Contacts of the helix formed by residues 244 - 260 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243B TYR* 1.3 73.0 - - - +
245B PRO* 1.3 63.7 - - - +
246B GLU* 2.6 47.4 + - + +
247B GLN* 2.6 54.8 + - + +
248B VAL* 3.0 9.8 + - - -
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Residues in contact with PRO 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B TYR 4.0 3.1 - - - +
244B THR* 1.3 90.0 - - - +
246B GLU* 1.3 57.2 + - - +
248B VAL* 4.3 6.0 - - + +
249B ALA* 2.8 38.1 + - - +
278B ASP* 5.5 2.0 - - - +
281B LEU* 3.9 26.0 - - + +
282B ASN* 3.5 25.4 - - - +
285B ALA* 3.0 22.2 - - + +
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Residues in contact with GLU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B THR* 2.6 38.5 + - + +
245B PRO* 1.3 83.2 - - - +
247B GLN* 1.3 59.3 + - + +
249B ALA* 3.5 3.3 - - - +
250B MET* 3.0 26.4 + - - +
285B ALA* 4.6 9.7 - - - +
289B CYS* 5.7 0.5 - - - +
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Residues in contact with GLN 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B LEU* 4.0 17.3 - - + -
242B LYS 3.7 4.0 + - - +
243B TYR* 3.0 22.0 - - + -
244B THR* 2.6 49.3 + - + +
246B GLU* 1.3 69.4 - - + +
248B VAL* 1.3 63.4 + - - +
249B ALA 2.9 4.5 - - - -
250B MET* 2.8 19.3 + - - +
251B ALA* 2.8 16.5 + - - +
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Residues in contact with VAL 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 4.6 3.4 - - + -
232B MET* 4.9 4.5 - - - -
233B VAL 3.2 8.7 - - - +
234B THR* 3.9 36.6 - - + -
243B TYR* 3.5 32.3 - - + +
244B THR 3.0 9.0 + - - +
245B PRO* 4.3 3.8 - - + +
247B GLN* 1.3 79.1 - - - +
249B ALA* 1.3 54.4 + - - +
252B THR* 2.7 30.5 + - - +
282B ASN* 3.0 38.1 - - + +
286B ILE* 4.7 1.0 - - + +
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B PRO 2.8 22.6 + - - +
246B GLU 3.5 3.1 - - - +
247B GLN 2.9 0.6 - - - -
248B VAL* 1.3 79.1 - - + +
250B MET* 1.3 59.8 + - - +
252B THR* 3.3 1.6 - - - -
253B VAL* 2.8 36.3 + - - +
282B ASN 4.5 0.2 - - - +
285B ALA* 3.6 5.4 - - + +
286B ILE* 3.2 45.1 - - + +
289B CYS* 4.7 3.8 - - + -
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Residues in contact with MET 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B GLU 3.0 14.1 + - - +
247B GLN* 2.8 15.6 + - - +
249B ALA* 1.3 66.0 - - - +
251B ALA* 1.3 69.6 + - - +
252B THR 2.7 2.9 + - - -
253B VAL 3.0 0.9 + - - -
254B THR* 2.8 36.8 + - - +
289B CYS* 3.6 14.3 - - - -
290B PRO* 5.2 9.9 - - + -
291B LEU* 3.1 36.8 - - + -
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B LEU* 3.6 37.7 - - + -
202B GLN* 3.2 33.9 - - + +
233B VAL* 3.7 9.9 - - + +
247B GLN 2.8 17.0 + - - +
250B MET* 1.3 76.5 - - - +
252B THR* 1.3 60.8 + - - +
254B THR* 3.6 3.3 - - - -
255B ALA* 3.3 11.4 + - - +
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Residues in contact with THR 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B ASN 5.1 1.3 - - - +
232B MET* 3.8 3.3 - - - +
233B VAL* 2.9 35.1 + - + +
248B VAL 2.7 20.8 + - - -
249B ALA* 3.3 9.2 + - - -
250B MET 2.7 1.0 + - - -
251B ALA* 1.3 75.5 - - - +
253B VAL* 1.3 63.1 + - - +
254B THR 3.1 1.9 + - - -
255B ALA* 3.2 5.7 + - - +
256B LEU* 2.8 30.9 + - + +
269B PHE* 3.2 39.7 - - + -
286B ILE* 3.9 7.8 - - + +
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Residues in contact with VAL 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B ALA 2.8 23.9 + - - +
252B THR* 1.3 68.9 - - + +
254B THR* 1.3 71.8 + - - +
256B LEU* 3.5 8.0 - - + +
257B HIS* 2.8 19.4 + - - -
286B ILE* 3.5 40.8 - - + +
