Contacts of the helix formed by residues 226 - 244 (chain D) in PDB entry 2XBM
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 226 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194D GLU* 4.8 5.2 - - - +
203D MET* 3.5 7.2 - - - +
225D GLY* 1.3 67.7 - - - -
227D ILE* 1.3 63.6 + - - +
228D VAL* 3.2 21.9 + - - +
229D SER* 3.3 27.2 + - - +
230D SER* 3.2 20.6 + - - -
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Residues in contact with ILE 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D ILE* 4.6 4.3 - - + +
193D LEU* 3.6 42.0 - - + +
194D GLU* 3.1 37.0 + - - +
197D GLN* 3.4 29.1 - - + +
203D MET* 3.7 17.0 - - - -
204D LEU* 4.0 24.0 - - + +
219D TRP* 6.3 0.4 - - + -
225D GLY 3.3 1.2 + - - -
226D ASN* 1.3 72.1 + - - +
228D VAL* 1.3 68.0 + - + +
230D SER* 3.2 5.7 + - - -
231D VAL* 3.0 31.7 + - + +
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Residues in contact with VAL 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D ILE* 4.0 37.5 - - + +
194D GLU* 4.1 16.4 - - - +
226D ASN* 3.2 12.5 + - - +
227D ILE* 1.3 79.4 - - - +
229D SER* 1.3 59.3 + - - +
231D VAL* 3.4 6.0 + - - +
232D ASN* 3.1 41.3 + - - +
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Residues in contact with SER 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D ASN* 3.3 32.6 + - - +
227D ILE 3.4 0.2 - - - -
228D VAL* 1.3 77.3 - - - +
230D SER* 1.3 61.7 + - - +
232D ASN* 3.1 11.6 + - - +
233D MET* 2.8 41.2 + - - +
236D ARG* 4.9 0.4 + - - -
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Residues in contact with SER 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D MET* 3.8 16.8 - - - +
204D LEU* 3.9 17.8 + - - +
217D MET* 4.6 2.5 - - - -
226D ASN 3.2 16.2 + - - -
227D ILE* 3.2 14.6 + - - -
229D SER* 1.3 76.6 + - - +
231D VAL* 1.3 64.2 + - - +
233D MET* 3.5 14.4 + - - +
234D VAL* 3.3 26.3 + - - +
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Residues in contact with VAL 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D PRO* 3.7 24.5 - - + +
185D TYR* 3.8 21.8 - - + -
190D ILE* 4.5 9.9 - - + -
204D LEU* 3.8 21.5 - - + -
215D HIS* 3.8 2.0 - - + -
217D MET* 3.6 26.9 - - + -
227D ILE 3.0 27.3 + - - +
228D VAL* 3.5 6.3 - - - +
230D SER* 1.3 75.2 + - - +
232D ASN* 1.3 67.4 + - - +
234D VAL* 3.2 6.6 + - - +
235D SER* 3.1 20.3 + - - +
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Residues in contact with ASN 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D THR* 5.5 2.8 + - - -
9D LEU* 5.0 14.6 + - + +
228D VAL* 3.1 35.6 + - - +
229D SER* 3.5 10.8 - - - +
231D VAL* 1.3 79.2 - - - +
233D MET* 1.3 57.0 + - - +
235D SER* 3.3 11.5 + - - -
236D ARG* 3.0 54.5 + - - +
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Residues in contact with MET 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D SER* 2.8 31.5 + - - +
230D SER* 3.7 13.7 - - - +
231D VAL 3.2 0.2 - - - -
232D ASN* 1.3 73.8 - - - +
234D VAL* 1.3 61.8 + - + +
236D ARG* 3.5 18.5 + - - +
237D LEU* 3.0 29.7 + - - +
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Residues in contact with VAL 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D ARG* 3.5 44.2 - - + +
215D HIS* 3.6 21.8 - - + +
217D MET* 3.6 17.5 - - + -
230D SER 3.3 15.3 - - - +
231D VAL 3.2 7.1 + - - +
233D MET* 1.3 77.6 - - - +
235D SER* 1.3 56.3 + - - +
237D LEU* 3.3 9.2 + - + +
238D LEU* 2.9 45.3 + - + +
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Residues in contact with SER 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D LEU* 3.8 24.7 - - - -
10D GLY* 3.4 15.6 + - - -
13D TRP* 5.0 1.8 - - - +
185D TYR* 4.6 3.1 - - - +
215D HIS* 2.8 27.6 + - - -
231D VAL* 3.1 11.4 + - - +
