Contacts of the helix formed by residues 223 - 249 (chain A) in PDB entry 4IKV
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 223 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A PRO 5.1 1.6 - - - +
222A LEU* 1.3 74.2 - - - +
224A PRO* 1.3 65.4 - - + +
225A ALA* 3.7 8.2 + - - +
226A GLU* 2.7 46.6 + - - +
227A LYS* 2.7 33.1 + - - +
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Residues in contact with PRO 224 (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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222A LEU 4.4 1.6 - - - +
223A THR* 1.3 87.3 - - - +
225A ALA* 1.3 60.5 + - - +
227A LYS* 3.4 13.5 + - + +
228A LYS* 3.1 22.9 + - - +
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Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A THR* 3.2 6.4 + - - +
224A PRO* 1.3 79.0 - - - +
226A GLU* 1.3 54.2 + - - +
228A LYS* 3.3 7.2 + - - +
229A LYS* 2.7 34.8 + - - +
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Residues in contact with GLU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ARG* 3.3 28.1 + - - +
221A PRO 3.7 5.0 - - - +
222A LEU* 3.5 18.0 - - + +
223A THR* 2.7 56.3 + - - +
225A ALA* 1.3 78.7 - - - +
227A LYS* 1.3 52.8 + - - +
229A LYS* 3.1 8.1 + - + +
230A ALA* 2.6 37.4 + - - +
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Residues in contact with LYS 227 (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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222A LEU* 3.3 47.1 - - + +
223A THR 2.7 19.3 + - - +
224A PRO* 3.7 11.4 - - + +
226A GLU* 1.3 72.5 - - - +
228A LYS* 1.3 58.0 + - - +
230A ALA* 3.9 2.1 - - - +
231A ALA* 3.0 27.7 + - - +
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Residues in contact with LYS 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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224A PRO 3.1 16.6 + - - +
225A ALA* 3.6 7.2 - - - +
227A LYS* 1.3 73.9 - - - +
229A LYS* 1.3 59.6 - - - +
231A ALA* 3.3 7.2 + - - +
232A ALA* 2.9 27.9 + - - +
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Residues in contact with LYS 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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225A ALA 2.7 17.4 + - - +
226A GLU* 3.4 10.5 - - + +
228A LYS* 1.3 74.5 - - - +
230A ALA* 1.3 60.3 + - - +
232A ALA* 3.1 8.4 + - - +
233A ILE* 3.0 35.7 + - + +
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Residues in contact with ALA 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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86A TRP* 4.0 29.4 - - + -
222A LEU* 4.2 11.2 - - + -
226A GLU 2.6 20.2 + - - +
227A LYS* 4.0 3.6 - - - +
229A LYS* 1.3 73.4 - - - +
231A ALA* 1.3 61.0 + - - +
233A ILE* 3.5 11.3 + - - +
234A MET* 3.2 31.9 + - + +
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Residues in contact with ALA 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 LYS 3.0 19.0 + - - +
228A LYS* 3.5 9.4 - - - +
230A ALA* 1.3 76.7 - - - +
232A ALA* 1.3 62.6 + - - +
234A MET* 3.3 13.7 + - - +
235A ALA* 3.1 20.6 + - - +
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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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228A LYS 2.9 14.7 + - - +
229A LYS* 3.1 11.4 + - - +
231A ALA* 1.3 75.1 - - - +
233A ILE* 1.3 61.0 + - + +
235A ALA* 3.0 10.5 + - - +
236A VAL* 2.9 31.4 + - + +
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Residues in contact with ILE 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 LYS* 3.0 23.7 + - + +
230A ALA* 3.8 9.0 - - - +
231A ALA 3.3 0.2 - - - -
232A ALA* 1.3 76.5 - - + +
234A MET* 1.3 59.2 + - + +
236A VAL* 3.1 13.5 + - + +
237A GLY* 2.9 24.4 + - - -
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Residues in contact with MET 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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86A TRP* 6.5 0.7 - - - -
230A ALA* 3.2 19.4 + - + +
231A ALA* 3.5 14.8 - - - +
232A ALA 3.2 0.2 - - - -
233A ILE* 1.3 78.0 - - + +
235A ALA* 1.3 57.8 + - - +
237A GLY* 3.4 2.5 + - - -
238A ALA* 2.9 27.1 + - - +
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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 ALA 3.1 11.5 + - - +
232A ALA* 3.0 13.6 + - - +
234A MET* 1.3 76.1 - - - +
236A VAL* 1.3 59.1 + - - +
238A ALA* 3.2 9.2 + - - +
239A VAL* 2.8 28.4 + - - +
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Residues in contact with VAL 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 ALA* 2.9 16.9 + - + +
233A ILE* 3.1 17.5 + - + +
235A ALA* 1.3 76.5 - - - +
237A GLY* 1.3 58.7 + - - +
239A VAL* 3.2 8.2 + - - +
240A VAL* 3.0 36.5 + - + +
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Residues in contact with GLY 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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233A ILE 2.9 13.4 + - - -
