Contacts of the helix formed by residues 244 - 260 (chain W) 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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243W TYR* 1.3 73.2 - - - +
245W PRO* 1.3 68.2 - - - +
246W GLU* 2.7 23.4 + - - +
247W GLN* 2.8 41.5 + - - +
248W VAL* 2.9 26.4 + - - +
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Residues in contact with PRO 245 (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 TYR 3.8 2.0 - - - +
244W THR* 1.3 88.7 - - - +
246W GLU* 1.3 66.8 + - - +
248W VAL* 3.1 3.5 + - + +
249W ALA* 2.5 38.8 + - - +
281W LEU* 4.6 16.8 - - + +
282W ASN* 4.0 24.7 - - - +
285W ALA* 3.9 17.9 - - + +
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Residues in contact with GLU 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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244W THR* 2.7 27.6 + - - +
245W PRO* 1.3 89.7 - - - +
247W GLN* 1.3 51.4 + - + +
249W ALA* 3.6 6.4 - - - +
250W MET* 2.5 38.2 + - - +
285W ALA* 4.7 7.1 - - + +
289W CYS* 4.8 3.0 - - - +
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Residues in contact with GLN 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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198W LEU* 3.9 13.1 - - + +
243W TYR* 3.4 22.6 - - + +
244W THR* 2.8 50.9 + - - +
246W GLU* 1.3 77.2 - - + +
248W VAL* 1.3 63.9 + - - +
250W MET* 3.4 5.9 - - - +
251W ALA* 2.9 26.7 + - - +
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Residues in contact with VAL 248 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198W LEU* 4.8 3.4 - - + -
232W MET* 4.5 6.1 - - + -
233W VAL 3.0 26.4 - - - +
234W THR* 3.2 24.0 - - + -
243W TYR* 3.6 23.6 - - + +
244W THR 2.9 22.8 + - - +
245W PRO* 3.4 8.5 - - + +
247W GLN* 1.3 76.8 - - - +
249W ALA* 1.3 53.7 + - - +
252W THR* 2.3 41.6 + - - +
282W ASN* 4.1 22.7 - - + +
286W ILE* 6.0 0.7 - - + -
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Residues in contact with ALA 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 PRO 2.5 20.9 + - - +
246W GLU* 3.7 5.8 - - - +
248W VAL* 1.3 74.2 - - - +
250W MET* 1.3 56.3 + - - +
252W THR* 4.0 0.2 - - - -
253W VAL* 2.8 36.6 + - - +
282W ASN 5.4 0.2 + - - -
285W ALA* 3.7 7.2 - - + -
286W ILE* 3.4 47.6 - - + +
289W CYS* 3.8 8.7 - - + -
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Residues in contact with MET 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 GLU 2.5 22.9 + - - +
247W GLN* 3.4 10.1 - - - +
248W VAL 3.2 0.2 - - - -
249W ALA* 1.3 70.7 - - - +
251W ALA* 1.3 58.5 + - - +
253W VAL* 4.2 0.2 - - - +
254W THR* 2.5 62.5 + - + +
289W CYS* 3.5 20.4 - - - -
290W PRO* 5.4 6.5 - - - -
291W LEU* 3.4 26.2 - - + -
364W SO4 5.6 4.9 - - - +
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Residues in contact with ALA 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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198W LEU* 4.2 17.0 - - + -
202W GLN* 3.2 31.3 - - - +
233W VAL* 3.6 21.0 - - + +
247W GLN 2.9 17.1 + - - +
248W VAL 4.2 0.9 - - - +
250W MET* 1.3 75.5 - - - +
252W THR* 1.3 63.4 + - - +
254W THR* 3.3 4.0 - - - -
255W ALA* 3.0 26.7 + - - +
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Residues in contact with THR 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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232W MET* 4.2 1.1 - - + +
233W VAL* 3.1 39.3 + - + +
248W VAL* 2.3 29.9 + - - +
249W ALA* 3.5 7.0 - - - -
251W ALA* 1.3 79.2 - - - +
253W VAL* 1.3 63.1 + - - +
255W ALA* 3.7 2.3 + - - +
256W LEU* 3.3 25.9 + - + +
269W PHE* 3.4 40.2 - - + -
286W ILE* 4.0 10.1 - - + -
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Residues in contact with VAL 253 (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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249W ALA 2.8 23.1 + - - +
252W THR* 1.3 71.5 - - - +
254W THR* 1.3 68.7 + - - +
256W LEU* 3.1 7.4 + - - +
257W HIS* 2.8 25.1 + - + +
286W ILE* 3.4 42.2 - - + +
289W CYS* 4.0 11.0 - - + -
291W LEU* 4.0 17.0 - - + -
