Contacts of the helix formed by residues 260 - 280 (chain A) in PDB entry 2J6U
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 260 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A SER* 2.8 8.1 + - - +
259A ARG* 1.3 78.6 - - - +
261A LEU* 1.3 68.9 + - - +
262A GLU* 3.5 16.5 + - - +
263A GLU* 2.9 54.7 + - - +
264A ILE* 3.1 14.8 + - - +
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Residues in contact with LEU 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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259A ARG 3.4 5.3 + - - -
260A ASN* 1.3 73.4 + - - +
262A GLU* 1.3 67.7 + - + +
264A ILE* 3.1 6.2 + - - +
265A LYS* 3.0 53.8 + - - +
319A VAL* 4.5 5.4 - - + -
322A LEU* 3.4 35.4 - - + -
323A GLN* 3.7 37.9 - - + +
326A LEU* 4.2 13.2 - - + -
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Residues in contact with GLU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ASN* 3.3 14.9 + - - +
261A LEU* 1.3 84.4 - - + +
263A GLU* 1.3 58.3 + - + +
265A LYS* 3.0 39.2 + - - +
266A PRO* 3.2 23.6 - - - +
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Residues in contact with GLU 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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254A MET* 5.1 0.9 - - - -
256A ARG* 5.0 13.8 + - - -
257A ASN 4.9 0.3 - - - +
258A SER* 3.0 28.5 + - - +
260A ASN* 2.9 38.5 + - - +
262A GLU* 1.3 77.4 - - - +
264A ILE* 1.3 63.8 + - - +
266A PRO* 3.5 7.4 - - - +
267A TYR* 3.4 22.6 - - + -
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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
----------------------------------------------------------
254A MET* 3.9 25.6 - - + -
258A SER* 3.9 26.7 - - - +
259A ARG 4.1 10.8 - - - -
260A ASN 3.2 16.6 - - - +
261A LEU 3.1 5.3 + - - +
263A GLU* 1.3 79.4 - - - +
265A LYS* 1.3 64.3 + - - +
266A PRO* 3.4 0.2 - - - -
267A TYR* 3.0 15.9 + - - +
268A LEU* 3.1 7.6 + - + -
322A LEU* 3.9 16.2 - - + -
326A LEU* 4.2 11.2 - - + -
333A ILE* 4.1 19.5 - - + -
336A ILE* 3.9 28.5 - - + -
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Residues in contact with LYS 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 LEU* 3.0 45.6 + - + +
262A GLU* 3.0 38.3 + - - +
264A ILE* 1.3 75.1 - - - +
266A PRO* 1.3 63.1 - - + +
268A LEU* 2.8 11.5 + - + +
269A PHE* 2.7 64.7 + - + -
319A VAL* 4.1 23.2 - - + +
322A LEU* 4.8 2.9 - - + +
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Residues in contact with PRO 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 GLU 3.2 20.0 - - - +
263A GLU* 3.5 8.3 - - - +
264A ILE 3.4 4.0 - - - -
265A LYS* 1.3 95.0 - - + +
267A TYR* 1.3 62.6 + - + +
269A PHE* 4.2 9.5 - - + +
270A ARG* 3.2 42.5 + - - +
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Residues in contact with TYR 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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252A VAL* 3.7 21.8 - - + +
253A THR 3.9 5.8 - - - -
254A MET* 3.5 42.8 - - + -
255A LYS* 3.1 34.8 + - + +
256A ARG 4.9 0.2 + - - -
263A GLU 3.4 26.9 - - - -
264A ILE 3.0 6.5 + - - +
266A PRO* 1.3 76.3 - - + +
268A LEU* 1.3 69.0 + - - +
270A ARG* 3.0 31.6 + - - +
271A ALA* 2.9 22.2 + - - +
336A ILE* 3.5 17.9 - - + -
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Residues in contact with LEU 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 ILE 3.1 8.7 + - - +
265A LYS* 2.8 10.5 + - - +
267A TYR* 1.3 79.8 - - - +
269A PHE* 1.3 70.9 + - + +
271A ALA* 3.0 9.2 + - - +
272A ILE* 3.0 22.1 + - + +
289A VAL* 4.3 5.6 - - + -
318A SER* 3.6 37.0 - - - +
319A VAL* 4.2 4.3 - - + +
322A LEU* 3.9 24.9 - - + -
336A ILE* 3.9 21.2 - - + +
337A GLY 4.2 11.2 - - - +
338A VAL* 3.6 31.0 - - + -
