Contacts of the helix formed by residues 252 - 268 (chain C) in PDB entry 1XPM
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 ASP 252 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225C ALA* 5.3 3.8 - - - -
250C ASN 4.1 0.6 + - - -
251C ALA* 1.3 77.1 - - - +
253C GLU* 1.3 59.8 + - - +
254C THR* 3.7 10.8 - - - -
255C THR* 3.0 36.8 + - - -
256C GLN* 2.9 25.3 + - - +
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Residues in contact with GLU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C ALA 5.6 0.4 - - - +
252C ASP* 1.3 70.8 - - - +
254C THR* 1.3 65.8 + - - +
256C GLN* 3.8 15.9 - - - +
257C GLU* 3.0 24.9 + - - +
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Residues in contact with THR 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C ASP* 3.2 9.9 - - - +
253C GLU* 1.3 78.1 - - - +
255C THR* 1.3 64.2 + - - +
257C GLU* 3.6 5.2 + - - +
258C ARG* 3.2 35.3 + - + +
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Residues in contact with THR 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C LEU 3.8 21.3 - - - +
225C ALA* 3.5 19.9 - - - +
251C ALA* 3.9 16.6 - - + -
252C ASP* 3.0 26.1 + - - -
254C THR* 1.3 76.4 - - - +
256C GLN* 1.3 59.8 + - - +
258C ARG* 3.2 16.4 + - - +
259C LEU* 2.9 52.0 + - + +
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Residues in contact with GLN 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C ILE* 2.6 45.9 + - + +
249C ASP* 3.4 14.1 + - - +
251C ALA* 3.6 10.5 - - + +
252C ASP 2.9 17.2 + - - +
253C GLU* 3.8 21.3 - - - +
255C THR* 1.3 77.0 - - - +
257C GLU* 1.3 61.7 + - - +
259C LEU* 4.2 1.7 - - - +
260C ARG* 3.0 67.7 + - - +
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Residues in contact with GLU 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C GLU 3.0 16.9 + - - +
254C THR* 3.9 5.6 - - - +
256C GLN* 1.3 77.0 - - - +
258C ARG* 1.3 63.8 + - - +
260C ARG* 3.5 8.0 + - - +
261C SER* 3.1 24.3 + - - -
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Residues in contact with ARG 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C LEU 3.9 2.4 + - - -
225C ALA* 3.0 33.3 + - - +
227C PHE 2.9 29.6 + - - -
228C ALA* 3.4 25.8 - - - +
254C THR* 3.2 30.3 + - - +
255C THR* 3.7 16.0 + - - +
257C GLU* 1.3 81.5 - - - +
259C LEU* 1.3 57.1 + - - +
261C SER* 3.2 6.9 + - - -
262C GLY* 2.9 25.3 + - - -
292C ARG* 3.7 13.9 + - - +
298C GLU* 5.9 1.8 - - - -
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Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C LEU* 4.0 19.1 - - + +
227C PHE* 3.8 18.4 - - + +
228C ALA 4.2 1.8 - - - +
229C SER* 3.6 34.6 + - - +
230C LEU* 4.1 22.1 + - + +
244C LEU* 4.2 16.5 - - + +
248C ILE* 4.3 18.6 - - + -
255C THR* 2.9 38.2 + - + +
256C GLN 4.2 2.0 - - - +
258C ARG* 1.3 74.6 - - + +
260C ARG* 1.3 61.5 + - - +
262C GLY* 3.4 2.3 + - - +
263C TYR* 3.0 27.5 + - - +
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Residues in contact with ARG 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C LYS* 3.7 15.3 + - - +
244C LEU* 4.1 8.7 - - + -
245C GLU* 2.7 43.6 + - - +
248C ILE* 3.3 17.8 - - + +
256C GLN* 3.0 54.1 + - - +
257C GLU* 3.9 7.2 - - - +
259C LEU* 1.3 76.1 - - - +
261C SER* 1.3 62.0 + - - +
263C TYR* 3.4 4.7 + - - +
264C GLU* 3.3 26.5 + - - +
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Residues in contact with SER 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C GLU* 3.1 20.0 + - - -
