Contacts of the helix formed by residues 243 - 261 (chain A) in PDB entry 6J95
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 MET 243 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A LEU* 4.7 1.8 - - + -
231A LEU* 3.8 19.1 - - + -
241A VAL* 3.6 26.0 - - + -
242A GLU* 1.3 72.0 - - - +
244A GLU* 1.3 59.0 + - - +
246A LEU* 3.3 13.3 + - + +
247A PHE* 2.9 76.9 + - + -
390A PHE* 5.6 1.6 - - + -
533A LEU* 4.1 12.3 - - + -
539A PHE* 4.3 8.7 - - + -
562A LEU* 2.8 24.8 + - + +
564A LEU* 3.5 31.9 - - + -
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Residues in contact with GLU 244 (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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242A GLU* 2.8 16.5 + - - +
243A MET* 1.3 78.0 - - - +
245A SER* 1.3 56.3 + - - +
247A PHE* 3.3 2.3 + - - +
248A SER* 3.0 28.3 + - - -
383A ALA* 5.1 3.3 - - + +
384A ALA* 5.9 2.0 - - - +
387A THR* 3.4 31.5 + - + +
556A ILE 4.5 1.7 - - - +
557A HIS* 3.4 23.3 - - + +
558A THR* 2.8 54.5 + - - +
561A GLY* 3.8 6.1 + - - -
562A LEU* 4.4 4.4 + - - +
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Residues in contact with SER 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A GLU* 3.0 24.9 + - - -
243A MET 3.4 0.2 - - - -
244A GLU* 1.3 76.1 - - - +
246A LEU* 1.3 62.8 + - - +
248A SER* 3.3 8.2 + - - -
249A ARG* 3.0 38.6 + - - +
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Residues in contact with LEU 246 (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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227A LEU* 4.0 17.9 - - + +
230A LYS* 3.7 32.3 - - + -
231A LEU* 3.9 28.3 - - + -
241A VAL* 4.1 13.9 - - + -
242A GLU 3.6 16.0 + - - +
243A MET* 3.3 19.0 + - + +
244A GLU 3.3 0.6 - - - -
245A SER* 1.3 79.0 - - - +
247A PHE* 1.3 58.6 + - - +
249A ARG* 3.2 9.0 + - + +
250A LEU* 2.9 27.4 + - - +
267A LEU* 3.9 7.3 - - + +
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Residues in contact with PHE 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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227A LEU* 4.0 13.7 - - + -
243A MET* 2.9 50.2 + - + +
244A GLU 3.8 3.4 - - - +
246A LEU* 1.3 75.7 - - - +
248A SER* 1.3 58.3 + - - +
250A LEU* 3.3 4.6 + - + +
251A THR* 3.0 34.5 + - - +
383A ALA* 3.9 16.6 - - - +
386A LEU* 3.4 44.6 - - + -
387A THR* 3.5 22.2 - - - +
390A PHE* 3.5 31.2 - + + -
529A ALA* 5.4 1.3 - - + -
533A LEU* 3.7 20.2 - - + -
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Residues in contact with SER 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLU* 3.0 15.3 + - - -
245A SER* 3.5 11.9 - - - -
246A LEU 3.2 0.2 - - - -
247A PHE* 1.3 76.6 - - - +
249A ARG* 1.3 60.8 + - - +
251A THR* 3.7 5.4 - - - -
252A LEU* 3.0 10.6 + - - +
278A TYR* 2.6 32.5 + - - -
379A HIS* 2.9 32.6 + - - -
380A GLU* 4.9 2.1 + - - -
383A ALA* 3.8 12.6 - - - +
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Residues in contact with ARG 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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245A SER* 3.0 29.9 + - - +
