Contacts of the helix formed by residues 239 - 253 (chain A) in PDB entry 3CTP
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 ASN 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ASN* 3.5 2.8 - - - +
213A ASP* 2.9 25.9 + - - -
237A VAL* 3.0 3.2 + - - +
238A PHE* 1.3 93.1 - - + +
240A ASP* 1.3 59.5 + - - +
241A ILE* 3.4 5.0 - - - +
242A ALA* 2.8 28.8 + - - +
243A ALA* 3.0 27.5 + - - +
266A PHE 3.2 13.0 - - - +
267A ASP* 3.5 7.4 - - - +
401A XLF 3.1 41.0 + - - +
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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
----------------------------------------------------------
239A ASN* 1.3 72.1 - - - +
241A ILE* 1.3 61.6 + - - +
243A ALA* 3.2 2.8 + - - +
244A ALA* 2.9 27.4 + - - +
266A PHE 2.8 25.8 + - - +
267A ASP* 3.8 2.1 + - + +
268A ASN* 2.9 27.1 + - - -
269A SER* 3.0 29.0 + - - +
271A ILE* 3.8 10.5 - - + +
272A GLY* 4.8 2.7 + - - +
279A LEU* 3.4 26.1 - - + +
281A THR* 2.6 24.2 + - - +
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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
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72A ASN* 3.6 31.9 - - - +
73A PRO* 4.0 26.5 - - + -
213A ASP* 4.0 0.4 - - - +
214A PHE* 3.5 43.7 - - + -
239A ASN* 3.4 11.7 - - - +
240A ASP* 1.3 74.7 - - - +
242A ALA* 1.3 68.5 + - - +
244A ALA* 3.2 11.3 + - - +
245A THR* 3.3 14.3 + - - +
267A ASP* 5.0 0.8 + - - -
269A SER* 4.8 1.4 + - - +
271A ILE* 3.9 17.2 - - + +
401A XLF 5.0 0.2 - - - +
270B PHE* 4.6 5.8 - - + -
274B LEU* 3.9 27.1 - - + -
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Residues in contact with ALA 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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210A PHE* 4.6 9.6 - - + -
213A ASP* 5.6 0.7 - - - +
214A PHE* 5.5 2.7 - - - +
218A MET* 5.2 5.6 - - - -
237A VAL* 3.7 18.8 - - + -
238A PHE* 3.8 24.0 - - + -
239A ASN* 2.8 19.7 + - - +
241A ILE* 1.3 77.5 - - - +
243A ALA* 1.3 63.8 + - - +
245A THR* 2.7 28.1 + - - -
246A VAL* 3.0 9.5 + - - +
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Residues in contact with ALA 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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237A VAL* 3.5 26.2 - - + +
239A ASN 3.0 15.7 + - - +
240A ASP* 3.2 9.6 + - - +
242A ALA* 1.3 78.1 - - - +
244A ALA* 1.3 56.9 + - - +
246A VAL* 3.1 2.3 + - - +
247A MET* 2.8 34.8 + - - +
263A ILE* 4.5 3.6 - - + -
265A GLY* 4.4 4.3 - - - -
279A LEU* 3.9 28.0 - - + -
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Residues in contact with ALA 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 12.4 + - - +
241A ILE 3.4 10.1 - - - +
242A ALA 3.2 0.4 - - - -
243A ALA* 1.3 76.0 - - - +
245A THR* 1.3 58.9 + - - +
247A MET* 3.5 3.0 + - - +
248A ARG* 3.0 27.9 + - - +
271A ILE* 4.0 18.2 - - + -
275A LEU* 3.8 31.2 - - + +
279A LEU* 5.3 0.4 - - - +
274B LEU* 3.8 19.5 - - + +
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Residues in contact with THR 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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210A PHE* 4.5 4.5 - - - -
214A PHE* 3.7 31.6 - - + -
218A MET* 4.2 23.8 - - + +
219A LEU* 4.3 8.7 - - + -
241A ILE 3.4 14.1 - - - +
242A ALA* 2.7 20.8 + - - -
244A ALA* 1.3 73.8 - - - +
246A VAL* 1.3 69.7 + - - +
248A ARG* 3.3 7.8 + - - +
249A ALA* 3.1 22.5 + - - +
274B LEU* 4.0 14.1 - - + -
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Residues in contact with VAL 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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178A ILE* 3.6 33.9 - - + -
210A PHE* 4.5 11.7 - - + -
223A ILE* 5.1 7.4 - - + -
226A MET* 4.6 3.5 - - + +
