Contacts of the helix formed by residues 257 - 275 (chain B) in PDB entry 1U2X
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 257 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B THR 3.2 16.6 - - - +
251B LYS* 3.8 17.6 + - + +
252B TYR* 3.7 8.5 - - - -
255B GLY 5.1 1.1 - - - -
256B LYS* 1.3 77.8 - - - +
258B ALA* 1.3 68.8 + - - +
259B ASN* 3.5 15.9 + - - +
260B TYR* 3.1 31.7 + - - +
261B TYR* 3.4 14.2 + - - -
263B ARG* 4.9 1.6 + - - -
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Residues in contact with ALA 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LEU* 4.5 7.4 - - + +
249B ARG 3.5 19.8 + - - +
250B THR* 3.1 11.6 + - - +
252B TYR* 4.5 2.9 - - - -
257B ASP* 1.3 74.8 - - - +
259B ASN* 1.3 64.2 + - - +
261B TYR* 3.2 6.2 + - - +
262B LEU* 2.9 27.1 + - + +
291B LEU* 3.6 27.4 - - + -
294B LYS* 4.5 14.8 - - + -
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Residues in contact with ASN 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ASP* 3.2 17.4 - - - +
258B ALA* 1.3 77.4 - - - +
260B TYR* 1.3 62.1 + - - +
262B LEU* 3.2 11.0 + - - +
263B ARG* 2.9 42.4 + - + +
294B LYS* 3.3 42.9 + - - +
298B ASN* 4.5 8.5 + - - +
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Residues in contact with TYR 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLU* 4.5 1.7 + - - -
256B LYS* 3.5 50.3 + - + -
257B ASP* 3.1 27.6 + - - +
259B ASN* 1.3 76.3 - - - +
261B TYR* 1.3 82.4 + + - +
263B ARG* 3.4 29.5 + - - +
264B ARG* 3.4 57.2 + - + +
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Residues in contact with TYR 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ARG* 3.0 45.1 + - + +
220B ILE 3.6 21.9 - - - +
221B GLU* 3.7 34.1 + - + +
248B LEU* 3.6 23.6 - - + -
252B TYR* 3.6 39.3 - + - -
256B LYS* 3.6 20.8 + - + +
257B ASP 3.4 12.4 + - - -
258B ALA 3.2 5.5 + - - +
260B TYR* 1.3 93.3 - + - +
262B LEU* 1.3 57.3 + - - +
264B ARG* 3.2 6.7 + - - +
265B ALA* 3.0 24.6 + - - +
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Residues in contact with LEU 262 (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 TYR* 4.4 8.5 - - + -
248B LEU* 3.9 22.0 - - + -
258B ALA* 2.9 27.3 + - + +
259B ASN* 3.2 8.2 + - - +
261B TYR* 1.3 73.7 - - - +
263B ARG* 1.3 65.9 + - - +
265B ALA* 3.6 3.9 - - + +
266B LYS* 3.0 30.2 + - - +
291B LEU* 5.2 0.4 - - + -
294B LYS* 3.6 26.7 - - + +
295B ILE* 4.2 8.7 - - + +
298B ASN* 3.6 34.2 - - + +
299B ILE* 4.1 28.9 - - + -
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Residues in contact with ARG 263 (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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257B ASP* 4.9 1.6 + - - -
259B ASN* 2.9 41.0 + - + +
260B TYR* 3.6 34.6 - - - +
261B TYR 3.3 0.2 - - - -
262B LEU* 1.3 75.5 - - - +
264B ARG* 1.3 62.8 + - + +
266B LYS* 3.5 25.0 + - - +
267B GLU* 3.1 29.9 + - - +
298B ASN* 5.4 0.9 - - - +
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Residues in contact with ARG 264 (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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221B GLU* 2.6 34.6 + - + +
222B THR 2.8 26.6 + - - +
224B GLU* 3.1 34.3 + - - +
227B LYS* 3.4 25.6 - - - +
260B TYR* 3.4 45.5 + - + +
261B TYR* 3.2 11.7 + - - +
262B LEU 3.2 0.4 - - - -
263B ARG* 1.3 76.7 - - + +
265B ALA* 1.4 61.6 + - - +
267B GLU* 3.3 19.3 + - - +
268B ASP* 3.1 30.9 + - - +
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Residues in contact with ALA 265 (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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34B TYR* 4.6 6.1 + - + +
220B ILE 6.0 1.1 - - - +
242B PHE* 5.2 0.2 - - - -
245B TYR* 3.8 31.5 + - + +
261B TYR 3.0 14.1 + - - +
262B LEU* 3.6 11.2 - - + +
263B ARG 3.2 0.2 - - - -
264B ARG* 1.4 78.1 - - - +
266B LYS* 1.3 60.8 + - - +
268B ASP* 3.3 12.8 + - - +
269B ILE* 3.2 28.0 + - - +
299B ILE* 3.8 10.3 - - + -
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Residues in contact with LYS 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B LEU 3.0 18.5 + - - +
263B ARG* 3.8 23.4 - - - +
264B ARG 3.4 0.4 - - - -
265B ALA* 1.3 72.7 - - - +
267B GLU* 1.3 63.2 + - - +
269B ILE* 3.3 10.5 + - + +
270B ILE* 3.1 32.8 + - + +
298B ASN* 2.7 55.3 + - + +
299B ILE* 4.9 1.8 - - + -
