Contacts of the helix formed by residues 246 - 266 (chain A) in PDB entry 2ODP
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 246 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A GLN 4.4 2.2 + - - -
244A SER 4.0 1.8 + - - -
245A VAL* 1.3 76.9 - - - +
247A GLU* 1.3 64.6 + - - +
248A ASN* 3.2 10.4 + - - +
249A ASP* 2.8 37.6 + - - -
250A PHE* 3.0 20.3 + - - +
308A TYR* 3.9 3.4 - - - -
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Residues in contact with GLU 247 (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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246A SER* 1.3 73.0 - - - +
248A ASN* 1.3 61.4 + - - +
250A PHE* 3.5 4.2 + - - +
251A LEU* 3.2 34.6 + - + +
307A ASN* 4.8 3.6 - - - +
308A TYR* 3.3 44.9 - - + +
309A LYS* 3.2 39.1 + - - +
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Residues in contact with ASN 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A SER* 3.1 8.7 + - - +
247A GLU* 1.3 78.7 - - - +
249A ASP* 1.3 66.1 + - - +
251A LEU* 3.3 22.4 + - - +
252A ILE* 3.2 24.6 + - - +
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Residues in contact with ASP 249 (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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244A SER 4.3 1.9 - - - +
245A VAL* 3.3 24.0 - - + -
246A SER* 2.8 33.1 + - - +
248A ASN* 1.3 76.2 - - - +
250A PHE* 1.3 55.5 + - - +
252A ILE* 3.0 13.7 + - - +
253A PHE* 2.9 31.2 + - + -
393A VAL 5.8 0.7 - - - +
394A GLY* 5.8 0.5 - - - -
395A LYS 5.0 4.0 + - - -
396A LEU* 3.9 35.8 + - + +
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Residues in contact with PHE 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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239A LEU* 3.9 28.5 - - + -
240A ASP 3.5 17.9 - - - -
241A ALA* 3.6 25.1 - - + -
245A VAL* 3.7 2.0 - - + +
246A SER 3.0 6.7 + - - +
247A GLU 3.6 9.2 - - - +
248A ASN 3.3 0.2 - - - -
249A ASP* 1.3 76.2 - - - +
251A LEU* 1.3 59.2 + - + +
253A PHE* 3.2 13.6 + + - +
254A LYS* 2.8 52.3 + - + +
277A THR* 3.8 22.0 - - + -
306A ALA* 3.8 8.7 - - + -
307A ASN 4.7 0.7 - - - -
308A TYR* 3.6 46.9 - + + -
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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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247A GLU* 3.2 24.7 + - + +
248A ASN* 3.4 24.9 - - - +
249A ASP 3.2 0.4 - - - -
250A PHE* 1.3 77.9 - - + +
252A ILE* 1.3 56.8 + - + +
254A LYS* 3.1 26.5 + - + +
255A GLU* 2.8 29.2 + - - +
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Residues in contact with ILE 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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248A ASN 3.4 14.8 - - - +
249A ASP* 3.0 13.2 + - - +
251A LEU* 1.3 73.6 - - + +
253A PHE* 1.3 60.0 + - - +
255A GLU* 3.4 17.6 - - - +
256A SER* 2.9 28.8 + - - -
393A VAL* 3.9 36.6 - - + +
394A GLY* 4.4 9.9 - - - -
420A GLN 5.9 0.7 - - - +
421A ASP* 5.1 6.3 - - + -
422A THR* 4.0 11.7 - - - +
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Residues in contact with PHE 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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239A LEU* 4.2 13.7 - - + -
240A ASP* 3.4 31.2 - - + -
245A VAL* 3.5 26.7 - - + -