258C ARG* 3.5 4.5 - - - -
260C ARG* 1.3 75.8 - - - +
262C GLY* 1.3 65.2 + - - +
264C GLU* 3.2 10.0 + - - +
265C ASP* 3.2 18.7 + - - +
292C ARG* 2.8 31.9 + - - -
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Residues in contact with GLY 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C SER* 3.4 23.1 - - - -
230C LEU 4.8 0.4 - - - -
258C ARG 2.9 14.7 + - - -
259C LEU 3.8 1.3 - - - -
260C ARG 3.3 0.2 - - - -
261C SER* 1.3 76.4 - - - +
263C TYR* 1.3 57.0 + - - +
265C ASP* 3.2 4.7 + - - +
266C ALA* 2.9 28.8 + - - +
288C LEU* 3.7 3.6 - - - +
292C ARG* 3.6 20.1 - - - +
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Residues in contact with TYR 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C SER* 4.4 0.2 + - - -
230C LEU 4.9 4.2 + - - -
232C PHE* 4.2 30.1 - + + -
234C VAL* 5.2 3.3 - - + +
236C PHE 4.5 0.2 + - - -
237C THR* 2.7 35.2 + - - -
240C GLY* 3.0 31.3 + - - -
241C LYS* 3.9 18.6 - - + -
244C LEU* 3.9 20.0 - - + -
259C LEU 3.0 14.1 + - - +
260C ARG 3.5 8.7 - - - +
261C SER 3.2 0.2 - - - -
262C GLY* 1.3 76.9 - - - +
264C GLU* 1.3 79.8 + - - +
266C ALA* 3.0 9.2 + - + +
267C VAL* 3.0 53.3 + - + +
271C ARG* 5.8 0.7 - - - -
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Residues in contact with GLU 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C LYS* 5.1 10.2 + - - +
260C ARG 3.3 12.1 + - - +
261C SER* 3.2 11.2 + - - +
263C TYR* 1.3 94.5 - - - +
265C ASP* 1.3 63.8 + - - +
267C VAL* 3.6 4.8 + - - +
268C ASP* 3.3 22.2 + - - +
271C ARG* 3.1 30.4 + - - -
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Residues in contact with ASP 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C SER* 3.2 5.5 + - - -
262C GLY 3.2 8.4 + - - +
263C TYR 3.2 0.4 - - - -
264C GLU* 1.3 80.0 - - - +
266C ALA* 1.3 53.1 + - - +
267C VAL 3.5 0.2 + - - -
268C ASP* 3.6 2.6 + - - +
287C SER* 2.6 35.2 + - - +
288C LEU* 4.2 5.8 - - + -
291C ASN* 3.6 27.0 + - + +
292C ARG* 2.8 54.9 + - + +
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Residues in contact with ALA 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C LEU 4.5 8.1 - - - +
231C CYS* 4.4 9.2 - - - -
232C PHE 5.7 0.4 - - - +
262C GLY 2.9 13.3 + - - +
263C TYR* 3.0 14.8 + - + +
265C ASP* 1.3 78.5 - - - +
267C VAL* 1.3 59.0 - - + +
268C ASP 3.4 0.2 - - - -
270C ASN* 3.1 3.1 - - - +
284C SER* 2.6 51.5 + - - +
287C SER* 3.2 4.3 - - - -
288C LEU* 3.9 16.3 - - + +
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Residues in contact with VAL 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C VAL* 3.8 20.2 - - + -
237C THR* 3.6 24.0 - - + -
263C TYR* 3.0 61.1 + - + +
264C GLU* 3.8 10.3 - - - +
266C ALA* 1.3 79.7 - - - +
268C ASP* 1.3 68.7 + - - +
269C TYR 3.4 1.8 - - - -
270C ASN* 3.2 8.6 + - + +
271C ARG* 3.1 34.6 + - - +
284C SER* 4.5 1.1 - - - +
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Residues in contact with ASP 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C GLU 3.3 12.7 + - - +
265C ASP* 3.7 6.1 - - - +
266C ALA 3.4 1.8 - - - -
267C VAL* 1.3 78.7 - - - +
269C TYR* 1.3 74.1 + - - +
271C ARG* 3.3 16.3 + - - +
272C TYR* 3.2 36.9 + - - -
287C SER* 3.4 9.4 - - - +
291C ASN* 3.4 25.6 + - - +
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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
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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