Contacts of the helix formed by residues 249 - 270 (chain A) in PDB entry 6AF6
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 SER 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A ALA 3.6 1.9 + - - -
245A LYS* 2.6 29.6 + - - -
246A GLY 4.6 3.1 - - - -
247A CYS 3.1 1.0 - - - -
248A LEU* 1.3 78.7 - - - +
250A ALA* 1.4 52.0 + - - +
251A LEU 3.0 1.3 - - - -
252A PHE* 2.8 40.7 + - - +
253A VAL 3.5 6.1 + - - -
301A LEU* 5.1 0.2 - - - -
322A LYS* 3.7 18.4 - - - +
325A ILE* 3.6 30.0 - - - +
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Residues in contact with ALA 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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70A ALA* 3.2 31.4 - - + +
73A ILE* 4.1 1.6 - - + -
74A GLU* 3.4 16.3 - - + +
247A CYS 3.1 17.1 + - - +
249A SER* 1.4 71.9 - - - +
251A LEU* 1.3 63.3 + - - +
253A VAL* 3.1 7.2 + - - +
254A GLY 3.0 18.9 + - - -
301A LEU* 3.7 29.5 - - + +
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Residues in contact with LEU 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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73A ILE* 3.5 19.7 - - + +
76A LEU* 3.9 6.7 - - + -
77A GLY* 3.5 35.2 - - - +
83A ILE* 4.2 24.1 - - + +
86A SER* 3.6 23.1 - - - +
87A PHE* 3.9 33.4 - - + +
90A CYS* 4.6 5.4 - - - -
248A LEU* 2.9 21.1 + - + +
250A ALA* 1.3 77.3 - - - +
252A PHE* 1.3 69.6 + - + +
254A GLY 3.3 0.7 + - - -
255A GLY* 3.0 22.9 + - - -
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Residues in contact with PHE 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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83A ILE* 3.8 23.6 - - + -
87A PHE* 4.4 7.2 - + - -
206A LEU* 5.5 2.0 - - + -
248A LEU* 4.1 18.6 - - + -
249A SER* 2.8 22.5 + - - +
251A LEU* 1.3 80.0 - - + +
253A VAL* 1.3 59.9 + - - +
255A GLY* 3.8 2.3 - - - +
256A LEU* 2.9 28.4 + - - +
325A ILE* 3.7 17.5 - - + -
326A SER* 5.9 0.2 - - - -
329A ALA* 4.4 11.1 - - + +
357A ASN 4.2 9.4 - - - -
358A MET* 3.5 35.3 - - + +
361A SER* 3.7 23.3 - - - -
364A PHE* 3.4 33.7 - + - -
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Residues in contact with VAL 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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74A GLU* 3.9 22.0 - - + +
249A SER 3.5 3.1 + - - +
250A ALA* 3.1 8.7 + - - +
252A PHE* 1.3 78.7 - - - +
254A GLY* 1.4 57.9 + - - +
256A LEU* 3.1 7.5 + - - +
257A ALA* 2.9 26.7 + - - +
294A LEU* 3.7 12.9 - - + +
297A CYS* 4.2 10.3 - - - -
298A ARG* 3.9 27.4 - - + -
301A LEU* 4.2 11.9 - - + -
325A ILE* 3.6 37.7 - - + -
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Residues in contact with GLY 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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74A GLU* 3.3 31.4 - - - +
78A LYS* 3.3 23.8 - - - +
250A ALA 3.0 11.5 + - - -
251A LEU 3.3 1.3 + - - -
253A VAL* 1.4 76.4 - - - +
255A GLY* 1.4 61.7 + - - +
257A ALA* 3.2 5.5 + - - +
258A ARG 3.1 18.4 + - - -
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Residues in contact with GLY 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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77A GLY 3.6 13.8 + - - -
83A ILE* 5.9 4.7 - - - -
251A LEU 3.0 14.6 + - - -
252A PHE* 3.4 4.7 + - - -
253A VAL 3.2 0.2 - - - -
254A GLY* 1.4 77.3 - - - +
