Contacts of the helix formed by residues 230 - 252 (chain w) in PDB entry 6AH0
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 PRO 230 (chain w).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227w PRO* 2.8 15.5 - - + +
228w GLY 4.7 2.1 - - - +
229w TRP* 1.3 80.4 - - - +
231w LYS* 1.3 66.2 + - - +
232w GLU 3.7 0.4 - - - -
233w THR* 3.6 6.1 + - - +
234w SER* 3.0 19.8 + - - -
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Residues in contact with LYS 231 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229w TRP 3.7 3.0 + - - -
230w PRO* 1.3 66.5 - - - +
232w GLU* 1.3 68.5 + - - +
233w THR 3.0 1.6 - - - -
234w SER* 2.9 13.9 + - - +
235w SER* 2.9 11.6 + - - -
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Residues in contact with GLU 232 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192w TYR* 5.8 11.7 - - - +
231w LYS* 1.3 72.1 - - - +
233w THR* 1.3 56.5 + - - +
235w SER* 3.4 1.5 + - - +
236w ALA* 2.9 27.2 + - - -
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Residues in contact with THR 233 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227w PRO 5.7 2.7 - - - -
230w PRO* 3.6 8.2 + - - -
231w LYS 3.0 1.2 + - - -
232w GLU* 1.3 77.0 - - - +
234w SER* 1.3 56.8 + - - +
236w ALA* 3.3 2.4 + - - +
237w LEU* 2.9 27.2 + - - -
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Residues in contact with SER 234 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228w GLY 5.7 3.8 - - - -
230w PRO 3.0 11.5 + - - -
231w LYS* 2.9 9.8 + - - +
233w THR* 1.3 71.7 - - - +
235w SER* 1.3 55.7 + - - +
237w LEU* 3.5 1.8 + - - +
238w THR* 3.0 25.3 + - - -
320w ILE* 5.9 2.8 - - - -
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Residues in contact with SER 235 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231w LYS 2.9 11.9 + - - -
232w GLU* 3.8 3.6 - - - +
234w SER* 1.3 73.9 - - - +
236w ALA* 1.3 65.9 + - - +
238w THR* 3.0 11.4 + - - +
239w HIS* 3.0 12.0 + - - -
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Residues in contact with ALA 236 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232w GLU 2.9 13.0 + - - -
233w THR* 3.7 3.4 - - - +
235w SER* 1.3 74.3 - - - +
237w LEU* 1.3 63.2 + - - +
239w HIS* 2.9 14.5 + - - +
240w ALA* 2.9 12.5 + - - -
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Residues in contact with LEU 237 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233w THR 2.9 19.0 + - - -
234w SER* 3.8 2.5 - - - +
236w ALA* 1.3 70.0 - - - +
238w THR* 1.3 61.9 + - - +
240w ALA* 3.9 1.5 - - - +
241w GLY* 2.9 22.5 + - - -
323w LEU 5.4 4.7 - - - +
324w GLU* 6.0 1.5 - - - -
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Residues in contact with THR 238 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234w SER 3.0 15.0 + - - -
235w SER* 3.0 4.9 + - - +
237w LEU* 1.3 76.8 - - - +
239w HIS* 1.3 62.8 + - - +
241w GLY* 3.2 0.7 + - - -
242w ALA* 3.0 21.0 + - - -
323w LEU* 6.0 6.1 - - - +
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Residues in contact with HIS 239 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235w SER 3.0 8.7 + - - -
236w ALA* 2.9 9.4 + - - +
238w THR* 1.3 72.3 - - - +
240w ALA* 1.3 57.3 + - - +
242w ALA* 3.4 2.0 + - - +
243w HIS* 3.0 24.6 + - - -
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Residues in contact with ALA 240 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236w ALA 2.9 13.1 + - - -
237w LEU* 3.9 2.2 - - - +
239w HIS* 1.3 73.0 - - - +
241w GLY* 1.3 65.1 + - - +
243w HIS* 3.0 4.0 + - - +
244w LEU* 2.9 20.3 + - - -
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Residues in contact with GLY 241 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237w LEU 2.9 18.5 + - - -
238w THR* 3.6 0.9 - - - -
