Contacts of the helix formed by residues 249 - 266 (chain A) in PDB entry 6BFN
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 TRP 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A LYS 4.9 14.3 + - - -
248A GLU* 1.3 85.6 + - - +
250A THR* 1.3 57.6 + - - +
252A VAL* 3.1 27.3 - - + +
253A LYS* 2.9 29.7 + - - +
282A GLY* 3.2 40.2 + - - -
284A TYR* 3.3 27.3 - + - -
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Residues in contact with THR 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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248A GLU* 3.5 24.2 - - + +
249A TRP* 1.3 73.0 - - - +
251A ALA* 1.3 62.9 + - - +
253A LYS* 3.2 25.0 - - - +
254A GLN* 2.9 27.4 + - - +
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Residues in contact with ALA 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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248A GLU* 3.0 22.1 + - + +
250A THR* 1.3 80.0 - - + +
252A VAL* 1.3 62.0 + - + +
253A LYS 3.1 0.2 - - - -
254A GLN* 3.0 9.1 + - - +
255A SER* 2.9 27.4 + - - -
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Residues in contact with VAL 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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223A PHE 5.5 2.9 - - - +
241A LEU* 3.6 24.6 - - + +
242A LYS* 4.8 21.3 - - + +
248A GLU 3.5 16.4 - - - +
249A TRP* 3.1 36.3 + - + +
251A ALA* 1.3 73.4 - - + +
253A LYS* 1.3 60.1 + - - +
255A SER* 3.0 11.5 + - - +
256A PHE* 2.9 28.9 + - - +
284A TYR* 4.6 5.8 - - + -
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Residues in contact with LYS 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 TRP* 2.9 16.9 + - - +
250A THR* 3.2 29.2 - - - +
251A ALA 3.1 0.2 - - - -
252A VAL* 1.3 81.1 - - - +
254A GLN* 1.3 56.9 + - - +
256A PHE* 3.2 7.1 - - - +
257A LEU* 2.9 48.2 + - + +
284A TYR* 2.4 52.8 + - + +
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Residues in contact with GLN 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 THR 2.9 13.2 + - - +
251A ALA* 3.0 11.8 + - - +
253A LYS* 1.3 74.7 - - - +
255A SER* 1.3 59.4 + - - +
257A LEU* 3.3 17.1 + - + +
258A THR* 2.9 41.0 + - - -
363A ARG* 3.1 29.3 + - - +
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Residues in contact with SER 255 (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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241A LEU* 4.3 9.0 - - - +
251A ALA 2.9 10.7 + - - -
252A VAL* 3.0 25.2 + - - +
254A GLN* 1.3 76.4 - - - +
256A PHE* 1.3 55.4 + - - +
259A GLU* 2.9 28.3 + - - +
360A GLY* 3.3 34.2 - - - -
361A LEU* 4.9 9.0 - - - -
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Residues in contact with PHE 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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241A LEU* 3.6 22.7 - - + -
252A VAL 2.9 15.6 + - - +
253A LYS* 3.2 12.1 - - + +
255A SER* 1.3 78.4 + - - +
257A LEU* 1.3 83.6 + - + +
259A GLU* 3.2 3.8 + - - +
260A VAL* 2.9 35.9 + - + +
277A TYR* 3.8 31.9 - + + -
278A CYS 4.2 0.9 - - - -
279A ALA* 4.1 17.0 - - + -
284A TYR* 3.8 26.7 - + + -
285A CYS 3.4 30.5 - - - -
286A LEU* 3.8 17.2 - - + +
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Residues in contact with LEU 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 LYS* 2.9 33.9 + - + +
254A GLN* 3.9 17.3 - - - +
256A PHE* 1.3 94.0 - - + +
258A THR* 1.3 58.2 + - - +
260A VAL* 3.4 6.2 + - + +
261A GLU* 2.9 32.1 + - - +
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Residues in contact with THR 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 GLN* 2.9 31.9 + - - +
255A SER 3.7 0.4 - - - -
256A PHE 3.2 0.2 - - - -
257A LEU* 1.3 76.3 - - - +
259A GLU* 1.3 57.7 + - - +
261A GLU* 3.3 8.1 + - - +
262A GLN* 2.9 43.6 + - + +
359A PHE 3.4 13.0 - - - +
360A GLY 3.3 24.9 + - - +
362A ALA 3.4 22.9 - - - +
363A ARG* 3.5 13.7 + - - +
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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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239A LYS* 2.9 25.1 + - - -
