Contacts of the helix formed by residues 264 - 282 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A HIS* 1.3 79.4 - - + +
265A SER* 1.3 63.5 + - - +
266A LEU* 3.6 20.5 - - + +
267A GLN* 2.9 40.6 + - - +
268A ARG* 3.2 34.1 + - - +
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Residues in contact with SER 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 3.3 34.0 + - - +
232A ASP* 2.3 29.1 + - - -
234A LEU* 3.1 37.7 + - - +
264A ASN* 1.3 73.8 - - - +
266A LEU* 1.3 60.3 + - - +
268A ARG* 4.3 0.8 - - - +
269A TRP* 2.8 32.2 + - - +
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Residues in contact with LEU 266 (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 GLU* 3.3 42.4 - - + +
228A LEU* 3.6 26.4 + - + +
229A VAL* 4.6 15.7 - - + -
264A ASN* 3.2 19.2 + - + +
265A SER* 1.3 77.4 - - - +
267A GLN* 1.3 58.8 + - + +
269A TRP* 3.3 2.1 + - - +
270A GLU* 2.9 33.3 + - - +
1411A GOL 5.3 0.4 - - - +
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Residues in contact with GLN 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A SER* 3.6 13.8 + - - +
263A HIS* 3.0 42.9 + - - +
264A ASN* 2.9 32.1 + - - +
266A LEU* 1.3 77.3 - - + +
268A ARG* 1.3 58.2 + - - +
270A GLU* 3.2 7.9 + - - +
271A HIS* 2.8 36.7 + - + +
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Residues in contact with ARG 268 (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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234A LEU* 2.7 33.2 + - + -
235A GLU* 3.3 24.0 + - - +
240A TRP* 3.9 10.0 - - - -
259A PHE* 2.6 79.3 + - + +
260A GLN 4.8 0.2 + - - -
262A SER* 3.1 32.5 + - - -
263A HIS 3.5 22.0 + - - -
264A ASN* 3.2 22.1 + - - +
265A SER 3.3 4.8 + - - +
266A LEU 3.2 0.2 - - - -
267A GLN* 1.3 76.0 - - - +
269A TRP* 1.3 58.6 + - - +
271A HIS* 3.1 4.8 + - - +
272A LEU* 2.8 25.1 + - - +
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Residues in contact with TRP 269 (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 PHE* 3.4 30.0 - + - -
228A LEU* 3.6 30.7 - - + -
233A ILE* 5.0 3.6 - - + -
234A LEU* 3.6 12.5 - - + +
243A ILE* 5.0 1.6 - - + -
265A SER 2.8 17.9 + - - +
266A LEU 3.7 3.4 - - - +
268A ARG* 1.3 75.8 - - - +
270A GLU* 1.3 60.8 + - - +
272A LEU* 3.1 37.6 + - + +
273A LYS* 2.8 53.8 + - + +
293A GLU* 3.5 25.1 - - + -
296A ILE* 3.7 34.8 - - + -
297A MET* 3.9 6.5 - - + -
1411A GOL 3.2 27.4 + - - -
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Residues in contact with GLU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU 2.9 18.7 + - - +
267A GLN* 3.2 8.5 + - - +
269A TRP* 1.3 78.9 - - - +
271A HIS* 1.3 61.1 + - - +
273A LYS* 2.9 42.1 + - - +
274A LYS* 3.2 48.2 + - - +
1411A GOL 4.5 5.4 + - - -
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Residues in contact with HIS 271 (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 LEU* 4.1 2.7 - - + -
258A SER* 3.8 35.0 + - - +
259A PHE* 4.6 1.8 - - + -
262A SER* 3.3 23.2 + - - -
267A GLN* 2.8 26.0 + - + +
268A ARG* 3.3 10.1 - - - +
270A GLU* 1.3 75.8 - - + +
272A LEU* 1.3 65.0 + - - +
274A LYS* 3.2 20.1 + - + +
275A VAL* 2.9 31.9 + - + +
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Residues in contact with LEU 272 (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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234A LEU* 5.1 1.8 - - + -
243A ILE* 3.5 31.2 - - + -
244A LEU* 5.9 0.4 - - + -
247A VAL* 5.4 4.0 - - + -
251A ILE* 6.1 0.4 - - + -
255A LEU* 3.6 24.7 - - + +
259A PHE* 4.5 12.6 - - + -
268A ARG 2.8 16.3 + - - +
269A TRP* 3.1 39.7 + - + +
271A HIS* 1.3 71.9 - - - +
273A LYS* 1.3 62.9 + - - +
275A VAL* 4.0 0.7 - - - +
276A ALA* 2.9 45.3 + - + +
293A GLU* 4.7 7.4 - - + +
296A ILE* 3.9 19.7 - - + -
