 0.2 - - - -
229J ARG* 1.3 99.5 + - - +
231J LEU* 1.4 57.4 + - - +
233J ARG* 3.3 24.7 + - - +
234J GLU* 3.0 29.3 + - - +
248J LYS* 4.7 8.5 + - - +
249J ILE* 4.6 12.9 - - + +
252J ALA* 3.6 31.3 - - + +
253J THR* 3.9 16.8 - - + -
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Residues in contact with LEU 231 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223J TYR* 3.9 12.6 - - + -
227J GLN 3.1 18.0 + - - +
228J LEU* 3.0 14.0 + - + +
230J GLU* 1.4 68.0 - - - +
232J GLU* 1.3 60.3 + - - +
234J GLU* 3.2 6.2 + - - +
235J TYR* 2.8 30.5 + - - +
249J ILE* 3.8 26.2 - - + -
255J LEU* 3.9 22.4 - - + -
260J ILE* 4.3 14.6 - - + -
263J TRP* 3.6 55.4 - - + +
264J PHE* 4.2 10.8 - - + -
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Residues in contact with GLU 232 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228J LEU* 2.7 32.3 + - + +
229J ARG* 3.8 4.9 - - - +
231J LEU* 1.3 73.6 - - - +
233J ARG* 1.3 62.3 + - - +
235J TYR* 3.8 4.9 - - - +
236J ALA* 3.0 26.7 + - - +
263J TRP* 3.4 19.2 - - + -
267J ARG* 3.2 37.9 + - - -
270J LYS* 5.2 5.9 + - - -
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Residues in contact with ARG 233 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E T 5.4 4.6 + - - -
10E A 4.7 8.1 + - - -
229J ARG* 2.8 28.0 + - - +
230J GLU* 3.7 25.5 + - - +
232J GLU* 1.3 75.0 - - - +
234J GLU* 1.3 73.3 + - - +
236J ALA* 3.5 5.8 + - - +
237J ALA* 3.3 18.4 + - - +
248J LYS* 3.5 25.9 - - - +
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Residues in contact with GLU 234 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E T 5.1 0.3 + - - -
230J GLU 3.0 12.4 + - - +
231J LEU 3.2 2.9 + - - +
233J ARG* 1.3 87.1 + - - +
235J TYR* 1.3 58.4 + - - +
237J ALA* 3.1 14.3 + - - +
238J ASN* 3.0 28.1 + - - +
241J ILE* 4.0 14.4 - - + -
245J LYS* 3.1 41.3 + - + +
248J LYS* 3.7 21.4 + - - -
249J ILE* 3.4 34.5 - - + +
264J PHE* 4.1 4.0 - - + -
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Residues in contact with TYR 235 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231J LEU 2.8 17.3 + - - +
232J GLU* 3.8 6.5 - - - +
233J ARG 3.3 0.2 - - - -
234J GLU* 1.3 72.7 - - - +
236J ALA* 1.3 68.4 + - - +
238J ASN* 3.1 23.5 + - - +
239J LYS* 3.5 34.9 + - + +
263J TRP* 3.8 11.0 - + + -
264J PHE* 3.9 22.1 - + + -
267J ARG* 3.4 51.6 - - + -
268J ARG* 3.6 20.6 - - + +
271J GLU* 2.6 44.1 + - - +
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Residues in contact with ALA 236 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232J GLU 3.0 17.3 + - - +
233J ARG* 3.7 7.9 - - + +
235J TYR* 1.3 82.2 - - - +
237J ALA* 1.3 58.3 + - - +
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Residues in contact with ALA 237 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233J ARG 3.3 9.4 + - - +
234J GLU* 3.1 23.2 + - - +
236J ALA* 1.3 80.6 - - - +
238J ASN* 1.3 61.7 + - + +
245J LYS* 5.8 2.7 - - - -
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Residues in contact with ASN 238 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234J GLU* 3.0 15.8 + - + +
235J TYR* 3.1 15.4 + - - +
237J ALA* 1.3 80.5 - - + +
239J LYS* 1.3 79.3 + - - +
240J PHE* 2.9 36.5 + - - +
242J THR* 4.7 12.3 - - - +
245J LYS* 5.9 8.2 - - + +
264J PHE* 3.5 7.3 - - - -
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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