234A MET* 3.4 4.9 + - - -
235A ALA 3.3 0.2 - - - -
236A VAL* 1.3 77.6 - - - +
238A ALA* 1.3 57.0 + - - +
240A VAL* 3.4 8.6 + - - +
241A ILE* 3.1 28.5 + - - +
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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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234A MET 2.9 17.3 + - - +
235A ALA* 3.4 10.8 - - - +
236A VAL 3.2 0.4 - - - -
237A GLY* 1.3 75.6 - - - +
239A VAL* 1.3 59.0 + - - +
241A ILE* 3.1 12.2 - - + +
242A ALA* 3.1 27.4 + - - +
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Residues in contact with VAL 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 2.8 12.7 + - - +
236A VAL* 3.2 10.5 + - - +
238A ALA* 1.3 75.6 - - - +
240A VAL* 1.3 57.9 - - + +
242A ALA* 3.3 6.3 + - - +
243A VAL* 2.8 33.1 + - - +
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Residues in contact with VAL 240 (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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236A VAL* 3.0 31.1 + - + +
237A GLY* 3.7 9.2 - - - +
238A ALA 3.4 0.2 - - - -
239A VAL* 1.3 77.4 - - + +
241A ILE* 1.3 61.1 + - - +
243A VAL* 3.5 10.2 - - + +
244A LEU* 3.2 35.5 + - + +
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Residues in contact with ILE 241 (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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237A GLY 3.1 20.2 + - - +
238A ALA* 3.1 22.0 - - + +
240A VAL* 1.3 75.3 - - - +
242A ALA* 1.3 64.3 + - - +
244A LEU* 3.2 16.1 + - + +
245A LEU* 3.0 46.7 + - + +
254A PHE* 5.6 4.5 - - + -
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Residues in contact with ALA 242 (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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238A ALA 3.1 19.8 + - - +
239A VAL* 3.5 8.1 - - - +
241A ILE* 1.3 78.1 - - - +
243A VAL* 1.3 62.2 + - - +
245A LEU* 3.1 22.0 + - - +
246A ALA* 3.2 13.3 + - - +
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Residues in contact with VAL 243 (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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239A VAL 2.8 17.8 + - - +
240A VAL* 3.5 15.7 - - + +
242A ALA* 1.3 74.1 - - - +
244A LEU* 1.3 68.9 + - + +
246A ALA* 3.6 8.3 + - + +
247A ILE* 3.3 39.6 + - + +
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Residues in contact with LEU 244 (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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240A VAL* 3.2 25.9 + - + +
241A ILE* 3.4 21.5 - - + +
242A ALA 3.1 0.4 - - - -
243A VAL* 1.3 82.4 - - + +
245A LEU* 1.3 55.9 + - + +
247A ILE* 3.0 11.1 + - + +
248A LEU* 2.7 65.4 + - + +
262A LEU* 5.8 8.1 - - + -
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Residues in contact with LEU 245 (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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241A ILE* 3.0 39.2 + - + +
242A ALA* 3.1 11.6 + - - +
244A LEU* 1.3 77.4 - - + +
246A ALA* 1.3 58.1 + - - +
248A LEU* 4.4 1.8 - - + +
249A ILE* 2.9 56.5 + - + +
254A PHE* 3.5 39.9 - - + -
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Residues in contact with ALA 246 (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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242A ALA 3.2 10.3 + - - +
243A VAL* 3.9 12.8 - - + +
244A LEU 3.3 0.2 - - - -
245A LEU* 1.3 77.5 - - - +
247A ILE* 1.3 59.3 + - + +
250A PRO* 3.2 24.0 - - - +
251A ASN* 5.5 0.2 + - - -
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Residues in contact with ILE 247 (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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243A VAL* 3.3 27.6 - - + +
244A LEU* 3.0 13.5 + - + +
246A ALA* 1.3 83.2 - - + +
248A LEU* 1.3 67.6 + - + +
249A ILE 3.6 0.2 - - - -
250A PRO* 3.8 2.2 - - - +
251A ASN* 2.8 33.9 + - - +
253A TRP* 4.1 18.2 - - + -
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Residues in contact with LEU 248 (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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244A LEU* 2.7 51.6 + - + +
245A LEU* 4.3 0.9 - - + +
247A ILE* 1.3 78.1 - - + +
249A ILE* 1.3 64.3 + - - +
251A ASN 3.4 2.1 + - - -
252A GLY 3.3 2.8 + - - -
253A TRP* 2.9 62.3 + - + +
254A PHE* 4.0 30.3 - - + +
258A THR* 4.7 14.1 - - + -
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Residues in contact with ILE 249 (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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245A LEU* 2.9 47.5 + - + +
248A LEU* 1.3 75.0 - - - +
250A PRO* 1.4 65.7 - - + +
252A GLY* 2.9 15.9 + - - -
254A PHE* 3.8 30.5 - - + -
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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
------------------------------------------------------------
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