302B PHE* 4.6 14.8 - - + -
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Residues in contact with GLU 267 (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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227B LYS* 2.8 42.9 + - - +
263B ARG* 3.1 20.9 + - - +
264B ARG* 3.3 15.5 + - - +
266B LYS* 1.3 73.9 - - - +
268B ASP* 1.3 63.6 + - - +
270B ILE* 3.2 13.1 + - + +
271B GLU* 3.0 31.9 + - + +
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Residues in contact with ASP 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR* 2.7 31.8 + - - +
221B GLU* 5.2 0.5 - - - -
222B THR* 2.7 30.5 + - - -
227B LYS* 3.6 12.6 + - - -
230B LEU* 3.0 26.3 - - + +
242B PHE* 4.5 7.2 - - + -
264B ARG* 3.1 20.9 + - - +
265B ALA* 3.5 7.7 - - - +
266B LYS 3.3 0.4 - - - -
267B GLU* 1.3 74.5 - - - +
269B ILE* 1.3 62.2 + - - +
271B GLU* 3.3 4.0 + - - +
272B PHE* 3.2 29.4 + - + -
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Residues in contact with ILE 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PHE* 3.9 20.0 - - + -
245B TYR* 4.6 2.5 - - - +
265B ALA 3.2 15.1 + - - +
266B LYS* 3.6 11.4 - - - +
267B GLU 3.3 0.2 - - - -
268B ASP* 1.3 79.6 - - - +
270B ILE* 1.3 57.1 + - + +
272B PHE* 3.3 1.2 + - - -
273B LYS* 2.8 49.7 + - + +
279B ILE* 3.8 10.3 - - + +
298B ASN 5.0 0.7 - - - +
299B ILE* 4.1 31.2 - - + +
302B PHE* 3.6 32.1 - - + +
303B VAL* 3.7 24.7 - - + -
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Residues in contact with ILE 270 (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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266B LYS* 3.1 28.1 + - + +
267B GLU* 3.5 11.2 - - + +
269B ILE* 1.3 77.3 - - + +
271B GLU* 1.3 73.8 - - - +
273B LYS* 4.0 3.9 - - - +
274B GLU* 3.0 28.5 + - + +
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Residues in contact with GLU 271 (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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227B LYS* 5.4 3.8 - - - +
230B LEU* 4.1 26.7 - - + -
231B GLY* 4.1 21.4 + - - +
267B GLU* 3.0 22.7 + - + +
268B ASP 3.6 7.0 - - - +
269B ILE 3.2 0.4 - - - -
270B ILE* 1.3 87.2 - - - +
272B PHE* 1.4 60.9 + - - +
274B GLU* 3.7 6.4 + - - +
275B LYS* 3.6 20.4 + - - +
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Residues in contact with PHE 272 (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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31B TYR* 3.6 37.5 - + + -
230B LEU* 4.0 33.2 - - + -
233B ILE* 4.0 14.6 - - + -
234B GLY* 3.9 26.9 - - - -
237B VAL* 4.2 4.5 - - + -
240B ALA* 4.3 4.3 - - + -
242B PHE* 3.8 21.5 - + - -
268B ASP* 3.2 25.2 + - + -
269B ILE 4.0 4.0 - - - +
271B GLU* 1.4 76.4 - - - +
273B LYS* 1.3 66.1 + - - +
275B LYS* 3.1 12.2 + - - -
277B VAL* 3.1 41.1 + - + +
279B ILE* 4.0 14.4 - - + -
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Residues in contact with LYS 273 (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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269B ILE* 2.8 32.9 + - + +
270B ILE* 3.4 5.4 + - - +
272B PHE* 1.3 72.8 - - - +
274B GLU* 1.3 62.7 + - - +
276B ASP* 3.1 15.2 + - - +
277B VAL 3.8 11.2 - - - +
279B ILE* 3.6 13.0 - - + -
301B PRO 5.7 0.2 + - - -
302B PHE* 2.8 33.8 + - - +
303B VAL* 4.0 5.4 + - - +
304B ASP* 3.6 36.5 + - - +
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Residues in contact with GLU 274 (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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270B ILE* 3.0 21.7 + - + +
271B GLU* 4.0 5.1 - - - +
272B PHE 3.2 0.6 - - - -
273B LYS* 1.3 76.9 - - - +
275B LYS* 1.3 89.4 + - - +
276B ASP* 3.2 10.3 + - - +
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Residues in contact with LYS 275 (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 GLY* 3.2 36.3 + - - +
234B GLY* 4.0 20.5 - - - +
235B LYS* 3.8 35.2 - - + +
237B VAL 5.4 0.5 - - - +
271B GLU* 3.6 14.7 + - - +
272B PHE 3.1 8.7 + - - +
274B GLU* 1.3 99.0 - - - +
276B ASP* 1.3 70.1 + - - +
277B VAL* 3.2 6.2 + - + +
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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
------------------------------------------------------------
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