246A LEU* 3.6 11.7 - - + +
248A SER* 1.3 74.6 - - - +
250A LEU* 1.3 63.2 + - - +
252A LEU 3.4 0.2 + - - -
253A ASP* 3.0 18.2 + - - -
266A SER* 2.9 59.0 + - - +
267A LEU* 3.8 16.6 - - + -
269A ASN 3.6 6.9 + - - -
270A ASP* 2.9 34.3 + - - -
274A ILE* 4.3 8.8 - - - +
278A TYR* 3.6 23.1 + - - -
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Residues in contact with LEU 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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223A ALA* 3.4 42.6 - - + +
224A SER* 3.7 9.0 - - - +
227A LEU* 4.0 23.3 - - + -
246A LEU 2.9 16.9 + - - +
247A PHE* 3.3 6.0 + - + +
249A ARG* 1.3 77.4 - - - +
251A THR* 1.3 59.3 + - + +
253A ASP* 3.3 3.5 + - - +
254A ILE* 3.0 39.3 + - + +
267A LEU* 3.8 14.3 - - + +
386A LEU* 3.9 28.3 - - + -
529A ALA* 4.2 15.7 - - + -
533A LEU* 5.9 0.2 - - + -
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Residues in contact with THR 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 PHE 3.0 17.1 + - - +
248A SER 3.2 1.6 + - - -
250A LEU* 1.3 74.9 - - + +
252A LEU* 1.3 58.9 + - - +
254A ILE* 3.9 1.3 - - - +
255A ILE* 3.0 32.1 + - - +
378A GLY 4.5 2.4 - - - +
379A HIS* 3.0 36.0 + - - -
382A SER* 3.8 15.5 - - - -
383A ALA* 3.5 22.6 - - - +
386A LEU* 4.1 14.6 - - + -
525A GLU* 3.9 18.0 - - - +
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Residues in contact with LEU 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 SER 3.0 18.8 + - - +
249A ARG 3.7 3.6 - - - +
251A THR* 1.3 75.1 + - - +
253A ASP* 1.3 65.8 + - - +
255A ILE* 3.3 3.2 + - - +
256A GLY 3.0 20.6 + - - -
264A PHE* 3.6 36.8 - - + -
266A SER* 3.8 23.3 - - - +
274A ILE* 4.4 9.9 - - + -
277A VAL* 4.1 17.9 - - + -
278A TYR* 3.9 24.2 - - + +
375A LEU* 4.1 9.6 - - + -
379A HIS* 3.5 25.7 + - + +
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Residues in contact with ASP 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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219A LEU* 5.1 1.3 - - - +
223A ALA* 5.1 1.8 - - + -
226A ARG* 3.4 25.5 + - - +
249A ARG 3.0 16.7 + - - +
250A LEU* 3.6 5.6 - - - +
252A LEU* 1.3 75.4 - - - +
254A ILE* 1.3 64.3 + - - +
256A GLY* 3.8 0.5 + - - -
257A LYS* 3.5 18.7 + - - +
262A TYR 4.6 2.4 - - - +
263A ASP* 5.6 0.9 - - - -
264A PHE* 3.6 9.3 + - - +
265A ASP* 3.4 12.5 + - - +
266A SER* 2.7 33.9 + - - -
267A LEU* 2.9 34.8 + - + +
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Residues in contact with ILE 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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219A LEU* 3.4 17.1 - - + +
220A PHE* 3.5 44.0 - - + +
223A ALA* 3.5 21.1 - - + -
224A SER* 4.9 2.0 - - - +
250A LEU* 3.0 42.3 + - + +
251A THR 3.9 3.8 - - - +
252A LEU 3.3 0.2 - - - -
253A ASP* 1.3 77.0 - - - +
255A ILE* 1.3 62.3 + - + +
257A LYS 3.3 2.3 + - - -
258A ALA* 2.9 24.3 + - - +
521A PHE* 4.4 4.9 - - + -
525A GLU* 3.5 34.3 - - + +
529A ALA* 6.2 0.9 - - + -
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Residues in contact with ILE 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 THR 3.0 20.8 + - - +
