Contacts of the helix formed by residues 252 - 268 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225D ALA* 5.5 4.2 - - - +
250D ASN 4.1 1.0 + - - -
251D ALA* 1.3 76.8 - - - +
253D GLU* 1.3 63.9 + - - +
254D THR* 3.9 11.2 + - - -
255D THR* 2.5 36.3 + - - -
256D GLN* 3.0 18.0 + - - +
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Residues in contact with GLU 253 (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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252D ASP* 1.3 74.4 - - - +
254D THR* 1.3 64.8 + - - +
256D GLN* 3.3 13.8 + - - +
257D GLU* 3.0 25.3 + - - +
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Residues in contact with THR 254 (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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252D ASP* 3.3 12.3 + - - -
253D GLU* 1.3 78.0 - - - +
255D THR* 1.3 63.6 + - - +
257D GLU* 3.5 5.4 + - - +
258D ARG* 3.1 37.2 + - + +
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Residues in contact with THR 255 (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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224D LEU* 3.8 22.0 - - + +
225D ALA* 3.7 18.2 - - - +
251D ALA* 3.8 18.6 - - + -
252D ASP* 2.5 33.6 + - - -
254D THR* 1.3 72.5 - - - +
256D GLN* 1.3 59.3 + - - +
258D ARG* 3.3 17.6 + - - +
259D LEU* 2.9 51.2 + - + +
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Residues in contact with GLN 256 (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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248D ILE* 2.6 43.3 + - + +
249D ASP* 3.5 12.7 + - - +
251D ALA* 3.5 12.4 + - + +
252D ASP 3.0 18.5 + - - +
253D GLU* 3.3 14.7 + - - +
255D THR* 1.3 76.6 - - - +
257D GLU* 1.3 61.7 + - - +
259D LEU* 4.2 3.5 - - - +
260D ARG* 3.0 66.6 + - - +
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Residues in contact with GLU 257 (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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253D GLU 3.0 16.9 + - - +
254D THR* 3.9 4.7 - - - +
256D GLN* 1.3 76.9 - - - +
258D ARG* 1.3 64.9 + - - +
260D ARG* 3.9 7.3 - - - +
261D SER* 3.0 27.6 + - - -
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Residues in contact with ARG 258 (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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224D LEU 3.9 2.0 + - - -
225D ALA* 3.1 33.7 + - - +
227D PHE 3.0 29.6 + - - -
228D ALA* 3.4 25.6 + - - +
254D THR* 3.1 41.9 + - + +
255D THR* 3.7 15.6 + - - +
256D GLN 3.3 0.2 - - - -
257D GLU* 1.3 77.7 - - - +
259D LEU* 1.3 58.3 + - - +
261D SER* 3.3 4.0 + - - -
262D GLY* 2.9 24.9 + - - -
292D ARG* 3.6 16.5 + - - +
298D GLU* 5.8 1.8 - - - -
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Residues in contact with LEU 259 (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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224D LEU* 4.0 19.1 - - + +
227D PHE* 3.7 20.0 - - + +
228D ALA 4.1 1.8 - - - +
229D SER* 3.7 29.8 + - - +
230D LEU* 4.1 25.8 + - + +
244D LEU* 4.3 15.7 - - + +
248D ILE* 4.1 20.0 - - + -
255D THR* 2.9 42.1 + - + +
256D GLN 4.2 1.8 - - - +
258D ARG* 1.3 71.2 - - - +
260D ARG* 1.3 60.8 + - - +
262D GLY* 3.4 2.2 + - - +
263D TYR* 3.0 28.4 + - - +
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Residues in contact with ARG 260 (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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241D LYS* 3.7 15.5 + - - +
244D LEU* 4.2 8.7 - - + -
245D GLU* 2.8 42.8 + - - +
248D ILE* 3.4 17.6 - - + +
256D GLN* 3.0 52.0 + - - +
257D GLU* 3.9 6.8 - - - +
259D LEU* 1.3 73.0 - - - +
261D SER* 1.3 66.8 + - - +
263D TYR* 3.3 4.0 + - - +
264D GLU* 3.2 27.2 + - - +
