Contacts of the helix formed by residues 239 - 253 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ASN* 3.5 2.2 - - - +
213B ASP* 2.9 26.1 + - - -
237B VAL* 3.0 2.5 + - - +
238B PHE* 1.3 92.4 - - - +
240B ASP* 1.3 61.2 + - - +
241B ILE* 3.4 5.5 + - - +
242B ALA* 2.8 28.2 + - - +
243B ALA* 2.9 27.2 + - - +
266B PHE 3.2 18.2 - - - +
267B ASP* 3.5 3.4 - - - +
401B XLF 3.1 41.5 + - - +
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Residues in contact with ASP 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ASN* 1.3 74.8 - - - +
241B ILE* 1.3 58.9 + - - +
243B ALA* 3.2 3.3 + - - +
244B ALA* 2.9 26.5 + - - +
266B PHE 2.8 23.6 + - - +
267B ASP* 3.8 2.3 + - + -
268B ASN* 2.9 25.6 + - - -
269B SER* 3.0 29.7 + - - +
271B ILE* 3.8 11.8 - - + +
272B GLY* 4.8 2.2 + - - -
275B LEU* 4.5 0.2 - - - +
279B LEU* 3.3 25.6 - - + +
281B THR* 2.6 24.4 + - - +
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Residues in contact with ILE 241 (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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270A PHE* 4.5 6.1 - - + -
274A LEU* 3.9 27.4 - - + -
72B ASN* 3.6 32.1 - - - +
73B PRO* 4.0 26.5 - - + -
213B ASP* 4.0 0.2 - - - +
214B PHE* 3.4 42.8 - - + -
239B ASN* 3.4 11.7 - - - +
240B ASP* 1.3 78.5 - - - +
242B ALA* 1.3 64.2 + - - +
244B ALA* 3.2 11.7 + - - +
245B THR* 3.3 13.9 + - - +
267B ASP* 5.0 0.8 + - - +
269B SER* 4.8 1.2 + - - +
271B ILE* 3.9 17.2 - - + +
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Residues in contact with ALA 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B PHE* 4.5 9.2 - - + -
213B ASP* 5.5 0.7 - - - +
214B PHE* 5.5 2.7 - - - +
218B MET* 5.5 4.7 - - - -
237B VAL* 3.7 19.3 - - + -
238B PHE* 3.7 25.4 - - + -
239B ASN* 2.8 23.6 + - - +
241B ILE* 1.3 72.2 - - + +
243B ALA* 1.3 63.7 + - - +
245B THR* 2.7 28.7 + - - -
246B VAL* 3.0 9.2 + - - +
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Residues in contact with ALA 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B VAL* 3.5 26.4 - - + +
239B ASN 2.9 15.9 + - - +
240B ASP 3.2 9.8 + - - +
242B ALA* 1.3 76.2 - - - +
244B ALA* 1.3 58.2 + - - +
246B VAL* 3.1 2.4 + - - +
247B MET* 2.9 34.5 + - - +
263B ILE* 4.5 3.5 - - + +
265B GLY* 4.4 4.3 - - - -
279B LEU* 3.8 28.5 - - + -
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Residues in contact with ALA 244 (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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274A LEU* 3.9 20.1 - - + +
240B ASP 2.9 13.4 + - - +
241B ILE 3.4 9.6 - - - +
242B ALA 3.2 0.2 - - - -
243B ALA* 1.3 76.4 - - - +
245B THR* 1.3 56.9 + - - +
247B MET* 3.4 2.3 + - - +
248B ARG* 3.0 28.1 + - - +
271B ILE* 4.0 17.3 - - + -
275B LEU* 3.8 35.6 - - + +
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Residues in contact with THR 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 4.0 14.4 - - + -
210B PHE* 4.4 10.6 - - - -
214B PHE* 3.7 31.6 - - + -
218B MET* 4.4 16.4 - - + -
219B LEU* 4.3 8.1 - - + -
241B ILE 3.5 13.9 - - - +
242B ALA* 2.7 21.5 + - - -
244B ALA* 1.3 74.0 - - - +
246B VAL* 1.3 68.6 + - - +
248B ARG* 3.3 8.8 + - - +
249B ALA* 3.1 22.3 + - - +
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Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ILE* 3.5 32.3 - - + -
210B PHE* 4.5 11.0 - - + -
223B ILE* 5.0 7.4 - - + -
226B MET* 5.2 6.5 - - + -
229B ILE* 5.3 1.3 - - + -
235B ILE* 4.6 12.6 - - + -
237B VAL* 4.3 15.0 - - + -
242B ALA 3.0 12.9 + - - +
243B ALA* 3.6 8.3 - - - +
245B THR* 1.3 85.1 + - - +
247B MET* 1.3 63.9 + - + +