249A ASP* 2.9 15.2 + - + -
250A PHE* 3.3 13.2 - + + +
252A ILE* 1.3 76.1 - - - +
254A LYS* 1.3 57.4 + - - +
256A SER* 3.4 2.5 + - - -
257A ALA* 2.9 30.7 + - - +
354A LEU* 3.5 35.1 - - + +
355A THR* 3.9 21.3 - - - -
393A VAL* 3.3 41.7 - - + -
396A LEU* 4.1 16.2 - - + -
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Residues in contact with LYS 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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239A LEU* 3.9 20.4 - - + -
250A PHE* 2.8 43.2 + - + +
251A LEU* 3.1 27.0 + - + +
253A PHE* 1.3 72.7 - - - +
255A GLU* 1.3 54.0 + - - +
257A ALA* 3.8 2.6 - - - +
258A SER* 2.8 38.9 + - - +
303A LEU* 3.1 28.5 - - + +
304A GLU* 2.9 24.2 + - - +
306A ALA* 2.9 20.1 + - + +
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Residues in contact with GLU 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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251A LEU 2.8 12.4 + - - +
252A ILE* 3.4 24.9 - - - +
254A LYS* 1.3 77.6 - - - +
256A SER* 1.3 62.0 + - - +
258A SER* 3.4 6.3 + - - -
259A LEU* 3.1 23.0 + - - +
422A THR* 3.1 30.3 + - + +
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Residues in contact with SER 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 ILE 2.9 16.1 + - - -
253A PHE 3.7 4.0 - - - -
255A GLU* 1.3 76.1 - - - +
257A ALA* 1.3 57.1 + - - +
259A LEU* 3.3 4.0 + - - +
260A MET* 3.0 35.2 + - - +
354A LEU* 4.5 6.3 - - - -
393A VAL* 3.7 28.3 - - - +
422A THR* 2.9 31.6 + - - -
425A LEU* 4.0 15.3 - - - +
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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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237A LEU* 3.9 13.4 - - + +
239A LEU* 4.1 6.7 - - + -
253A PHE 2.9 17.7 + - - +
254A LYS 3.8 0.7 - - - +
256A SER* 1.3 76.1 - - - +
258A SER* 1.3 56.1 + - - +
260A MET* 3.2 13.1 + - - +
261A VAL* 3.0 32.6 + - - +
303A LEU* 3.7 30.1 - - + -
354A LEU* 4.1 11.1 - - + +
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Residues in contact with SER 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 LYS* 2.8 26.3 + - - +
255A GLU* 3.6 7.6 - - - -
256A SER 3.4 0.2 - - - -
257A ALA* 1.3 68.4 - - - +
259A LEU* 1.3 60.5 + - - +
261A VAL* 3.3 2.3 + - - +
262A ASP* 2.8 31.5 + - - +
300A ILE* 3.8 20.8 - - - +
303A LEU* 3.6 20.7 - - - +
304A GLU* 5.2 6.1 + - - +
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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 GLU 3.1 13.6 + - - +
256A SER 3.3 6.7 + - - +
258A SER* 1.3 75.5 - - - +
260A MET* 1.3 64.9 + - + +
262A ASP* 3.5 6.5 - - - +
263A ARG* 2.9 28.7 + - + +
422A THR* 3.9 20.0 - - + -
423A LYS* 6.1 0.2 - - - -
425A LEU* 4.0 19.5 - - + -
426A HIS* 3.7 47.1 - - + -
429A PHE* 4.7 8.1 - - + -
669A PHE* 4.3 10.2 - - + -
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Residues in contact with MET 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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235A LEU* 5.3 3.6 - - + -
237A LEU* 4.2 16.2 - - + -
256A SER 3.0 25.6 + - - +
257A ALA* 3.2 14.8 + - - +
259A LEU* 1.3 76.6 - - + +
261A VAL* 1.3 58.0 + - - +
264A ILE* 2.9 31.8 + - - +
352A ILE* 3.8 31.9 - - + -
354A LEU* 4.2 16.8 - - + -
391A ILE* 5.0 0.4 - - - -
