Contacts of the helix formed by residues 245 - 268 (chain A) in PDB entry 1PUF
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 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A ALA* 4.0 0.4 - - - -
244A LEU* 1.3 77.2 - - - +
246A GLU* 1.3 63.9 + - - +
247A ARG* 3.4 10.7 + - - +
248A GLN* 2.9 41.0 + - - +
249A VAL* 3.0 21.7 + - - +
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Residues in contact with GLU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ARG* 4.4 5.4 - - - +
235A ARG* 3.4 36.4 + - - +
236A TYR* 3.4 30.1 + - - +
239A ALA* 3.9 20.7 - - + +
245A THR* 1.3 74.1 - - - +
247A ARG* 1.3 57.2 + - - +
249A VAL* 3.2 0.7 + - - +
250A LYS* 2.9 26.6 + - - +
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Residues in contact with ARG 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A THR* 3.1 10.4 + - - +
246A GLU* 1.3 79.1 - - - +
248A GLN* 1.3 64.5 + - + +
250A LYS* 3.2 22.8 + - - +
251A ILE* 2.9 56.0 + - + +
13D A 4.1 1.4 - - - +
14D C 2.2 64.4 + - - +
15D G 4.9 2.4 + - - -
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Residues in contact with GLN 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A LYS* 4.0 19.5 - - + +
210A CYS* 5.3 1.8 - - - +
212A TYR* 3.4 26.0 + - + +
243A ASN 4.9 0.2 - - - +
244A LEU* 3.4 21.8 - - + +
245A THR* 2.9 49.3 + - + +
247A ARG* 1.3 78.4 - - + +
249A VAL* 1.3 57.5 + - - +
251A ILE* 3.8 7.4 - - - +
252A TRP* 2.9 29.5 + - - +
13D A 2.9 33.3 + - - +
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Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A LEU* 4.3 5.2 - - + -
230A LEU* 3.7 19.3 - - + -
235A ARG* 3.8 15.5 - - + +
238A VAL* 4.3 20.6 - - + -
239A ALA* 3.7 26.9 - - + +
244A LEU* 4.2 17.5 - - + -
245A THR 3.0 17.8 + - - +
246A GLU 3.7 6.7 - - - +
247A ARG 3.2 0.2 - - - -
248A GLN* 1.3 75.0 - - - +
250A LYS* 1.3 65.3 + - - +
252A TRP* 3.2 6.0 + - - +
253A PHE* 3.1 31.8 + - + -
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Residues in contact with LYS 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A LEU* 4.0 11.7 - - - -
235A ARG* 3.9 17.9 - - - +
246A GLU 2.9 15.7 + - - +
247A ARG* 3.5 26.4 - - - +
249A VAL* 1.3 76.7 - - - +
251A ILE* 1.3 66.3 + - - +
253A PHE* 3.4 5.0 + - - +
254A GLN* 3.1 53.7 + - - +
23E G 5.9 0.6 - - - +
24E C 3.9 38.5 + - + +
25E G 3.9 8.3 + - - +
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Residues in contact with ILE 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ARG* 2.9 63.3 + - + +
248A GLN* 3.9 6.1 - - - +
250A LYS* 1.3 82.2 - - - +
252A TRP* 1.3 59.6 + - - +
254A GLN* 3.2 16.6 + - + +
255A ASN* 2.8 48.0 + - - +
12D T 5.5 2.5 - - + -
13D A 3.6 21.5 - - + +
14D C 4.3 18.8 - - + +
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Residues in contact with TRP 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A TYR* 3.7 27.8 - + + +
217A THR* 4.4 16.2 + - + +
220A LEU* 3.7 42.1 - - + +
221A GLU* 3.5 36.8 - - + -
224A PHE* 4.2 5.2 - - + -
244A LEU* 6.4 0.2 - - + -
248A GLN 2.9 19.1 + - - +
249A VAL* 3.2 7.6 + - - +
251A ILE* 1.3 78.0 - - - +
253A PHE* 1.3 79.3 + + - +
255A ASN* 3.3 8.4 + - + +
256A ARG* 2.8 51.3 + - + -
12D T 3.9 17.5 + - - -
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Residues in contact with PHE 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A LEU* 4.2 14.6 - - + -
223A GLU* 3.6 12.3 - - + -
224A PHE* 3.5 48.5 - + + -
227A ASN 3.6 14.4 - - - -
228A MET 3.5 18.4 - - - -
230A LEU* 3.4 47.6 - - + +
249A VAL* 3.1 14.7 + - + +
250A LYS 3.7 8.1 - - - +
252A TRP* 1.3 96.6 - + - +
254A GLN* 1.3 60.1 + - - +
256A ARG* 3.2 3.4 + - - +
257A ARG* 3.0 37.5 + - - +
25E G 6.1 0.4 - - - +
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Residues in contact with GLN 254 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A LYS* 3.1 33.2 + - - +
251A ILE* 3.2 21.9 + - + +
253A PHE* 1.3 76.6 - - - +
255A ASN* 1.3 63.0 + - - +
257A ARG* 3.3 28.5 + - - +
258A MET* 3.2 25.9 + - - +
14D C 5.4 7.8 + - - +
24E C 4.1 6.9 - - - +
25E G 2.8 24.5 + - - +
26E T 3.4 36.7 + - + +
27E C 5.6 1.7 + - - +
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Residues in contact with ASN 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ILE* 2.8 30.8 + - - +
252A TRP* 3.7 7.4 - - + +
254A GLN* 1.3 73.9 - - - +
256A ARG* 1.3 57.7 + - - +
258A MET* 3.0 11.8 + - - +
259A LYS* 2.9 27.6 + - - +
12D T 3.5 33.7 - - + +
13D A 2.9 47.9 + - - +
14D C 4.0 6.2 + - - -
28E G 4.4 1.7 - - - +