241A LEU* 5.7 0.2 - - - +
255A SER 2.9 18.4 + - - +
256A PHE 3.8 3.1 - - - +
258A THR* 1.3 73.3 - - - +
260A VAL* 1.3 67.1 + - - +
263A LEU* 2.9 50.1 + - + +
286A LEU* 3.2 18.3 - - + +
288A TYR* 2.6 28.9 + - - +
358A ASP 3.7 6.6 + - - -
359A PHE* 3.5 27.7 + - - +
360A GLY* 3.7 11.7 + - - +
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Residues in contact with VAL 260 (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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197A PRO* 3.7 32.1 - - + -
256A PHE* 2.9 41.9 + - + +
257A LEU* 3.7 7.4 - - + +
259A GLU* 1.3 76.3 - - - +
261A GLU* 1.3 62.9 + - - +
263A LEU* 3.9 0.5 - - - +
264A SER* 2.8 30.2 + - - +
274A PHE* 4.2 13.2 - - + -
277A TYR* 4.1 13.0 - - + -
286A LEU* 3.6 22.7 - - + -
195B PRO* 5.8 0.4 - - + -
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Residues in contact with GLU 261 (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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257A LEU 2.9 18.4 + - - +
258A THR* 3.7 7.1 - - - +
260A VAL* 1.3 77.6 - - - +
262A GLN* 1.3 79.4 + - - +
264A SER* 3.1 9.1 + - - -
265A ARG* 3.0 27.7 + - + +
364A PHE* 4.8 7.1 - - - -
194B ARG 5.6 5.3 - - - -
195B PRO* 4.4 24.4 - - + +
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Residues in contact with GLN 262 (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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258A THR* 2.9 26.6 + - + +
259A GLU 4.4 0.9 - - - +
261A GLU* 1.3 94.3 + - - +
263A LEU* 1.3 60.9 + - - +
265A ARG* 3.2 5.1 + - - +
266A PHE* 2.8 56.7 + - - +
336A LEU* 3.8 16.5 - - + +
359A PHE* 4.3 21.1 - - + -
362A ALA* 4.1 22.5 + - + -
363A ARG* 5.6 0.2 - - - +
364A PHE* 3.6 28.4 - - - +
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Residues in contact with LEU 263 (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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259A GLU* 2.9 39.2 + - + +
260A VAL 4.3 0.2 - - - +
262A GLN* 1.3 74.0 - - - +
264A SER* 1.3 55.6 + - - +
266A PHE 3.5 11.8 - - - +
271A ILE* 3.9 22.2 - - + -
272A VAL* 4.1 11.9 - - + +
274A PHE* 3.8 26.5 - - + -
288A TYR* 3.5 32.3 - - + -
359A PHE* 3.6 30.7 - - + -
267B ARG* 2.6 31.3 + - - -
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Residues in contact with SER 264 (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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196A PHE* 5.3 8.8 - - - -
197A PRO* 3.3 27.9 - - - +
260A VAL 2.8 20.6 + - - -
261A GLU 3.1 10.3 + - - -
263A LEU* 1.3 78.1 - - - +
265A ARG* 1.3 61.6 + - - +
267A ARG* 4.4 5.4 - - - +
274A PHE* 4.2 5.0 - - - -
195B PRO* 3.7 22.9 - - - -
196B PHE 4.9 2.9 - - - +
197B PRO* 5.5 3.6 - - - +
267B ARG* 3.3 18.9 + - - +
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Residues in contact with ARG 265 (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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261A GLU* 3.0 15.1 + - + +
262A GLN* 3.2 10.1 + - - +
264A SER* 1.3 79.4 - - - +
266A PHE* 1.3 82.8 + - + +
267A ARG* 3.6 5.0 + - - +
332A ASP* 3.0 37.6 + - - -
333A SER 5.5 2.4 + - - -
364A PHE* 4.4 15.2 - - - -
195B PRO* 5.2 2.6 - - + +
196B PHE* 4.4 21.8 + - - +
197B PRO 4.6 2.2 + - - -
198B PHE* 3.8 52.0 + - + +
199B CYS 5.0 3.4 + - - +
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Residues in contact with PHE 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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262A GLN* 2.8 28.9 + - + +
263A LEU* 3.5 15.1 - - + +
265A ARG* 1.3 99.4 - - + +
267A ARG* 1.3 61.1 + - - +
271A ILE* 4.1 22.7 - - + +
272A VAL 5.3 1.0 - - - +
328A PHE* 3.8 18.8 - + - -
329A LEU* 3.6 29.4 - - + -
332A ASP* 3.3 38.6 - - + -
336A LEU* 3.5 40.8 - - + -
359A PHE* 5.0 4.0 - + + -
364A PHE* 4.5 3.8 - + - -
198B PHE* 4.3 9.4 - + - -
267B ARG* 4.9 1.0 + - - -
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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