252A LEU* 3.4 11.2 - - - +
254A ILE* 1.3 79.6 - - + +
256A GLY* 1.3 61.3 + - - +
258A ALA* 4.4 0.9 - - - +
259A VAL* 2.9 56.4 + - + +
374A MET 3.7 17.7 - - - +
375A LEU* 3.6 32.1 - - + +
378A GLY* 3.9 24.9 - - - +
379A HIS* 4.0 5.4 - - + -
521A PHE* 4.2 18.4 - - + -
525A GLU* 5.6 0.7 - - - +
601A HEM 4.1 13.5 - - + -
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Residues in contact with GLY 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 LEU 3.0 11.2 + - - -
253A ASP 4.3 0.2 - - - -
255A ILE* 1.3 80.0 - - - +
257A LYS* 1.3 58.5 + - - +
260A PHE* 3.3 22.9 + - - -
261A ASN 3.3 6.1 + - - -
262A TYR 3.0 25.0 + - - -
264A PHE* 3.7 27.1 - - - -
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Residues in contact with LYS 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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216A MET* 5.9 0.3 - - - +
219A LEU* 3.8 27.4 - - + -
253A ASP 3.5 10.5 + - - +
254A ILE 3.3 7.7 + - - +
255A ILE 3.2 0.4 - - - -
256A GLY* 1.3 76.1 - - - +
258A ALA* 1.3 64.8 + - - +
261A ASN* 3.1 44.5 + - - +
262A TYR 3.0 10.6 + - - +
263A ASP* 3.2 39.8 + - - +
349A PRO* 6.2 3.4 - - - -
350A SER* 3.9 5.2 - - - -
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Residues in contact with ALA 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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212A TYR* 2.8 29.1 + - - +
216A MET* 3.6 20.0 - - - -
219A LEU* 3.8 3.5 - - + +
254A ILE 2.9 15.8 + - - +
255A ILE* 4.0 3.1 - - - +
257A LYS* 1.3 77.1 - - - +
259A VAL* 1.3 61.4 + - + +
350A SER* 3.3 5.9 - - - -
351A ILE 3.2 15.4 + - - -
521A PHE* 3.5 28.5 - - + -
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Residues in contact with VAL 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 ILE* 2.9 46.4 + - + +
258A ALA* 1.3 80.9 - - + +
260A PHE* 1.3 80.7 + - + +
350A SER* 3.8 1.1 - - - -
351A ILE* 3.3 17.5 + - + +
352A LEU* 2.9 28.9 + - - +
371A LEU* 3.8 26.9 - - + +
374A MET* 4.1 25.1 - - + -
375A LEU 4.7 0.4 - - - +
601A HEM 4.7 1.6 - - + -
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Residues in contact with PHE 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 GLY* 3.3 19.1 + - - -
259A VAL* 1.3 96.6 - - + +
261A ASN* 1.3 72.5 + - - +
262A TYR* 3.2 22.0 + + + -
264A PHE* 4.3 11.7 - + - -
317A ILE* 6.3 0.7 - - + -
320A THR* 6.2 0.7 - - + -
321A LEU* 3.7 28.0 - - + -
324A LEU* 3.6 31.7 - - + +
350A SER* 4.0 1.8 - - - -
352A LEU* 3.9 27.6 - - + +
371A LEU* 4.0 16.8 - - + -
375A LEU* 4.0 39.9 - - + -
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Residues in contact with ASN 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 LYS* 3.1 51.2 + - - +
260A PHE* 1.3 80.4 - - - +
262A TYR* 1.3 57.9 + - - +
263A ASP* 4.2 2.4 + - - +
324A LEU* 4.1 9.8 - - + +
331A MET* 5.7 1.2 - - - -
347A ARG 5.0 3.9 + - - +
348A ASP* 3.3 43.5 + - - +
349A PRO* 5.4 2.8 - - - +
350A SER* 3.6 4.8 - - - +
352A LEU* 6.0 0.7 - - + -
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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