Contacts of the helix formed by residues 238 - 259 (chain A) in PDB entry 3DTC
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 PRO 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A LYS* 5.7 2.5 - - - -
236A ARG 4.0 4.7 - - - +
237A ILE* 1.3 89.0 - - + +
239A PRO* 1.3 72.1 - - + +
240A ASP* 3.3 11.9 - - - +
241A ILE* 3.1 30.9 + - + -
242A LEU* 2.9 25.7 + - - +
285A LEU* 5.2 6.3 - - + -
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Residues in contact with PRO 239 (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 ILE 3.8 2.3 - - - +
238A PRO* 1.3 86.9 - - + +
240A ASP* 1.3 64.9 + - - +
242A LEU* 3.3 8.7 + - + +
243A VAL* 2.9 37.5 + - + +
375A PRO* 6.3 3.6 - - + -
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Residues in contact with ASP 240 (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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238A PRO* 3.7 17.2 - - - +
239A PRO* 1.3 82.3 - - + +
241A ILE* 1.3 79.3 + - - +
243A VAL* 3.1 8.4 + - - +
244A ASN* 2.9 29.0 + - - +
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Residues in contact with ILE 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ILE* 4.7 6.7 - - + -
238A PRO* 3.1 29.9 + - + +
240A ASP* 1.3 87.4 - - - +
242A LEU* 1.3 59.7 + - - +
244A ASN* 4.5 6.5 - - + +
245A TRP* 3.1 58.9 + - + +
285A LEU* 3.6 27.6 - - + +
286A SER* 4.2 15.0 - - - -
287A ASN 5.1 2.0 - - - +
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Residues in contact with LEU 242 (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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236A ARG* 6.4 0.4 - - - -
237A ILE* 3.3 33.0 - - + +
238A PRO 2.9 15.6 + - - +
239A PRO* 3.5 9.4 - - + +
240A ASP 3.1 0.2 - - - -
241A ILE* 1.3 75.8 - - - +
243A VAL* 1.3 64.4 + - + +
245A TRP* 3.5 3.2 + - - +
246A ALA* 3.1 20.1 + - - +
342A LEU* 3.2 37.9 - - + +
343A LEU* 3.3 35.7 - - + +
375A PRO* 6.1 0.4 - - + -
378A PHE* 3.3 28.3 - - + -
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Residues in contact with VAL 243 (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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239A PRO* 2.9 30.2 + - + +
240A ASP* 3.1 6.5 + - - +
242A LEU* 1.3 75.7 - - + +
244A ASN* 1.3 66.0 + - - +
246A ALA* 3.3 3.1 + - - +
247A VAL* 3.0 34.3 + - + +
375A PRO* 6.2 1.3 - - + -
378A PHE* 3.9 25.8 - - + -
403A LEU* 4.0 28.7 - - + +
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Residues in contact with ASN 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 ASP 2.9 15.9 + - - +
241A ILE* 3.9 9.9 - - + +
242A LEU 3.4 0.2 - - - -
243A VAL* 1.3 78.6 - - - +
245A TRP* 1.3 67.2 + - + +
247A VAL* 3.6 8.0 - - - +
248A GLN* 2.8 58.4 + - - +
251A ARG* 4.9 7.3 - - - +
288A LYS 4.5 0.5 - - - +
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Residues in contact with TRP 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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228A LEU* 3.5 31.6 - - + -
231A VAL* 4.6 8.7 - - + -
232A LEU* 4.4 4.3 - - + -
237A ILE* 4.1 30.1 - - + -
241A ILE* 3.1 27.3 + - + +
242A LEU* 3.8 5.4 - - - +
243A VAL 3.2 0.6 - - - -
244A ASN* 1.3 93.3 + - - +
246A ALA* 1.3 64.9 + - - +
247A VAL 3.1 1.8 - - - -
248A GLN* 3.3 11.1 + - - +
249A ILE* 3.0 30.3 + - - +
