Contacts of the helix formed by residues 243 - 263 (chain A) in PDB entry 3UVV
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 GLU 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A PRO* 3.4 2.5 - - + +
242A CYS* 1.4 84.5 - - - +
244A ASP* 1.4 58.8 + - - +
246A ILE* 2.7 38.3 + - + +
247A ILE* 3.1 23.5 + - + +
331A ILE* 6.2 2.2 - - + -
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Residues in contact with ASP 244 (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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240A LEU* 5.2 2.2 - - + -
241A PRO* 3.7 20.8 + - + +
243A GLU* 1.4 76.2 - - - +
245A GLN* 1.3 55.6 + - - +
247A ILE* 3.7 2.5 + - - +
248A LEU* 3.3 32.0 + - - +
329A GLY 3.6 5.9 - - - +
330A LEU* 3.4 26.9 - - + +
331A ILE* 2.8 35.3 + - - +
332A CYS* 2.6 42.6 + - - +
336A ILE* 4.7 3.1 - - + -
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Residues in contact with GLN 245 (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 LYS* 5.9 3.8 - - - +
237A PHE* 3.2 68.9 - - + +
238A SER* 3.8 9.3 - - - +
240A LEU* 2.8 27.4 - - + +
241A PRO 2.9 26.6 + - - +
242A CYS* 4.0 7.9 - - - +
244A ASP* 1.3 70.9 - - - +
246A ILE* 1.4 62.6 + - + +
248A LEU* 4.1 2.7 - - - -
249A LEU* 3.3 24.7 + - + +
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Residues in contact with ILE 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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242A CYS 3.5 13.2 + - - +
243A GLU* 2.7 33.2 + - + +
245A GLN* 1.4 72.9 - - + +
247A ILE* 1.4 58.8 + - + +
248A LEU 3.4 0.2 - - - -
249A LEU* 3.3 14.0 + - + +
250A LYS* 2.9 57.8 + - + +
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Residues in contact with ILE 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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243A GLU* 3.1 37.1 + - + +
244A ASP* 3.7 8.5 - - - +
246A ILE* 1.4 78.3 - - + +
248A LEU* 1.4 59.0 + - - +
250A LYS* 3.3 8.5 + - + +
251A GLY* 3.0 26.5 + - - -
327A ARG* 3.8 23.2 - - + -
328A THR 3.3 23.8 - - - +
329A GLY 3.2 24.7 - - - +
330A LEU* 3.8 9.6 - - + -
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Residues in contact with LEU 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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237A PHE* 4.1 13.0 - - + -
240A LEU* 3.7 29.6 - - + -
244A ASP 3.3 17.0 + - - +
245A GLN 4.4 0.2 - - - +
247A ILE* 1.4 77.7 - - - +
249A LEU* 1.3 62.5 + - - +
251A GLY* 3.5 0.5 + - - -
252A CYS* 3.2 30.8 + - - +
322A LEU* 3.4 31.3 - - + +
323A MET* 4.3 2.5 - - - -
324A SER* 3.4 24.9 - - - +
327A ARG* 4.4 9.6 + - + +
330A LEU* 3.9 17.7 - - + -
336A ILE* 4.0 20.4 - - + -
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Residues in contact with LEU 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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227A VAL* 3.7 28.3 - - + +
228A VAL* 3.8 37.0 - - + -
231A ALA* 4.2 6.1 - - + -
237A PHE* 3.5 24.7 - - + -
245A GLN* 3.3 28.2 + - - +
246A ILE* 3.3 18.5 + - + +
247A ILE 3.3 0.6 - - - -
248A LEU* 1.3 80.9 - - - +
250A LYS* 1.3 56.7 + - + +
252A CYS* 4.3 5.8 - - - -
253A CYS* 3.3 29.6 + - + +
322A LEU* 4.8 0.9 - - + -
402A VAL* 4.7 1.6 - - - +
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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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246A ILE* 2.9 39.5 + - + +