425A LEU* 3.8 24.2 - - + -
429A PHE* 3.6 51.2 - - + -
432A MET* 5.0 1.3 - - - -
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Residues in contact with VAL 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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235A LEU* 5.2 0.9 - - + -
237A LEU* 3.5 22.4 - - + -
257A ALA 3.0 18.6 + - - +
258A SER 3.6 6.7 - - - +
260A MET* 1.3 73.5 - - - +
262A ASP* 1.3 64.5 + - - +
264A ILE* 3.2 9.8 - - - +
265A PHE* 2.9 42.4 + - + -
273A VAL* 4.2 6.7 - - + -
296A MET* 4.2 2.0 - - + -
299A VAL* 3.8 25.1 - - + -
300A ILE* 3.5 25.4 - - + -
303A LEU* 3.9 11.7 - - + -
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Residues in contact with ASP 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 SER 2.8 21.0 + - - +
259A LEU* 3.5 7.6 - - - +
261A VAL* 1.3 75.3 - - - +
263A ARG* 1.3 62.1 + - - +
265A PHE* 3.4 2.9 + - - +
266A SER* 3.2 18.2 + - - -
296A MET* 4.2 16.9 - - + +
300A ILE* 4.6 2.0 - - + +
573A ARG* 4.7 2.3 + - - -
668A ARG* 3.5 30.4 + - - +
669A PHE* 3.3 25.2 - - + -
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Residues in contact with ARG 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* 2.9 20.2 + - + +
262A ASP* 1.3 74.3 - - - +
264A ILE* 1.3 65.5 + - - +
266A SER* 2.6 38.8 + - - -
267A PHE* 3.4 30.1 - - - -
426A HIS* 5.7 1.1 - - + -
429A PHE* 3.8 25.4 - - + -
430A GLU* 2.8 42.2 + - - +
433A LEU* 4.0 6.5 - - + -
445A VAL* 5.7 1.0 - - - +
446A GLY 2.9 25.5 + - - +
448A MET* 3.7 12.6 - - - +
669A PHE* 3.6 46.0 + - + +
670A ARG* 5.9 0.8 - - - +
1C NAG 3.7 2.6 - - - +
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Residues in contact with ILE 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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225A ILE* 4.1 12.3 - - + -
227A ILE* 3.8 15.9 - - + -
233A LEU* 4.1 15.9 - - + -
235A LEU* 4.4 19.1 - - + -
260A MET 2.9 15.0 + - - +
261A VAL* 3.2 19.5 - - - +
263A ARG* 1.3 78.2 - - - +
265A PHE* 1.3 76.6 + - + +
266A SER 3.2 1.6 + - - -
267A PHE* 3.7 13.2 + - - -
269A ILE* 4.1 15.1 - - + +
271A VAL* 4.3 14.6 - - + +
273A VAL* 4.6 1.1 - - + -
429A PHE* 4.0 10.7 - - + -
433A LEU* 3.8 29.6 - - + -
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Residues in contact with PHE 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 VAL* 2.9 37.0 + - + +
262A ASP 4.0 0.7 - - - +
264A ILE* 1.3 81.4 - - + +
266A SER* 1.3 58.2 + - - +
267A PHE 3.2 1.9 + - - -
268A GLU* 3.7 11.3 + - - +
269A ILE 5.6 2.2 - - - +
271A VAL* 3.7 31.2 - - + -
273A VAL* 3.8 22.9 - - + -
293A SER 4.1 7.9 - - - -
294A ARG 3.5 25.6 - - - -
295A ASP 4.3 0.7 - - - -
296A MET* 3.6 47.3 - - + -
299A VAL* 4.5 2.2 - - + -
573A ARG* 2.7 29.8 + - - +
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Residues in contact with SER 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 ASP* 3.2 9.3 + - - -
263A ARG* 2.6 45.8 + - - -
265A PHE* 1.3 77.5 - - - +
267A PHE* 1.3 60.9 + - - +
268A GLU* 3.4 0.7 - - - -
442A ILE* 4.7 0.2 - - - +
445A VAL* 4.9 0.2 - - - +
573A ARG* 3.8 8.3 - - - +
668A ARG 3.9 10.5 - - - -
669A PHE* 3.7 25.1 - - - -
670A ARG* 3.4 34.5 + - - +
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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