240w ALA* 1.3 72.8 - - - +
242w ALA* 1.3 65.0 + - - +
244w LEU* 3.1 3.8 + - - -
245w ASP* 3.0 21.1 + - - -
323w LEU* 4.7 9.4 - - - -
326w GLN 5.9 0.2 - - - -
327w ILE* 4.5 23.1 + - - -
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Residues in contact with ALA 242 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238w THR 3.0 13.3 + - - -
239w HIS* 3.7 3.8 - - - +
241w GLY* 1.3 74.5 - - - +
243w HIS* 1.3 63.6 + - - +
245w ASP* 3.3 1.3 + - - +
246w LEU* 3.0 20.8 + - - -
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Residues in contact with HIS 243 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239w HIS 3.0 14.8 + - - -
240w ALA* 3.0 4.7 + - - +
242w ALA* 1.3 77.2 - - - +
244w LEU* 1.3 62.1 + - - +
246w LEU* 3.3 0.7 + - - -
247w SER* 2.9 22.2 + - - -
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Residues in contact with LEU 244 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240w ALA 2.9 13.2 + - - -
241w GLY* 3.1 3.5 + - - -
243w HIS* 1.3 74.1 - - - +
245w ASP* 1.3 57.2 + - - +
247w SER* 3.4 1.4 + - - +
248w ALA* 2.9 25.6 + - - -
330w TYR* 5.8 6.3 - - - +
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Residues in contact with ASP 245 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241w GLY 3.0 13.4 + - - -
242w ALA 3.8 2.2 - - - -
244w LEU* 1.3 73.1 - - - +
246w LEU* 1.3 65.6 + - - +
248w ALA* 3.0 11.8 + - - +
249w PHE* 3.0 12.0 + - - -
330w TYR* 6.1 3.8 - - - +
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Residues in contact with LEU 246 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242w ALA 3.0 14.2 + - - -
243w HIS* 3.8 2.5 - - - +
245w ASP* 1.3 75.6 - - - +
247w SER* 1.3 55.4 + - - +
249w PHE* 3.9 0.6 - - - +
250w SER* 2.9 27.7 + - - -
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Residues in contact with SER 247 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243w HIS 2.9 17.1 + - - -
244w LEU* 3.7 2.0 - - - +
246w LEU* 1.3 77.0 - - - +
248w ALA* 1.3 62.8 + - - +
250w SER* 3.2 1.8 + - - +
251w SER* 2.9 22.2 + - - -
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Residues in contact with ALA 248 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244w LEU 2.9 15.2 + - - -
245w ASP* 3.0 4.4 + - - +
247w SER* 1.3 78.6 - - - +
249w PHE* 1.3 62.6 + - - +
251w SER* 3.1 8.5 + - - -
252w TRP* 3.3 9.9 + - - -
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Residues in contact with PHE 249 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245w ASP 3.0 12.7 + - - -
246w LEU* 3.9 1.6 - - - +
248w ALA* 1.3 74.9 - - - +
250w SER* 1.3 61.5 + - - +
251w SER 3.3 0.2 - - - -
252w TRP 3.5 20.8 - - - +
253w GLU* 3.6 6.4 + - - -
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Residues in contact with SER 250 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246w LEU 2.9 18.3 + - - -
247w SER* 3.6 2.2 - - - +
248w ALA 3.1 0.4 - - - -
249w PHE* 1.3 79.4 - - - +
251w SER* 1.3 58.9 + - - +
252w TRP 3.5 0.3 + - - -
253w GLU* 4.3 5.0 + - - -
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Residues in contact with SER 251 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176w GLU 5.7 1.6 - - - -
177w ARG* 5.2 13.9 - - - +
247w SER 2.9 13.1 + - - -
248w ALA 3.1 3.6 + - - -
250w SER* 1.3 76.9 - - - +
252w TRP* 1.3 56.4 + - - +
253w GLU 3.9 1.3 + - - -
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Residues in contact with TRP 252 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248w ALA 3.3 10.7 + - - -
249w PHE* 3.5 10.9 - - - +
251w SER* 1.3 79.5 - - - +
253w GLU* 1.3 65.3 + - - +
254w GLU 3.2 3.8 + - - +
255w LEU* 3.3 14.7 + - - +
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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