276A ILE* 4.7 5.4 - - + -
285A LEU* 3.8 41.8 + - + -
288A LYS* 4.3 22.7 + - + +
290A LEU* 3.8 23.4 - - + +
342A LEU* 4.3 13.5 - - + -
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Residues in contact with ALA 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 LEU 3.1 16.3 + - - +
243A VAL 3.3 4.9 + - - +
245A TRP* 1.3 75.8 - - - +
247A VAL* 1.3 56.9 + - - +
249A ILE* 3.6 2.8 + - - -
250A ALA* 2.8 21.0 + - - +
335A TYR* 2.6 32.0 + - - +
339A LEU* 3.6 19.5 - - + -
342A LEU* 4.1 9.5 - - + +
378A PHE* 4.3 10.5 - - + -
403A LEU* 3.8 10.5 - - + -
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Residues in contact with VAL 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 VAL* 3.0 30.4 + - + +
244A ASN* 3.6 8.7 - - - +
246A ALA* 1.3 74.2 - - - +
248A GLN* 1.3 55.7 + - - +
250A ALA* 3.0 4.5 + - - +
251A ARG* 2.7 72.5 + - - +
400A LEU* 4.1 9.6 - - + -
403A LEU* 3.8 34.5 - - + +
404A THR* 5.4 7.9 - - + +
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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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202A ASN* 3.0 34.8 + - - +
244A ASN* 2.8 47.7 + - - +
245A TRP* 3.8 9.8 - - - +
247A VAL* 1.3 77.5 - - - +
249A ILE* 1.3 61.9 + - - +
251A ARG* 3.2 14.2 + - - +
252A GLY 3.0 18.0 + - - -
288A LYS 2.9 23.6 + - - -
289A ILE* 3.5 7.7 - - - +
290A LEU* 2.8 37.1 + - + +
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Residues in contact with ILE 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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202A ASN* 5.6 0.2 - - - -
228A LEU* 4.3 12.8 - - + -
245A TRP 3.0 20.8 + - - +
246A ALA* 3.8 3.8 - - - +
248A GLN* 1.3 75.0 - - - +
250A ALA* 1.3 62.7 + - - +
252A GLY* 3.1 3.0 + - - +
253A MET* 2.9 29.8 + - + +
269A LEU* 4.6 2.7 - - + -
274A ILE* 4.1 20.6 - - + -
290A LEU* 3.9 23.3 - - + -
292A ILE* 3.8 8.1 - - + +
335A TYR* 3.6 24.7 - - + -
338A LEU* 4.2 31.0 - - + -
342A LEU* 4.5 9.6 - - + -
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Residues in contact with ALA 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 ALA 2.8 19.7 + - - +
247A VAL* 3.0 6.7 + - - +
249A ILE* 1.3 77.3 - - - +
251A ARG* 1.3 50.2 + - - +
253A MET* 3.3 1.9 + - - +
254A ASN* 2.8 35.2 + - - +
335A TYR* 3.8 12.1 - - + +
396A PHE* 3.9 22.5 - - + +
399A ILE* 4.4 3.8 - - + -
400A LEU* 3.6 21.9 - - + +
403A LEU* 4.3 5.4 - - + -
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Residues in contact with ARG 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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200A HIS* 3.9 13.7 + - + +
202A ASN* 3.5 18.9 - - - +
244A ASN* 4.9 6.5 - - - +
247A VAL* 2.7 43.3 + - - +
248A GLN* 3.4 21.7 - - - +
250A ALA* 1.3 69.7 - - - +
252A GLY* 1.3 66.4 + - - +
254A ASN* 3.2 9.3 + - - +
255A TYR* 2.9 23.9 + - - +
400A LEU* 4.0 16.7 - - + +
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Residues in contact with GLY 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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200A HIS* 4.3 4.7 - - - -
202A ASN* 3.9 13.4 - - - +
203A ILE* 3.5 18.5 - - - +
248A GLN 3.0 11.1 + - - -
249A ILE 3.6 3.1 - - - -
251A ARG* 1.3 76.4 - - - +
253A MET* 1.3 61.4 + - - +
255A TYR* 3.3 4.3 + - - +
256A LEU* 3.1 19.1 + - - +