232D ASN* 3.4 14.2 + - - -
233D MET 3.3 0.2 - - - -
234D VAL* 1.3 77.6 - - - +
236D ARG* 1.3 56.2 + - - +
238D LEU* 3.3 2.5 + - - +
239D LEU* 2.9 36.7 + - - +
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Residues in contact with ARG 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D LEU* 3.7 27.1 - - + +
229D SER* 4.9 0.8 + - - -
232D ASN* 3.0 51.2 + - - +
233D MET* 3.9 21.1 - - - +
235D SER* 1.3 74.6 - - - +
237D LEU* 1.3 57.3 + - - +
239D LEU* 3.4 6.3 + - - +
240D ASN* 2.9 45.2 + - - +
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Residues in contact with LEU 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D ARG* 5.5 8.7 - - + +
233D MET 3.0 19.1 + - - +
234D VAL* 3.3 10.3 + - + +
236D ARG* 1.3 77.4 - - - +
238D LEU* 1.3 72.3 + - + +
240D ASN* 3.5 7.5 + - + +
241D ARG* 3.3 69.7 + - + +
244D MET* 5.2 7.0 - - + -
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Residues in contact with LEU 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D TRP* 3.7 19.5 - - + +
28D TYR* 2.9 27.3 + - - +
206D ARG* 4.0 14.1 - - - +
212D ASN* 3.5 39.3 - - + +
214D THR 3.9 15.9 - - - +
215D HIS* 3.9 20.4 - - + -
234D VAL* 2.9 35.9 + - + +
235D SER 3.9 2.5 - - - +
237D LEU* 1.3 82.9 - - + +
239D LEU* 1.3 66.2 + - - +
241D ARG* 3.2 13.9 + - - +
242D PHE* 3.7 1.4 - - - -
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Residues in contact with LEU 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 3.5 46.2 - - + +
12D LYS* 4.3 13.0 - - + -
13D TRP* 3.7 31.6 - - + +
16D LYS* 4.3 18.4 - - + +
235D SER 2.9 18.3 + - - +
236D ARG* 3.7 5.2 - - - +
238D LEU* 1.3 75.3 - - - +
240D ASN* 1.3 65.1 + - - +
242D PHE* 3.2 36.0 + - + +
243D THR* 4.2 3.8 + - - -
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Residues in contact with ASN 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D ARG* 2.9 27.7 + - - +
237D LEU* 3.7 8.8 - - + +
239D LEU* 1.3 79.2 - - - +
241D ARG* 1.3 56.8 + - - +
242D PHE 3.2 0.8 + - - -
243D THR* 3.4 10.3 + - - -
244D MET* 3.1 45.7 + - + +
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Residues in contact with ARG 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D TYR* 3.6 21.2 - - + -
31D SER* 3.7 17.4 + - - +
32D GLY* 3.5 22.7 + - - -
33D ILE* 3.8 15.4 - - - +
206D ARG* 5.4 3.2 - - - +
210D SER 5.5 0.2 + - - -
212D ASN* 2.7 46.8 + - - +
237D LEU* 3.3 48.5 + - - +
238D LEU* 3.2 11.5 + - - +
239D LEU 3.2 1.6 - - - -
240D ASN* 1.3 74.2 - - - +
242D PHE* 1.3 64.0 + - - +
244D MET* 3.8 31.1 - - + +
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Residues in contact with PHE 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D TRP* 3.5 28.0 - + - -
16D LYS* 4.0 23.8 - - + -
17D LEU* 3.9 18.8 - - - -
20D LEU* 3.8 36.6 - - + -
28D TYR* 3.7 32.1 - + - -
238D LEU 3.7 4.9 - - - -
239D LEU* 3.2 32.7 + - + +
240D ASN 3.2 0.6 - - - -
241D ARG* 1.3 79.6 - - - +
243D THR* 1.3 64.3 + - + +
244D MET 3.6 4.2 + - - +
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Residues in contact with THR 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D LEU 4.3 3.3 + - - -
240D ASN* 3.4 15.9 + - - -
242D PHE* 1.3 77.1 - - + +
244D MET* 1.3 63.7 + - - +
245D THR* 3.4 6.1 + - - +
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Residues in contact with MET 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D SER* 4.7 3.1 + - - +
237D LEU* 4.7 7.0 - - + +
240D ASN* 3.1 46.4 + - + +
241D ARG* 3.8 35.5 - - + +
242D PHE 3.4 4.0 - - - +
243D THR* 1.3 78.0 - - - +
245D THR* 1.3 68.5 + - - +
246D HIS* 3.4 3.3 + - - -
247D ARG* 4.9 20.6 - - - -
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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