247A ILE* 3.7 8.3 - - + +
249A LEU* 1.3 75.4 - - - +
251A GLY* 1.3 66.4 + - - +
252A CYS 3.5 0.2 + - - -
253A CYS* 3.6 13.0 + - - +
254A MET 4.8 1.2 + - - -
401A GLU 2.7 28.4 + - - -
402A VAL* 3.3 35.6 + - + +
403A PHE* 5.2 4.3 - - - -
404A GLU 3.7 14.5 + - - -
405A ASP* 4.4 10.7 + - - +
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Residues in contact with GLY 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 ILE 3.0 13.6 + - - -
250A LYS* 1.3 77.8 - - - +
252A CYS* 1.3 57.3 + - - +
253A CYS 3.7 0.2 + - - -
254A MET* 4.8 2.8 + - - +
255A GLU* 3.0 20.3 - - - +
327A ARG* 3.4 31.2 + - - -
376A GLY* 5.8 0.2 - - - -
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Residues in contact with CYS 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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227A VAL* 5.0 2.9 - - - -
248A LEU 3.2 24.4 + - - +
249A LEU* 4.3 6.5 - - - -
251A GLY* 1.3 76.6 - - - +
253A CYS* 1.3 70.4 + - - +
254A MET 3.5 0.9 - - - -
255A GLU* 3.2 11.3 + - - +
256A ILE* 3.0 43.2 + - + +
321A LEU* 3.6 29.8 - - + +
322A LEU* 3.7 23.1 - - - -
327A ARG* 3.8 1.5 - - - +
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Residues in contact with CYS 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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224A ILE* 3.9 23.8 - - - -
227A VAL* 4.0 18.9 - - + +
228A VAL* 6.3 0.4 - - - -
249A LEU* 3.3 23.5 + - - +
250A LYS 3.9 2.7 - - - +
251A GLY 3.5 2.2 - - - -
252A CYS* 1.3 77.0 - - - +
254A MET* 1.3 57.3 + - - +
256A ILE* 3.3 2.9 + - - +
257A MET* 2.9 53.1 + - - +
402A VAL* 3.7 28.7 - - + -
403A PHE* 4.3 0.7 - - + -
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Residues in contact with MET 254 (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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250A LYS 4.8 0.8 + - - -
251A GLY 4.8 2.3 + - - +
252A CYS 3.5 0.4 - - - -
253A CYS* 1.3 74.4 - - - +
255A GLU* 1.4 53.9 - - - +
257A MET* 3.3 18.2 + - - +
258A SER* 2.7 61.3 + - - +
290A LEU* 4.4 5.2 - - + -
293A VAL* 4.5 0.4 - - + -
297A ILE* 3.9 10.3 - - + -
375A ILE* 4.2 10.3 - - + +
376A GLY* 4.4 11.2 - - - +
379A HIS* 3.7 35.9 - - + +
403A PHE* 3.9 17.8 - - + -
501A T3 3.8 46.9 - - + -
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Residues in contact with GLU 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 GLY 3.0 20.5 - - - +
252A CYS* 3.2 11.2 + - - +
254A MET* 1.4 77.1 - - - +
256A ILE* 1.4 52.2 + - - +
258A SER* 3.2 2.5 + - - -
259A LEU* 2.8 30.5 + - - +
321A LEU* 3.9 19.4 - - + +
327A ARG* 2.7 28.0 + - - -
372A LEU* 3.4 45.6 - - + +
373A ARG* 3.0 28.4 + - - +
375A ILE* 5.9 0.2 - - - -
376A GLY* 4.0 19.3 - - - -
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Residues in contact with ILE 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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227A VAL* 3.8 20.2 - - + +
230A PHE* 4.8 9.6 - - + -
252A CYS* 3.0 37.7 + - + +
253A CYS 3.7 3.6 - - - +
255A GLU* 1.4 78.1 - - - +
257A MET* 1.3 52.8 + - - +
259A LEU* 3.4 7.3 + - - +
260A ARG* 2.7 63.1 + - - +
318A GLN* 3.7 49.1 - - + +
321A LEU* 4.4 8.3 - - + -
322A LEU* 4.7 3.6 - - + -
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Residues in contact with MET 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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220A ILE* 4.1 28.9 - - + -