256A LEU* 1.3 55.8 + - - +
258A ARG* 3.4 5.5 + - - +
259A LEU* 2.9 28.1 + - - +
354A HIS* 4.0 19.5 - - - -
358A MET* 5.8 0.4 - - - -
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Residues in contact with LEU 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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252A PHE 2.9 17.8 + - - +
253A VAL* 3.1 5.6 + - - +
255A GLY* 1.3 72.8 - - - +
257A ALA* 1.3 61.4 + - - +
259A LEU* 4.1 13.2 - - + -
260A LEU* 2.8 29.1 + - + +
290A MET* 4.5 13.5 - - + +
293A ARG* 4.6 5.2 - - + -
294A LEU* 3.8 40.8 - - + +
297A CYS* 4.6 9.9 - - - -
325A ILE 5.9 0.2 - - - +
328A TYR* 4.7 10.5 - - + +
329A ALA* 5.1 7.0 - - + +
332A SER* 3.4 38.6 - - - +
354A HIS* 4.8 2.6 - - - +
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Residues in contact with ALA 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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74A GLU* 5.5 0.7 - - - +
78A LYS* 4.1 21.8 - - + +
253A VAL 2.9 13.3 + - - +
254A GLY* 3.5 11.0 - - - +
256A LEU* 1.3 78.6 - - - +
258A ARG* 1.3 60.2 + - - +
260A LEU* 3.5 2.1 + - - +
261A GLU* 3.2 28.5 + - - +
294A LEU* 3.9 23.5 - - + +
298A ARG* 4.6 12.8 - - - +
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Residues in contact with ARG 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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17A TYR* 5.9 0.6 + - - -
21A CYS* 5.8 1.0 - - - -
25A ASP* 4.3 7.3 + - - -
77A GLY 4.6 4.9 - - - -
78A LYS* 3.1 39.7 + - + +
79A GLY* 3.5 19.8 + - - -
80A SER 4.1 2.2 - - - +
81A ARG* 3.2 43.7 - - - +
254A GLY 3.1 12.6 + - - +
255A GLY* 3.6 8.7 - - - +
257A ALA* 1.3 72.9 - - - +
259A LEU* 1.3 68.0 + - - +
261A GLU* 3.2 7.8 + - - +
262A THR* 3.1 29.4 + - - +
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Residues in contact with LEU 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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255A GLY 2.9 18.3 + - - +
256A LEU* 3.6 8.7 - - + +
258A ARG* 1.3 78.7 - - - +
260A LEU* 1.3 57.0 + - - +
262A THR* 3.3 6.4 + - - -
263A THR* 2.8 33.5 + - - +
290A MET* 3.9 7.6 - - + -
329A ALA 5.3 0.4 - - - +
332A SER* 3.5 39.0 - - - +
333A GLY* 3.9 0.4 - - - +
336A ALA* 3.6 24.0 - - + -
351A LEU* 3.8 22.4 - - + -
354A HIS* 3.6 37.0 - - + +
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Residues in contact with LEU 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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256A LEU* 2.8 24.1 + - + +
257A ALA 3.9 4.3 - - - +
259A LEU* 1.3 72.9 - - - +
261A GLU* 1.3 61.2 + - + +
263A THR* 3.2 0.6 + - - -
264A LEU* 2.9 45.6 + - + +
287A ILE* 3.9 30.1 - - + +
290A MET* 4.1 28.9 - - + +
291A LYS* 3.8 38.8 - - + +
294A LEU* 3.8 19.7 - - + -
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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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17A TYR* 5.5 1.2 + - - -
78A LYS* 2.9 39.8 + - - -
257A ALA* 3.2 10.3 + - - +
258A ARG* 3.6 9.0 - - - +
260A LEU* 1.3 77.9 - - + +
262A THR* 1.3 62.9 + - - +
264A LEU* 3.5 9.2 + - + +
265A GLU* 3.1 37.5 + - - +
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Residues in contact with THR 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 ARG* 3.1 20.0 + - - +
259A LEU* 3.6 10.7 - - - +
261A GLU* 1.3 76.6 - - - +
263A THR* 1.3 63.7 + - - +