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Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A TRP* 2.8 38.9 + - + +
270A GLU* 2.9 42.4 + - - +
272A LEU* 1.3 79.3 - - + +
274A LYS* 1.3 58.7 + - + +
276A ALA* 3.8 3.3 - - - +
277A SER* 2.8 37.6 + - - +
293A GLU* 3.6 31.6 - - + +
1411A GOL 3.5 35.4 + - - -
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Residues in contact with LYS 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A GLU* 3.2 34.0 + - - +
271A HIS* 3.2 20.6 + - + +
273A LYS* 1.3 76.5 - - + +
275A VAL* 1.3 58.9 + - + +
277A SER* 3.4 6.0 + - - -
278A ARG* 2.9 53.9 + - - +
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Residues in contact with VAL 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ILE* 3.8 33.0 - - + -
254A GLU* 3.8 30.5 - - + +
255A LEU* 3.7 23.1 - - + -
258A SER* 5.4 2.5 - - - +
271A HIS* 2.9 23.8 + - + +
272A LEU 4.0 0.4 - - - +
274A LYS* 1.3 75.3 - - + +
276A ALA* 1.3 53.9 + - - +
278A ARG* 3.2 27.7 + - + +
279A TYR* 2.8 32.7 + - - +
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Residues in contact with ALA 276 (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 VAL* 6.1 0.4 - - + -
251A ILE* 4.9 4.9 - - + +
272A LEU* 2.9 28.8 + - + +
273A LYS* 3.8 4.0 - - - +
275A VAL* 1.3 74.9 - - - +
277A SER* 1.3 66.5 + - - +
279A TYR* 3.0 18.9 + - - +
280A GLN* 3.2 17.7 + - - +
290A PRO 4.7 1.1 - - - +
292A LEU* 4.1 31.8 - - + +
293A GLU* 4.9 6.5 - - + +
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Residues in contact with SER 277 (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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273A LYS* 2.8 29.6 + - - +
274A LYS* 3.7 6.3 - - - -
276A ALA* 1.3 71.8 - - - +
278A ARG* 1.3 63.8 + - - +
280A GLN* 3.1 34.5 + - - +
281A ASN* 3.8 9.4 - - - +
293A GLU* 5.3 3.8 + - - -
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Residues in contact with ARG 278 (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 GLU* 3.1 27.9 + - - -
274A LYS* 2.9 41.9 + - - +
275A VAL* 3.5 21.3 - - - +
277A SER* 1.3 76.9 - - - +
279A TYR* 1.3 63.3 + - - +
280A GLN 3.2 0.7 + - - -
281A ASN* 3.5 24.1 + - - +
282A ASN* 4.0 10.6 + - - +
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Residues in contact with TYR 279 (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 PRO* 3.6 31.1 - - + +
250A THR* 3.4 22.0 + - + +
251A ILE* 3.6 23.8 - - + -
275A VAL 2.8 12.8 + - - +
276A ALA* 3.0 15.7 + - - +
278A ARG* 1.3 78.7 - - - +
280A GLN* 1.3 62.5 + - + +
281A ASN 3.5 0.5 + - - -
282A ASN* 3.5 29.4 + - - +
290A PRO* 5.2 13.5 - - + -
292A LEU* 4.2 16.6 - - + -
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Residues in contact with GLN 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ALA 3.4 11.9 - - - +
277A SER* 3.1 23.8 + - - +
279A TYR* 1.3 78.3 - - + +
281A ASN* 1.3 69.3 + - - +
282A ASN 3.4 6.1 + - - +
290A PRO* 2.7 46.6 - - + +
291A TRP* 3.3 33.6 - - - -
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Residues in contact with ASN 281 (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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277A SER 3.8 10.2 + - - +
278A ARG* 3.9 17.1 + - - +
279A TYR 3.4 0.8 - - - -
280A GLN* 1.3 80.9 - - - +
282A ASN* 1.3 63.4 + - - +
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Residues in contact with ASN 282 (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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278A ARG 4.0 12.2 + - - +
279A TYR* 3.5 29.6 + - - +
280A GLN 4.0 4.8 - - - +
281A ASN* 1.3 82.4 - - - +
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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