292A ILE* 3.6 17.5 - - - -
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Residues in contact with MET 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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249A ILE* 2.9 20.1 + - + +
250A ALA 3.7 0.7 - - - +
252A GLY* 1.3 73.4 - - - +
254A ASN* 1.3 61.0 + - - +
256A LEU* 3.4 22.1 + - + +
257A HIS* 2.9 37.4 + - - +
266A HIS* 3.9 21.5 - - + -
269A LEU* 4.0 25.6 - - + -
292A ILE* 3.1 44.4 - - + -
331A ASP* 4.5 7.2 - - - +
396A PHE* 3.4 45.3 - - + -
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Residues in contact with ASN 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 ALA 2.8 18.1 + - - +
251A ARG* 3.2 6.8 + - - +
253A MET* 1.3 77.4 - - - +
255A TYR* 1.3 60.2 + - - +
257A HIS* 3.9 2.3 - - - +
258A ASP* 3.2 30.8 + - - +
259A GLU* 3.6 27.4 + - - +
396A PHE* 3.9 13.7 - - + +
397A THR* 3.3 26.0 + - - +
400A LEU* 4.0 23.4 - - + +
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Residues in contact with TYR 255 (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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197A MET 4.5 1.6 + - - -
198A LEU* 3.7 26.1 - - + +
199A LYS* 3.1 51.8 + - - +
200A HIS* 3.6 36.3 - - + +
203A ILE* 4.1 3.1 - - + -
251A ARG 2.9 11.9 + - - +
252A GLY 3.4 7.6 - - - +
253A MET 3.2 0.2 - - - -
254A ASN* 1.3 74.5 - - - +
256A LEU* 1.3 80.5 + - + +
259A GLU* 3.2 53.2 + - + +
260A ALA* 3.5 18.1 + - + +
261A ILE* 5.6 2.1 - - - +
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Residues in contact with LEU 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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198A LEU* 4.1 22.0 - - + -
203A ILE* 3.6 31.9 - - + -
252A GLY 3.1 6.1 + - - +
253A MET* 3.6 32.8 - - + +
255A TYR* 1.3 93.1 - - + +
257A HIS* 1.3 62.4 + - + +
258A ASP* 3.6 0.3 + - - -
260A ALA* 4.7 3.4 - - - +
262A VAL 4.0 3.1 - - - +
263A PRO* 3.7 2.4 - - - +
264A ILE* 2.8 54.7 + - + +
266A HIS* 4.9 1.6 - - + -
295A PHE* 3.7 25.6 - - + -
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Residues in contact with HIS 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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253A MET* 2.9 21.7 + - - +
254A ASN* 3.9 4.9 - - - +
255A TYR 3.3 0.2 - - - -
256A LEU* 1.3 79.8 - - + +
258A ASP* 1.3 69.9 + - - +
263A PRO* 3.4 18.8 - - - +
264A ILE 3.2 20.4 - - - +
265A ILE* 4.0 7.7 - - + +
328A LYS* 3.1 62.7 + - + +
331A ASP* 3.0 23.8 + - + +
332A VAL* 4.6 1.3 - - + +
395A SER* 6.2 0.2 - - - -
396A PHE* 3.4 37.8 + + + +
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Residues in contact with ASP 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 ASN* 3.2 22.2 + - - +
257A HIS* 1.3 85.2 - - - +
259A GLU* 1.3 73.9 + - - +
260A ALA 4.6 2.2 - - - +
262A VAL 6.2 0.2 - - - -
263A PRO* 5.2 2.2 - - - -
328A LYS* 3.1 23.9 + - - +
395A SER* 6.0 2.4 - - - -
397A THR* 4.7 5.1 + - - -
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Residues in contact with GLU 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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200A HIS* 5.2 4.3 - - - -
254A ASN* 3.6 33.2 + - - +
255A TYR* 3.2 42.8 + - + +
258A ASP* 1.3 91.4 - - - +
260A ALA* 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