Contacts of the helix formed by residues 244 - 260 (chain X) in PDB entry 1XDM
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 244 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242X LYS* 4.3 0.6 - - - +
243X TYR* 1.3 72.0 - - - +
245X PRO* 1.3 68.9 - - - +
246X GLU* 2.7 41.3 + - + -
247X GLN* 2.8 54.4 + - + +
248X VAL* 2.9 11.4 + - - +
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Residues in contact with PRO 245 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243X TYR 4.3 2.9 - - - +
244X THR* 1.3 88.3 - - - +
246X GLU* 1.3 61.7 + - - +
248X VAL* 4.1 8.2 - - + +
249X ALA* 3.1 14.6 + - - +
278X ASP* 5.9 2.2 - - - +
281X LEU* 4.3 24.9 - - + -
282X ASN* 3.3 26.6 - - - +
285X ALA* 2.8 34.6 - - + +
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Residues in contact with GLU 246 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244X THR* 2.7 34.3 + - + -
245X PRO* 1.3 88.8 - - - +
247X GLN* 1.3 58.6 + - + +
249X ALA* 3.3 5.6 - - - +
250X MET* 3.0 27.5 + - - +
285X ALA* 4.4 10.5 - - - +
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Residues in contact with GLN 247 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198X LEU* 3.8 15.4 - - + +
241X LYS* 6.0 4.2 - - - +
242X LYS 3.7 4.6 + - - +
243X TYR* 2.9 42.8 - - + +
244X THR* 2.8 23.5 + - + +
246X GLU* 1.3 72.9 - - + +
248X VAL* 1.3 67.3 + - - +
249X ALA 3.0 1.7 + - - -
250X MET* 3.0 6.3 + - - +
251X ALA* 2.9 26.9 + - - +
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Residues in contact with VAL 248 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198X LEU* 4.1 6.9 - - + +
232X MET* 4.9 5.4 - - + -
233X VAL* 3.1 26.7 - - - +
234X THR* 4.4 13.7 - - + -
243X TYR* 3.7 23.3 - - + +
244X THR 2.9 16.5 + - - +
245X PRO* 4.1 6.7 - - + +
247X GLN* 1.3 76.3 - - - +
249X ALA* 1.3 62.2 + - - +
252X THR* 2.8 33.9 + - - +
282X ASN* 3.6 31.0 - - + +
286X ILE* 5.9 0.4 - - + -
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Residues in contact with ALA 249 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245X PRO 3.1 20.5 + - - +
246X GLU* 3.3 6.7 - - - +
247X GLN 3.0 0.4 - - - -
248X VAL* 1.3 76.9 - - - +
250X MET* 1.3 70.3 + - - +
252X THR* 3.1 4.2 + - - -
253X VAL* 2.9 25.2 + - - +
282X ASN* 5.1 0.8 - - - +
285X ALA* 3.4 32.8 - - + +
286X ILE* 3.7 14.8 - - + +
289X CYS* 4.3 4.7 - - + -
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Residues in contact with MET 250 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246X GLU 3.0 13.9 + - - +
247X GLN* 3.6 8.5 - - - +
249X ALA* 1.3 72.7 - - - +
251X ALA* 1.3 65.6 + - - +
252X THR 2.9 0.9 + - - -
254X THR* 2.4 59.9 + - + +
289X CYS* 3.6 12.0 - - - -
290X PRO* 5.1 4.9 - - - -
291X LEU* 3.2 43.3 - - + -
364X SO4 6.2 0.2 - - - +
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Residues in contact with ALA 251 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198X LEU* 3.5 26.2 - - + -
202X GLN* 3.7 21.2 - - + +
233X VAL* 3.2 20.9 - - + -
247X GLN 2.9 18.4 + - - +
250X MET* 1.3 76.5 - - - +
252X THR* 1.3 61.0 + - - +
254X THR* 3.5 5.9 - - - -
255X ALA* 3.1 22.0 + - - +
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Residues in contact with THR 252 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231X ASN 5.2 1.6 - - - +
232X MET* 3.9 4.0 - - - +
233X VAL* 2.9 35.3 + - + +
248X VAL* 2.8 22.6 + - - +
249X ALA 3.3 4.0 - - - -
250X MET 2.9 3.6 + - - -
251X ALA* 1.3 74.3 - - - +
253X VAL* 1.3 61.1 + - + +
255X ALA* 3.4 4.8 + - - +
256X LEU* 2.9 33.7 + - + +
269X PHE* 3.4 37.9 - - + -
286X ILE* 4.1 8.5 - - + +
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Residues in contact with VAL 253 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249X ALA 2.9 19.9 + - - +
250X MET 2.9 0.2 + - - -
252X THR* 1.3 70.8 - - - +