289B CYS* 3.9 15.9 - - + -
291B LEU* 3.8 17.9 - - + -
292B PRO 4.0 3.6 - - - +
293B LYS* 3.8 28.0 - - + -
295B TRP* 4.8 7.6 - - + -
297B LEU* 4.9 1.1 - - + -
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Residues in contact with THR 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLU* 5.0 0.9 - - - +
202B GLN* 3.2 22.0 - - - +
250B MET* 2.8 36.4 + - - +
251B ALA* 3.6 5.1 - - - -
253B VAL* 1.3 78.8 - - - +
255B ALA* 1.3 57.0 + - - +
257B HIS* 2.5 45.1 + - + -
258B ARG* 3.0 28.0 - - - +
291B LEU* 4.3 5.4 - - - +
364B SO4 3.6 9.9 + - - +
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Residues in contact with ALA 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLN* 4.0 7.9 - - + -
205B THR* 4.5 17.0 - - + -
206B GLU* 3.2 36.3 - - + +
209B LEU* 5.2 1.1 - - - -
233B VAL* 4.5 2.5 - - + -
251B ALA 3.5 10.3 - - - +
252B THR 3.2 7.6 + - - +
254B THR* 1.3 79.7 - - - +
256B LEU* 1.3 61.9 + - - +
258B ARG* 3.2 9.1 + - - +
259B THR* 2.9 23.0 + - - +
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Residues in contact with LEU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B THR* 5.7 1.8 - - + -
209B LEU* 3.8 15.3 - - + -
228B LEU* 4.3 6.5 - - + -
230B PRO* 4.5 6.7 - - + -
252B THR* 2.8 24.5 + - + +
253B VAL* 3.5 11.2 - - + +
254B THR 2.9 0.2 + - - -
255B ALA* 1.3 74.7 - - + +
257B HIS* 1.3 55.8 + - - +
258B ARG 3.2 0.5 + - - -
259B THR* 4.2 1.3 - - - -
260B VAL* 2.9 55.5 + - + +
267B ILE* 3.5 24.9 - - + -
269B PHE* 3.1 36.1 - - + -
295B TRP* 3.6 14.4 - - + -
297B LEU* 3.8 6.5 - - + -
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Residues in contact with HIS 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLU* 3.9 18.5 + - - +
261A PRO* 4.8 0.7 - - - -
262A ALA* 3.5 21.2 + - + -
263A ALA* 2.8 68.6 + - + +
253B VAL 2.8 10.1 + - - +
254B THR* 2.5 50.0 + - + -
256B LEU* 1.3 72.2 - - - +
258B ARG* 1.3 62.4 + - - +
259B THR 5.3 0.2 - - - -
260B VAL 4.9 1.3 - - - -
291B LEU* 3.8 19.6 - - + +
292B PRO* 3.4 39.0 - - + +
295B TRP* 3.9 10.8 - - + -
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Residues in contact with ARG 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ASN* 5.8 1.5 + - - +
222A TYR* 4.1 17.8 - - - +
223A LEU* 3.5 23.3 - - + +
224A GLU* 2.4 46.2 + - - -
261A PRO* 3.1 24.7 - - - +
263A ALA* 4.0 4.9 - - - -
202B GLN* 4.3 0.2 - - - +
206B GLU* 3.2 31.0 + - - +
254B THR* 3.0 31.8 - - - +
255B ALA* 3.4 4.9 - - - +
256B LEU 3.1 0.4 - - - -
257B HIS* 1.3 82.6 - - - +
259B THR* 1.3 67.5 + - + +
364B SO4 2.6 49.5 + - - -
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Residues in contact with THR 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ASN* 3.8 15.5 - - - +
261A PRO* 4.9 7.0 - - - +
206B GLU* 3.1 37.2 - - + +
209B LEU* 3.4 32.8 - - - +
210B ALA* 4.2 7.2 - - + +
213B TYR* 4.2 8.3 - - - +
255B ALA 2.9 15.1 + - - +
256B LEU 3.8 0.3 + - - -
258B ARG* 1.3 82.9 - - + +
260B VAL* 1.3 61.9 + - - +
261B PRO* 2.9 15.8 - - - +
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Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A PRO* 5.6 2.2 - - - +
262A ALA* 5.4 4.2 + - - +
209B LEU* 4.0 5.6 - - + -
213B TYR* 3.6 32.5 - - + +
228B LEU* 3.5 27.8 - - + -
256B LEU* 2.9 32.9 + - + +
257B HIS* 4.9 1.9 - - - -
259B THR* 1.3 76.4 - - - +
261B PRO* 1.4 58.4 - - - +
264B VAL* 3.9 14.8 - - + -
267B ILE* 4.3 5.2 - - + -
294B PRO* 5.1 0.3 - - - +
295B TRP* 2.7 44.2 + - + +
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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