292W PRO 3.9 9.6 - - - +
293W LYS* 3.8 24.0 - - + -
295W TRP* 5.0 4.5 - - + -
297W LEU* 4.5 7.0 - - + -
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Residues in contact with THR 254 (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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202W GLN* 3.0 15.3 - - - +
250W MET* 2.5 52.9 + - + +
251W ALA* 3.3 6.5 - - - -
253W VAL* 1.3 76.2 - - - +
255W ALA* 1.3 64.0 + - - +
257W HIS* 2.5 24.9 + - - -
258W ARG* 3.0 39.2 - - - +
291W LEU* 3.3 11.3 - - + +
364W SO4 3.4 6.7 + - - +
224X GLU* 4.7 4.0 - - - +
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Residues in contact with ALA 255 (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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202W GLN* 4.2 8.1 - - + +
205W THR* 4.6 17.3 - - + -
206W GLU* 3.3 37.7 - - + +
233W VAL* 5.2 0.9 - - + -
251W ALA 3.0 13.6 + - - +
252W THR* 3.9 4.3 - - - +
254W THR* 1.3 77.6 - - - +
256W LEU* 1.3 55.3 + - + +
258W ARG* 2.8 32.6 + - - +
259W THR* 3.0 12.1 + - + +
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Residues in contact with LEU 256 (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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205W THR* 5.9 1.3 - - + -
209W LEU* 4.0 14.6 - - + +
228W LEU* 4.0 9.4 - - + -
230W PRO* 4.6 5.4 - - + -
231W ASN 5.8 0.2 - - - +
233W VAL* 6.5 0.2 - - + -
252W THR* 3.3 19.7 + - + +
253W VAL* 3.1 6.0 + - - +
255W ALA* 1.3 79.3 - - + +
257W HIS* 1.3 57.5 + - - +
258W ARG 3.2 0.2 - - - -
259W THR* 3.1 5.4 + - - -
260W VAL* 2.9 63.2 + - + +
267W ILE* 3.9 19.3 - - + -
269W PHE* 3.4 37.9 - - + -
295W TRP* 3.5 10.9 - - + -
297W LEU* 4.4 7.6 - - + -
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Residues in contact with HIS 257 (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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253W VAL 2.8 16.0 + - - +
254W THR* 2.5 36.4 + - - -
255W ALA 2.9 0.6 + - - -
256W LEU* 1.3 72.9 - - - +
258W ARG* 1.3 51.0 + - + +
259W THR 3.6 0.2 - - - -
260W VAL 4.4 1.6 - - - -
291W LEU* 4.3 12.1 - - + +
292W PRO* 3.7 43.9 - - + +
295W TRP* 3.7 13.9 - - + -
224X GLU* 3.5 23.6 + - + +
262X ALA* 2.7 24.5 + - + -
263X ALA* 2.7 71.9 + - + +
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Residues in contact with ARG 258 (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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202W GLN* 3.1 6.3 + - - -
206W GLU* 3.3 26.5 + - - +
210W ALA* 5.2 0.9 - - - +
254W THR* 3.0 25.2 + - - +
255W ALA* 2.8 18.1 + - - +
257W HIS* 1.3 77.9 - - - +
259W THR* 1.3 63.2 + - + +
364W SO4 2.7 34.2 + - - -
217X ASN* 4.7 6.7 + - - +
221X VAL 5.9 0.8 + - - -
222X TYR* 4.5 14.5 - - - +
223X LEU* 3.4 29.9 - - + +
224X GLU* 2.7 41.6 + - - -
261X PRO* 3.4 27.2 - - - +
263X ALA* 3.4 9.2 - - + -
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Residues in contact with THR 259 (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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206W GLU* 3.3 47.6 - - + +
209W LEU* 3.5 20.6 - - + +
210W ALA* 4.1 14.6 - - - +
213W TYR* 4.1 9.3 - - - +
255W ALA 3.0 18.4 + - - +
256W LEU* 3.1 12.5 - - - -
258W ARG* 1.3 84.0 - - + +
260W VAL* 1.3 74.6 + - - +
261W PRO* 3.5 9.7 - - - +
217X ASN* 4.5 3.8 - - - +
261X PRO* 4.9 5.5 - - - +
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Residues in contact with VAL 260 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209W LEU* 3.7 8.1 - - + -
213W TYR* 3.5 30.1 - - + +
228W LEU* 3.8 3.6 - - + -
256W LEU* 2.9 46.0 + - + +
257W HIS 4.4 7.3 - - - +
259W THR* 1.3 82.0 + - - +
261W PRO* 1.4 71.2 - - + +
262W ALA 4.0 0.7 + - - -
264W VAL* 4.3 5.4 - - + -
267W ILE* 3.8 13.0 - - + -
295W TRP* 3.3 33.6 + - + +
261X PRO* 5.3 2.0 - - - -
262X ALA* 4.4 5.7 + - - +
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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
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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