223A ALA* 4.2 14.8 - - - -
224A ILE* 4.1 19.3 - - + -
227A VAL* 3.6 17.3 - - + -
253A CYS* 2.9 29.2 + - - +
254A MET* 3.6 20.0 - - - +
256A ILE* 1.3 74.9 - - - +
258A SER* 1.4 52.2 + - - +
260A ARG* 3.3 3.1 + - - -
261A ALA 2.8 28.2 + - - -
403A PHE* 3.8 29.6 - - + -
501A T3 3.3 35.1 - - + -
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Residues in contact with SER 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 MET* 2.7 36.9 + - - +
255A GLU* 3.4 4.5 - - - -
257A MET* 1.4 67.4 - - - +
259A LEU* 1.4 54.8 + - - +
261A ALA* 3.1 6.9 + - - +
262A ALA* 2.6 39.1 + - - +
297A ILE* 3.7 12.8 - - - +
300A LEU* 5.5 0.4 - - - -
372A LEU* 4.4 9.0 - - - -
375A ILE* 3.1 34.5 - - - +
501A T3 4.3 3.8 - - - +
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Residues in contact with LEU 259 (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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255A GLU 2.8 20.0 + - - +
256A ILE* 3.6 4.3 - - - +
258A SER* 1.4 71.1 - - - +
260A ARG* 1.3 63.5 + - - +
262A ALA* 3.9 4.4 - - - -
263A VAL* 3.1 46.8 + - + +
300A LEU* 5.3 0.2 - - - -
304A LEU* 4.1 15.5 - - + -
309A LEU* 5.2 2.2 - - + -
314A VAL* 4.3 11.9 - - + -
317A LEU* 3.8 42.2 - - + -
318A GLN* 3.8 27.4 - - + -
321A LEU* 4.0 12.1 - - + -
372A LEU* 3.8 15.6 - - + +
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Residues in contact with ARG 260 (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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173A HIS* 3.2 32.4 + - - +
176A THR* 3.1 43.3 + - - +
177A ASN* 3.7 21.4 + - - +
226A ARG* 4.4 1.6 - - - +
227A VAL* 3.8 18.9 - - - +
230A PHE* 4.0 4.9 - - - +
256A ILE* 2.7 40.0 + - - +
257A MET 3.5 2.0 - - - +
259A LEU* 1.3 72.5 - - - +
261A ALA* 1.3 60.2 + - - +
263A VAL* 3.3 20.4 - - + +
264A ARG* 3.3 15.1 + - - +
314A VAL* 5.4 0.9 - - + -
318A GLN* 3.3 31.6 + - - +
501A T3 3.2 35.8 + - - +
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Residues in contact with ALA 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 MET 2.8 17.0 + - - +
258A SER* 3.4 4.5 - - - +
260A ARG* 1.3 76.4 - - - +
262A ALA* 1.4 60.9 + - - +
264A ARG* 3.2 18.4 + - - +
272A LEU* 3.2 21.5 - - + +
273A THR 4.3 5.6 + - - +
274A LEU* 4.5 7.2 - - + -
297A ILE* 4.3 5.8 - - + -
501A T3 3.7 39.5 - - + +
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Residues in contact with ALA 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 SER 2.6 22.4 + - - +
259A LEU* 3.9 3.8 - - - +
261A ALA* 1.4 70.5 - - - +
263A VAL* 1.4 61.7 + - - +
264A ARG 3.5 0.5 + - - -
265A TYR* 3.5 9.1 - - - +
272A LEU* 3.7 10.9 - - - +
297A ILE* 4.0 10.9 - - + +
300A LEU* 4.3 16.6 - - + -
301A GLY* 3.2 38.9 - - - +
304A LEU* 4.4 8.1 - - + +
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Residues in contact with VAL 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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173A HIS* 6.1 0.7 - - + +
177A ASN* 5.8 4.9 - - - +
183A TRP* 5.1 3.1 - - - -
259A LEU* 3.1 31.3 + - + +
260A ARG* 3.3 22.9 - - - +
262A ALA* 1.4 75.1 - - - +
264A ARG* 1.3 69.5 + - + +
265A TYR 3.3 6.7 + - - +
304A LEU* 4.5 12.6 - - + -
309A LEU* 4.6 9.6 - - + -
314A VAL* 4.0 27.8 - - + -
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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