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Residues in contact with ARG 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A GLU* 2.9 38.6 + - - -
224A PHE* 3.4 39.2 - - + -
225A LEU* 5.4 2.0 - - - +
252A TRP* 2.8 43.6 + - + +
253A PHE 3.5 5.4 - - - +
255A ASN* 1.3 73.5 - - - +
257A ARG* 1.3 63.0 + - - +
259A LYS* 3.3 29.4 + - - +
260A MET* 3.1 29.0 + - - +
263A ILE* 5.6 5.0 - - - +
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Residues in contact with ARG 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A PHE* 3.8 18.4 - - + -
228A MET* 2.9 25.2 + - + -
229A TYR* 3.4 41.5 - - - +
230A LEU 5.1 0.4 - - - +
253A PHE* 3.0 31.0 + - - +
254A GLN* 3.5 22.6 - - - +
255A ASN 3.2 0.4 - - - -
256A ARG* 1.3 76.9 - - - +
258A MET* 1.3 68.8 + - + +
260A MET* 3.4 20.6 + - + +
261A LYS* 3.1 21.3 + - - +
25E G 3.5 26.5 + - - -
26E T 2.8 39.8 + - - +
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Residues in contact with MET 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A GLN 3.2 14.9 + - - +
255A ASN* 3.0 14.6 + - - +
257A ARG* 1.3 81.5 - - + +
259A LYS* 1.3 60.3 + - - +
261A LYS* 3.3 35.7 + - + +
262A LYS* 2.8 27.9 + - - +
26E T 3.8 39.5 - - + +
27E C 3.5 35.9 - - + +
28E G 5.7 4.7 - - - +
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Residues in contact with LYS 259 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A ASN 2.9 12.3 + - - +
256A ARG* 3.6 33.6 - - - +
257A ARG 3.3 0.2 - - - -
258A MET* 1.3 74.5 - - - +
260A MET* 1.3 60.5 + - - +
262A LYS* 3.1 13.5 + - + +
263A ILE* 2.9 51.6 + - + +
10D T 5.5 1.1 - - - -
11D T 3.0 41.7 + - - +
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Residues in contact with MET 260 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A PHE* 4.6 2.5 - - + -
228A MET* 3.0 39.7 - - + -
256A ARG* 3.1 24.4 + - - +
257A ARG* 3.6 23.8 - - + +
259A LYS* 1.3 77.6 - - - +
261A LYS* 1.3 55.9 + - - +
263A ILE* 3.4 7.9 + - - +
264A ASN* 3.0 44.1 + - - +
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Residues in contact with LYS 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A ARG 3.1 13.4 + - - +
258A MET* 3.4 30.8 - - + +
259A LYS 3.2 0.2 - - - -
260A MET* 1.3 78.6 - - - +
262A LYS* 1.3 64.3 + - - +
264A ASN* 3.3 5.7 + - - +
265A LYS* 3.0 26.6 + - + +
27E C 2.8 52.4 + - - +
28E G 4.5 4.8 + - - -
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Residues in contact with LYS 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A MET 2.8 13.9 + - - +
259A LYS* 3.1 15.9 + - + +
261A LYS* 1.3 81.1 - - - +
263A ILE* 1.3 64.3 + - + +
265A LYS* 3.4 5.7 + - - +
266A ASP* 3.1 22.1 + - + +
278B SER* 3.6 33.6 + - - +
281B SER* 6.3 0.6 - - - -
282B ASN* 5.0 11.8 + - - +
10D T 4.3 22.2 - - - +
11D T 6.1 6.3 - - + -
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Residues in contact with ILE 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ARG* 5.6 4.5 - - - +
259A LYS* 2.9 46.0 + - + +
260A MET* 3.8 7.2 - - - +
262A LYS* 1.3 78.8 - - + +
264A ASN* 1.3 68.1 + - - +
266A ASP* 3.1 17.7 + - + +
267A ARG* 3.2 29.7 + - + +
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Residues in contact with ASN 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A MET* 3.0 34.2 + - - +
261A LYS* 3.9 5.4 - - - +
263A ILE* 1.3 81.8 - - - +
265A LYS* 1.3 59.4 + - - +
267A ARG* 3.7 14.6 - - - +
268A ALA* 3.1 31.9 + - - +
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Residues in contact with LYS 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A LYS* 3.0 20.2 + - + +
262A LYS* 3.8 6.5 - - - +
264A ASN* 1.3 76.0 - - - +
266A ASP* 1.3 63.0 + - - +
267A ARG 3.1 1.0 + - - -
268A ALA* 3.9 14.1 + - - +
269A LYS* 4.6 2.8 + - - -
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Residues in contact with ASP 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A LYS* 3.1 14.3 + - + +
263A ILE* 3.1 16.0 + - - +
265A LYS* 1.3 79.2 - - - +
267A ARG* 1.3 59.9 + - + +
269A LYS* 5.1 4.3 + - - +
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Residues in contact with ARG 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ILE* 3.2 30.4 + - + +
264A ASN* 3.4 15.7 + - - +
265A LYS 3.1 0.4 - - - -
266A ASP* 1.3 81.7 - - + +
268A ALA* 1.3 58.4 + - - +
269A LYS* 2.9 15.0 + - - +
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Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A ASN 3.1 17.2 + - - +
265A LYS* 3.9 7.6 + - - +
267A ARG* 1.3 74.3 - - + +
269A LYS* 1.3 64.0 + - - +
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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