254X THR* 1.3 67.5 + - - +
256X LEU* 4.2 5.2 - - - +
257X HIS* 2.8 27.0 + - - -
286X ILE* 3.9 22.4 - - + +
289X CYS* 3.6 29.4 - - + -
291X LEU* 3.9 8.3 - - + -
292X PRO 3.6 8.5 - - - +
293X LYS* 3.2 35.4 - - + -
295X TRP* 4.7 8.3 - - + -
297X LEU* 4.8 2.0 - - + -
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Residues in contact with THR 254 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224W GLU* 4.6 1.3 - - + +
202X GLN* 3.9 7.6 - - - +
250X MET* 2.4 56.5 + - + +
251X ALA* 3.5 5.9 + - - -
253X VAL* 1.3 75.2 - - - +
255X ALA* 1.3 55.1 + - - +
257X HIS* 2.6 32.9 + - + -
258X ARG* 2.7 52.6 - - - +
291X LEU* 4.7 1.3 - - - +
364X SO4 4.5 7.2 - - - +
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Residues in contact with ALA 255 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202X GLN* 4.1 10.7 + - + -
205X THR* 4.7 17.0 - - + -
206X GLU* 3.6 29.3 - - + +
209X LEU* 4.7 1.5 - - - +
233X VAL* 5.6 1.3 - - + -
251X ALA 3.1 10.4 + - - +
252X THR* 3.5 10.8 - - - +
253X VAL 3.1 0.2 - - - -
254X THR* 1.3 78.6 - - - +
256X LEU* 1.3 66.6 + - + +
258X ARG* 3.4 7.3 + - - +
259X THR* 3.2 22.9 + - - +
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Residues in contact with LEU 256 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205X THR* 5.2 3.4 - - + -
209X LEU* 3.6 24.7 - - + -
228X LEU* 4.7 0.2 - - + -
230X PRO* 4.5 14.1 - - + -
231X ASN 6.1 0.4 - - - +
252X THR* 2.9 32.3 + - + +
253X VAL* 3.1 4.0 + - - +
255X ALA* 1.3 79.5 - - + +
257X HIS* 1.3 57.1 + - - +
258X ARG 3.0 3.0 + - - -
259X THR* 4.0 2.9 - - - -
260X VAL* 3.0 32.9 + - + +
267X ILE* 3.7 16.2 - - + -
269X PHE* 3.6 33.2 - - + -
295X TRP* 3.5 20.8 - - + -
297X LEU* 3.7 17.0 - - + -
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Residues in contact with HIS 257 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224W GLU* 3.1 31.6 + - + +
261W PRO* 3.8 0.4 - - - +
262W ALA* 3.2 27.0 + - + +
263W ALA* 2.8 51.7 + - - +
253X VAL 2.8 20.3 + - - +
254X THR* 2.6 40.9 + - + -
256X LEU* 1.3 71.6 - - - +
258X ARG* 1.3 58.5 + - + +
259X THR 3.5 0.4 - - - -
260X VAL 5.2 0.7 - - - -
291X LEU* 3.7 18.5 - - + +
292X PRO* 3.6 34.7 - - + +
295X TRP* 3.7 12.8 - - + -
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Residues in contact with ARG 258 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217W ASN* 4.8 6.6 + - - +
222W TYR* 4.0 12.9 - - - +
223W LEU* 3.6 17.0 - - + +
224W GLU* 2.5 54.6 + - - +
261W PRO* 3.3 20.7 - - - +
263W ALA* 3.5 10.8 - - + -
202X GLN* 3.9 5.5 + - - -
206X GLU* 2.9 24.9 + - - +
254X THR* 2.7 35.2 + - - +
255X ALA 3.7 5.4 - - - +
256X LEU 3.0 0.8 - - - -
257X HIS* 1.3 78.2 - - - +
259X THR* 1.3 64.4 + - + +
364X SO4 2.7 43.9 + - - -
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Residues in contact with THR 259 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217W ASN* 3.9 13.5 - - - +
259W THR 5.7 0.2 - - - +
261W PRO* 4.3 10.4 - - - +
206X GLU* 3.4 36.6 - - + +
209X LEU* 3.5 19.0 - - + +
210X ALA* 4.3 8.5 - - - +
213X TYR* 4.7 4.9 - - - +
255X ALA 3.2 18.0 + - - +
257X HIS 5.2 0.2 - - - -
258X ARG* 1.3 85.8 - - + +
260X VAL* 1.3 80.2 + - - +
261X PRO* 3.0 18.8 - - - +
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Residues in contact with VAL 260 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261W PRO* 5.7 0.9 - - - -
262W ALA 5.3 4.0 + - - -
209X LEU* 3.9 9.6 - - + -
213X TYR* 3.8 20.9 - - + +
228X LEU* 3.6 24.5 - - + -
256X LEU* 3.0 20.0 + - + +
257X HIS* 5.2 0.9 - - - -
259X THR* 1.3 84.9 + - - +
261X PRO* 1.3 75.1 - - - +
264X VAL* 3.6 28.0 - - + -
267X ILE* 4.0 10.5 - - + -
294X PRO* 5.3 0.2 - - - +
295X TRP* 2.8 25.9 + - + +
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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