229A ILE* 5.3 4.0 - - + -
235A ILE* 4.7 9.6 - - + -
237A VAL* 4.2 16.4 - - + -
242A ALA 3.0 14.0 + - - +
243A ALA* 3.5 8.3 - - - +
245A THR* 1.3 85.9 + - - +
247A MET* 1.3 62.5 + - + +
249A ALA* 3.2 7.9 + - - +
250A LEU* 3.0 38.9 + - + +
263A ILE* 5.1 3.6 - - + -
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Residues in contact with MET 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 ALA 2.8 20.9 + - - +
244A ALA* 3.8 4.9 - - - +
246A VAL* 1.3 76.7 - - - +
248A ARG* 1.3 58.8 + - - +
250A LEU* 3.3 7.4 + - - +
251A LYS* 2.8 42.9 + - - +
257A ILE* 4.0 20.0 - - + -
263A ILE* 4.2 15.5 - - + -
275A LEU* 4.4 19.3 - - + -
276A TYR 4.3 4.5 - - - +
277A PRO* 3.5 39.7 - - + +
279A LEU* 4.0 18.8 - - - -
322A THR* 3.6 22.7 - - + -
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Residues in contact with ARG 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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218A MET 4.7 1.0 + - - -
219A LEU* 2.8 54.8 + - - +
221A GLU 5.5 2.4 + - - -
244A ALA 3.0 18.6 + - - +
245A THR* 3.5 7.9 + - - +
247A MET* 1.3 77.2 - - - +
249A ALA* 1.3 67.4 + - - +
251A LYS* 3.3 12.0 + - - +
252A LYS* 3.0 47.7 + - + +
273B GLU* 2.6 61.0 + - - +
274B LEU* 4.2 14.4 - - + +
275B LEU 5.8 0.4 - - - +
276B TYR* 5.4 3.5 - - + -
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Residues in contact with ALA 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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223A ILE* 6.2 1.3 - - + -
226A MET* 3.8 25.6 - - + -
245A THR 3.1 13.1 + - - +
246A VAL* 3.2 10.3 + - - +
248A ARG* 1.3 83.6 - - - +
250A LEU* 1.3 59.2 + - - +
252A LYS* 3.3 13.4 + - - +
253A ARG* 3.0 24.5 + - - +
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Residues in contact with LEU 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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226A MET* 3.5 22.2 - - + +
229A ILE* 3.8 15.9 - - + -
230A VAL* 4.4 6.7 - - - +
235A ILE* 4.4 5.6 - - + -
246A VAL* 3.0 28.0 + - + +
247A MET* 3.6 7.0 - - - +
249A ALA* 1.3 77.2 - - - +
251A LYS* 1.3 62.7 + - - +
253A ARG* 3.0 15.8 + - + +
254A GLY 3.3 0.2 + - - -
255A VAL* 3.1 48.5 + - + +
257A ILE* 4.1 15.0 - - + -
261A VAL* 4.1 9.2 - - + -
263A ILE* 4.0 26.5 - - + -
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Residues in contact with LYS 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 MET* 2.8 41.1 + - - +
248A ARG* 3.3 8.5 + - - +
250A LEU* 1.3 73.1 - - - +
252A LYS* 1.3 58.1 + - - +
254A GLY* 2.9 19.9 + - - -
255A VAL 4.3 14.1 - - - +
257A ILE* 5.0 6.3 - - + -
275A LEU* 5.2 6.1 - - - +
276A TYR* 2.3 39.6 + - - +
277A PRO* 4.4 8.1 - - - -
251B LYS* 5.6 2.2 - - - +
274B LEU 5.6 2.8 + - - +
276B TYR* 3.9 61.1 + - + +
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Residues in contact with LYS 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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248A ARG* 3.0 45.9 + - + +
249A ALA* 3.6 11.2 - - - +
250A LEU 3.2 0.4 - - - -
251A LYS* 1.3 76.7 - - - +
253A ARG* 1.3 60.6 + - + +
254A GLY 3.3 1.0 + - - -
273B GLU* 4.7 8.7 + - - -
275B LEU 5.3 1.6 + - - -
276B TYR* 4.4 17.4 - - + -
278B SER* 4.1 13.9 + - - +
321B GLU* 3.2 32.9 + - - +
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Residues in contact with ARG 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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226A MET* 3.9 26.0 + - + +
227A LYS* 2.9 48.1 + - - +
249A ALA 3.0 19.5 - - - +
250A LEU* 3.0 10.4 + - + +
252A LYS* 1.3 77.0 - - + +
254A GLY* 1.3 62.4 + - - +
255A VAL* 3.3 12.9 + - + +
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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