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Residues in contact with SER 261 (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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257D GLU* 3.0 21.8 + - - -
258D ARG* 3.6 4.7 - - - -
260D ARG* 1.3 78.0 - - - +
262D GLY* 1.3 63.6 + - - +
264D GLU* 3.3 10.4 + - - +
265D ASP* 3.3 18.4 + - - +
292D ARG* 3.1 25.8 + - - -
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Residues in contact with GLY 262 (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* 3.5 22.0 - - - -
258D ARG 2.9 15.5 + - - -
259D LEU 3.8 1.1 - - - -
260D ARG 3.3 0.2 - - - -
261D SER* 1.3 77.9 - - - +
263D TYR* 1.3 56.0 + - - +
265D ASP* 3.2 4.4 + - - +
266D ALA* 2.9 28.1 + - - +
288D LEU* 3.7 4.0 - - - +
292D ARG* 3.6 20.4 - - - +
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Residues in contact with TYR 263 (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* 4.4 0.6 + - - -
230D LEU 4.9 3.8 + - - +
232D PHE* 4.2 29.8 - + + -
234D VAL* 5.0 4.1 - - + +
237D THR* 2.8 29.3 + - - -
240D GLY* 2.9 33.0 + - - -
241D LYS* 3.8 19.1 - - + -
244D LEU* 3.9 19.7 - - + -
259D LEU 3.0 14.1 + - - +
260D ARG 3.5 8.5 - - - +
261D SER 3.2 0.2 - - - -
262D GLY* 1.3 77.2 - - - +
264D GLU* 1.3 77.5 + - - +
266D ALA* 3.1 8.7 + - + +
267D VAL* 3.0 57.5 + - + +
271D ARG* 6.0 0.9 - - - -
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Residues in contact with GLU 264 (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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241D LYS* 5.0 10.7 + - - +
260D ARG 3.2 14.4 + - - +
261D SER* 3.6 10.3 - - - +
262D GLY 3.3 0.4 - - - -
263D TYR* 1.3 93.1 - - - +
265D ASP* 1.3 63.1 + - - +
267D VAL* 3.6 4.8 + - - +
268D ASP* 3.3 21.3 + - - +
271D ARG* 3.1 29.6 + - - -
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Residues in contact with ASP 265 (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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261D SER* 3.3 5.8 + - - -
262D GLY 3.2 9.1 + - - +
263D TYR 3.2 0.6 - - - -
264D GLU* 1.3 79.3 - - - +
266D ALA* 1.3 53.0 + - - +
267D VAL 3.6 0.2 + - - -
268D ASP* 3.6 7.1 + - - +
287D SER* 2.7 34.7 + - - +
288D LEU* 4.2 5.6 - - + -
291D ASN* 3.6 24.0 + - + +
292D ARG* 2.7 55.8 + - + +
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Residues in contact with ALA 266 (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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230D LEU 4.5 7.2 - - - +
231D CYS* 4.5 8.3 - - - -
232D PHE 5.8 0.2 - - - +
262D GLY 2.9 16.9 + - - +
263D TYR* 3.1 11.6 + - + +
265D ASP* 1.3 78.3 - - - +
267D VAL* 1.3 57.7 - - + +
270D ASN* 3.2 0.5 - - - +
284D SER* 2.7 49.4 + - - +
287D SER* 3.2 7.6 - - - -
288D LEU* 3.9 17.3 - - + +
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Residues in contact with VAL 267 (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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234D VAL* 3.8 20.4 - - + -
237D THR* 3.7 23.6 - - + -
263D TYR* 3.0 58.1 + - + +
264D GLU* 3.8 10.1 - - - +
266D ALA* 1.3 78.3 - - - +
268D ASP* 1.3 68.4 + - - +
269D TYR 3.4 2.0 - - - -
270D ASN* 3.2 10.2 + - + +
271D ARG* 3.1 33.5 + - - +
284D SER* 4.5 1.3 - - - +
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Residues in contact with ASP 268 (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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264D GLU 3.3 12.1 + - - +
265D ASP* 3.6 6.5 - - - +
266D ALA 3.4 1.6 - - - -
267D VAL* 1.3 79.3 - - - +
269D TYR* 1.3 74.5 + - - +
271D ARG* 3.3 15.6 + - - +
272D TYR* 3.2 36.5 + - - -
287D SER* 3.4 9.6 - - - +
291D ASN* 3.3 27.5 + - - +
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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