265A GLU* 3.4 10.6 + - - +
266A TYR* 3.1 21.5 + - - +
340A PHE* 3.8 20.6 - - + -
349A LEU* 6.2 2.7 - - + +
351A LEU* 4.6 12.8 - - + -
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Residues in contact with THR 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 LEU* 2.8 18.9 + - - +
260A LEU* 3.7 4.0 - - - -
262A THR* 1.3 75.0 - - - +
264A LEU* 1.3 60.0 + - - +
266A TYR* 3.2 3.1 + - - +
267A ALA* 2.9 27.8 + - - +
287A ILE* 3.9 16.8 - - + -
290A MET* 3.7 16.6 - - - +
336A ALA* 3.5 22.5 - - - +
339A THR* 3.7 35.1 - - + +
340A PHE* 4.1 11.2 - - + -
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Residues in contact with LEU 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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260A LEU* 2.9 45.5 + - + +
261A GLU* 3.8 8.5 - - + +
263A THR* 1.3 74.9 - - - +
265A GLU* 1.3 64.7 + - + +
267A ALA* 3.2 5.7 + - + +
268A LYS* 3.1 52.2 + - - +
287A ILE* 3.6 23.6 - - + -
291A LYS* 6.2 0.9 - - + -
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Residues in contact with GLU 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* 3.1 30.1 + - - +
262A THR* 3.7 8.0 - - - +
264A LEU* 1.3 75.6 - - + +
266A TYR* 1.3 62.7 + - - +
268A LYS* 3.3 11.2 + - + +
269A ALA* 3.1 23.8 + - - +
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Residues in contact with TYR 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 THR 3.1 8.6 + - - +
263A THR 3.2 4.0 + - - +
265A GLU* 1.3 77.5 - - - +
267A ALA* 1.3 59.9 + - - +
269A ALA* 4.4 5.4 - - + +
270A ARG* 2.9 74.0 + - + +
277A ILE* 4.2 3.4 - - + -
339A THR* 3.9 13.9 - - + -
340A PHE* 3.4 71.1 + + + -
343A ALA* 3.9 17.6 - - + +
349A LEU* 6.1 0.7 - - + -
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Residues in contact with ALA 267 (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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263A THR 2.9 10.7 + - - +
264A LEU* 3.2 5.1 + - + +
266A TYR* 1.3 76.9 - - - +
268A LYS* 1.3 60.2 + - + +
270A ARG 4.2 0.2 - - - +
276A ALA* 3.5 7.3 - - - +
277A ILE* 3.6 17.5 + - + +
278A GLY* 3.0 37.1 + - - +
283A VAL* 4.4 0.7 - - + -
287A ILE* 3.5 32.1 - - + -
339A THR* 4.3 6.0 - - + +
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Residues in contact with LYS 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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264A LEU* 3.1 41.6 + - + +
265A GLU* 3.7 8.8 - - + +
267A ALA* 1.3 82.0 - - + +
269A ALA* 1.3 59.5 + - - +
271A GLN* 3.8 5.7 + - - -
276A ALA* 3.5 18.3 - - - +
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Residues in contact with ALA 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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265A GLU 3.1 16.6 + - - +
266A TYR* 4.0 7.9 - - + +
268A LYS* 1.3 77.2 - - - +
270A ARG* 1.3 65.1 + - - +
271A GLN* 3.4 17.0 + - - +
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Residues in contact with ARG 270 (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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266A TYR* 2.9 58.2 + - + +
269A ALA* 1.3 75.5 - - - +
271A GLN* 1.3 65.2 + - - +
272A GLN* 3.6 36.5 + - - +
276A ALA* 3.3 3.3 - - - +
277A ILE* 2.8 45.5 + - + +
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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