249B ALA* 3.2 8.2 + - - +
250B LEU* 3.0 37.6 + - + +
263B ILE* 5.0 4.0 - - + -
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Residues in contact with MET 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ALA 2.9 17.4 + - - +
244B ALA* 3.8 5.4 - - - +
246B VAL* 1.3 76.5 - - + +
248B ARG* 1.3 58.4 + - - +
250B LEU* 3.7 7.5 - - - +
251B LYS* 2.8 50.5 + - - +
257B ILE* 4.0 18.1 - - + +
263B ILE* 4.3 15.3 - - + -
275B LEU* 4.1 28.5 - - + -
276B TYR 4.3 1.1 - - - +
277B PRO* 3.6 37.5 - - + +
279B LEU* 4.1 12.1 - - - -
322B THR* 3.7 23.8 - - + -
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Residues in contact with ARG 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A GLU* 2.8 57.4 + - - +
274A LEU* 3.5 25.8 - - - +
275A LEU 5.8 1.1 - - - +
276A TYR* 5.7 3.3 - - + -
218B MET 4.7 1.4 + - - -
219B LEU* 2.9 49.0 + - - +
221B GLU 5.5 2.0 + - - -
244B ALA 3.0 12.1 + - - +
245B THR* 3.5 11.7 + - - +
246B VAL 3.2 0.2 - - - -
247B MET* 1.3 77.2 - - - +
249B ALA* 1.3 60.7 + - - +
251B LYS* 3.2 10.6 + - - +
252B LYS* 2.9 59.3 + - + +
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ILE* 6.2 0.7 - - + -
226B MET* 3.8 27.7 - - + +
245B THR 3.1 11.0 + - - +
246B VAL* 3.5 9.6 - - - +
248B ARG* 1.3 86.5 - - - +
250B LEU* 1.3 63.0 + - - +
252B LYS* 3.3 17.4 + - - +
253B ARG* 3.4 18.5 + - - +
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Residues in contact with LEU 250 (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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226B MET* 3.6 21.8 - - + +
229B ILE* 3.9 15.7 - - + -
230B VAL* 4.4 7.2 - - + +
235B ILE* 4.5 4.0 - - + -
246B VAL* 3.0 27.3 + - + +
247B MET* 3.7 6.1 - - - +
248B ARG 3.3 0.2 - - - -
249B ALA* 1.3 76.2 - - - +
251B LYS* 1.3 64.4 + - - +
253B ARG* 3.0 15.0 + - - +
255B VAL* 3.1 46.6 + - + +
257B ILE* 3.9 25.4 - - + -
261B VAL* 4.0 15.3 - - + -
263B ILE* 4.0 14.4 - - + -
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Residues in contact with LYS 251 (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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251A LYS* 5.6 2.6 - - - +
276A TYR* 4.1 54.9 + - + +
247B MET* 2.8 43.9 + - - +
248B ARG* 3.7 7.0 - - - +
250B LEU* 1.3 77.5 - - - +
252B LYS* 1.3 57.8 + - - +
253B ARG 2.9 0.2 - - - -
254B GLY* 2.8 20.6 + - - +
255B VAL 4.4 13.0 - - - +
257B ILE* 5.1 6.5 - - + -
275B LEU* 5.5 4.0 - - - -
276B TYR* 2.2 38.2 + - - +
277B PRO* 3.8 6.4 - - - +
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Residues in contact with LYS 252 (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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273A GLU* 3.5 18.0 + - - -
276A TYR* 4.9 12.9 - - + -
278A SER* 5.4 4.8 + - - -
321A GLU* 5.3 10.1 + - - +
248B ARG* 2.9 57.6 + - + +
249B ALA* 3.7 9.6 - - - +
250B LEU 3.3 0.4 - - - -
251B LYS* 1.3 75.5 - - - +
253B ARG* 1.3 61.3 + - + +
254B GLY 3.3 0.8 + - - -
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Residues in contact with ARG 253 (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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226B MET* 3.9 31.1 - - + +
227B LYS* 2.9 46.8 + - - +
249B ALA 3.5 10.5 - - - +
250B LEU* 3.0 9.7 + - - +
251B LYS 2.9 1.0 - - - -
252B LYS* 1.3 80.2 - - + +
254B GLY* 1.3 61.7 + - - +
255B VAL* 3.4 12.0 + - + +
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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
------------------------------------------------------------
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