Contacts of the helix formed by residues 264 - 279 (chain C) in PDB entry 4BPU
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 264 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263C HIS* 1.3 78.8 - - - +
265C SER* 1.3 62.7 + - - +
266C LEU* 3.9 21.1 - - + +
267C GLN* 3.0 43.4 + - - +
268C ARG* 3.1 33.0 + - - +
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Residues in contact with SER 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C LEU* 3.4 33.2 - - - +
232C ASP* 2.3 28.7 + - - -
234C LEU* 2.9 40.6 + - - +
264C ASN* 1.3 74.8 - - - +
266C LEU* 1.3 56.0 + - - +
268C ARG* 3.3 1.4 + - - +
269C TRP* 2.8 35.3 + - - +
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Residues in contact with LEU 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C GLU* 3.8 34.8 - - + +
228C LEU* 4.0 26.0 - - + +
229C VAL* 4.1 26.0 - - + -
264C ASN* 3.4 23.5 - - + +
265C SER* 1.3 73.9 - - - +
267C GLN* 1.3 60.8 + - + +
269C TRP* 3.3 3.1 + - - +
270C GLU* 2.9 31.9 + - - +
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Residues in contact with GLN 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C SER* 3.6 13.4 + - - +
263C HIS* 3.0 44.7 + - - +
264C ASN* 3.0 36.3 + - - +
266C LEU* 1.3 76.0 - - + +
268C ARG* 1.3 59.0 + - - +
270C GLU* 3.1 8.4 + - - +
271C HIS* 2.9 37.1 + - + -
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Residues in contact with ARG 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C LEU* 2.8 39.1 + - + -
235C GLU* 3.4 13.9 + - - +
240C TRP* 3.6 16.1 - - - -
259C PHE* 2.8 77.1 + - + -
262C SER* 3.2 33.2 + - - -
263C HIS 3.5 7.1 + - - -
264C ASN* 3.1 39.0 + - - +
265C SER 3.3 6.8 + - - +
266C LEU 3.2 0.4 - - - -
267C GLN* 1.3 73.3 - - - +
269C TRP* 1.3 61.8 + - - +
271C HIS* 3.3 4.1 + - - +
272C LEU* 2.8 25.5 + - - +
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Residues in contact with TRP 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C PHE* 3.5 32.6 - + - -
224C GLU* 6.2 0.2 - - + -
228C LEU* 3.6 28.7 - - + -
233C ILE* 5.4 2.9 - - + -
234C LEU* 3.8 11.6 - - + +
243C ILE* 5.1 1.6 - - + -
265C SER 2.8 17.0 + - - +
266C LEU 3.6 4.9 - - - +
267C GLN 3.2 0.2 - - - -
268C ARG* 1.3 77.6 - - - +
270C GLU* 1.3 58.5 + - - +
272C LEU* 3.1 36.7 + - + +
273C LYS* 2.8 65.1 + - + +
293C GLU* 3.5 42.1 + - + -
296C ILE* 4.0 23.3 - - + -
297C MET* 3.9 8.9 - - + -
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Residues in contact with GLU 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C GLU* 5.7 1.0 - - - +
266C LEU 2.9 14.7 + - - +
267C GLN* 3.5 11.4 - - - +
269C TRP* 1.3 77.9 - - - +
271C HIS* 1.3 58.6 + - + +
273C LYS* 3.3 35.5 + - - +
274C LYS* 3.0 59.7 + - - +
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Residues in contact with HIS 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C LEU* 4.5 1.6 - - + -
258C SER* 4.4 28.8 + - - +
259C PHE* 4.8 3.4 - - + -
262C SER* 3.7 21.2 + - - -
267C GLN* 2.9 23.4 + - + -
268C ARG* 3.5 9.4 - - - +
270C GLU* 1.3 75.1 - - + +
272C LEU* 1.3 66.4 + - - +
274C LYS* 3.1 18.0 + - + +
275C VAL* 2.8 35.3 + - + +
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Residues in contact with LEU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C LEU* 5.5 1.8 - - + -
243C ILE* 3.8 18.2 - - + -
244C LEU* 5.9 0.9 - - + -
247C VAL* 5.3 5.2 - - + -
255C LEU* 4.1 24.8 - - + +
259C PHE* 4.6 12.1 - - + -
268C ARG 2.8 17.2 + - - +
269C TRP* 3.1 38.8 + - + +
271C HIS* 1.3 71.7 - - - +
273C LYS* 1.3 61.6 - - - +
275C VAL* 3.9 0.9 - - - +
276C ALA* 2.8 40.7 + - + +
292C LEU* 5.2 2.7 - - + -
293C GLU* 4.5 11.4 - - + +
296C ILE* 3.8 28.3 - - + -
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Residues in contact with LYS 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C GLU* 5.8 1.8 + - - -
269C TRP* 2.8 46.0 + - + +
270C GLU* 3.4 38.2 + - - +
272C LEU* 1.3 78.8 - - - +
274C LYS* 1.3 58.0 + - + +
276C ALA* 3.7 3.9 - - - +
277C SER* 2.8 36.7 + - - +
293C GLU* 3.5 40.7 - - + +
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Residues in contact with LYS 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C GLU* 3.0 45.8 + - - +
271C HIS* 3.1 19.0 + - + +
273C LYS* 1.3 77.6 - - + +
275C VAL* 1.3 58.5 + - + +
277C SER* 3.3 6.6 + - - -
278C ARG* 2.9 38.9 + - + +
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Residues in contact with VAL 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C ILE* 4.4 26.2 - - + -
254C GLU* 4.1 35.4 - - + +
255C LEU* 3.6 28.0 - - + -
258C SER* 5.5 1.8 - - - +
271C HIS* 2.8 30.9 + - + +
272C LEU 3.9 2.5 - - - +
274C LYS* 1.3 72.3 - - + +
276C ALA* 1.3 63.0 + - - +
278C ARG* 3.4 17.6 + - - +
279C TYR* 3.1 21.3 + - - +
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Residues in contact with ALA 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C ILE* 5.7 1.6 - - - -
272C LEU* 2.8 29.4 + - + +
273C LYS* 3.7 5.2 - - - +
275C VAL* 1.3 75.8 - - - +
277C SER* 1.3 66.4 + - - +
279C TYR* 3.0 26.3 + - - +
290C PRO 5.0 7.3 - - - +
292C LEU* 4.6 26.5 - - + +
293C GLU* 4.9 8.1 - - + +
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Residues in contact with SER 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C LYS* 2.8 25.2 + - - +
274C LYS* 3.6 6.7 - - - -
276C ALA* 1.3 77.9 - - - +
278C ARG* 1.3 62.9 + - - +
279C TYR 3.4 3.8 + - - -
293C GLU* 5.2 3.8 + - - -
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Residues in contact with ARG 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C GLU* 2.7 32.3 + - - -
274C LYS* 2.9 21.4 + - + +
275C VAL* 3.7 19.6 + - - +
277C SER* 1.3 78.1 - - - +
279C TYR* 1.3 63.8 + - - +
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Residues in contact with TYR 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C PRO* 3.9 26.4 - - + +
250C THR* 4.3 15.9 + - - -
251C ILE* 4.3 21.5 - - + -
275C VAL 3.1 13.1 + - - +
276C ALA* 3.0 20.9 + - - +
277C SER 4.1 3.6 - - - -
278C ARG* 1.3 81.2 - - - +
290C PRO* 4.9 21.3 - - + -
292C LEU* 4.8 14.1 - - + -
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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