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Residues in contact with PHE 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 LYS* 2.7 50.1 + - + +
266A PRO* 4.2 6.3 - - + +
268A LEU* 1.3 78.8 - - + +
270A ARG* 1.3 52.0 + - - +
272A ILE* 3.0 12.4 + - + +
273A GLU* 2.7 40.0 + - + +
315A TYR* 3.3 45.7 + + + +
318A SER* 4.1 7.9 - - - -
319A VAL* 3.8 31.4 - - + -
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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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252A VAL* 5.5 10.1 - - + +
266A PRO* 3.2 28.9 + - - +
267A TYR* 3.2 46.4 - - - +
269A PHE* 1.3 77.9 - - - +
271A ALA* 1.3 62.9 + - - +
273A GLU* 3.3 7.0 + - + +
274A GLU* 3.1 46.3 + - + +
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Residues in contact with ALA 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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250A ARG* 3.6 36.3 - - + +
251A ILE* 4.8 1.1 - - - +
252A VAL* 5.2 4.9 - - + +
267A TYR 2.9 11.4 + - - +
268A LEU* 3.0 11.2 + - - +
270A ARG* 1.3 78.5 - - - +
272A ILE* 1.3 52.4 + - - +
274A GLU* 3.4 1.6 + - - +
275A SER* 2.7 38.3 + - - -
336A ILE 4.5 2.7 - - - +
337A GLY* 4.0 12.8 - - - -
338A VAL* 3.8 7.9 - - + -
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Residues in contact with ILE 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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268A LEU* 3.0 17.9 + - + +
269A PHE* 3.0 17.2 + - + +
271A ALA* 1.3 75.1 - - - +
273A GLU* 1.3 66.5 + - - +
275A SER* 3.1 3.6 + - - -
276A TYR* 2.9 40.1 + - + +
311A LYS* 4.6 2.0 - - + -
314A ALA* 4.0 16.2 - - + +
315A TYR* 3.6 31.9 - - + -
318A SER* 3.5 35.2 - - - +
338A VAL* 3.7 23.6 - - + -
340A PHE* 4.8 4.5 - - + -
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Residues in contact with GLU 273 (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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269A PHE* 2.7 18.5 + - + +
270A ARG* 3.7 8.1 - - - +
272A ILE* 1.3 72.9 - - - +
274A GLU* 1.3 64.1 + - + +
276A TYR* 3.6 4.3 + - - +
277A TYR* 3.2 20.4 + - - +
311A LYS* 3.1 32.3 + - - +
315A TYR* 2.2 41.0 + - - +
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Residues in contact with GLU 274 (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 ARG* 2.6 47.7 + - + -
252A VAL* 5.9 1.3 - - - -
270A ARG* 3.1 32.3 + - + +
271A ALA 3.9 2.7 - - - +
273A GLU* 1.3 75.7 - - + +
275A SER* 1.3 67.5 + - - +
276A TYR 3.1 1.6 - - - -
277A TYR* 3.2 8.2 + - - +
278A LYS* 3.1 30.5 + - + +
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Residues in contact with SER 275 (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 ILE* 3.8 7.1 - - - +
249A GLY* 3.7 6.1 - - - -
250A ARG* 3.3 26.2 + - - +
271A ALA 2.7 23.8 + - - -
272A ILE 3.6 4.5 - - - -
274A GLU* 1.3 77.0 - - - +
276A TYR* 1.3 58.0 + - - +
278A LYS* 3.3 7.6 + - - +
279A LEU* 2.9 30.9 + - - +
338A VAL* 3.5 7.3 - - - +
340A PHE* 3.8 26.5 - - - -
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Residues in contact with TYR 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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272A ILE* 2.9 25.4 + - + +
273A GLU 3.8 3.4 - - - +
275A SER* 1.3 73.8 - - - +
277A TYR* 1.3 67.5 + - - +
278A LYS 3.1 1.3 - - - -
279A LEU* 3.1 34.3 + - + +
280A ASP* 3.6 6.1 + - - +
283A ILE* 5.9 5.4 - - + -
284A PRO* 4.5 4.5 - - + +
309A ILE* 2.5 32.0 + - - +
310A SER* 3.3 8.4 + - - -
311A LYS* 3.6 50.9 - - + +
314A ALA* 4.0 10.0 - - + +
340A PHE* 3.5 31.1 - + - -
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Residues in contact with TYR 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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82A GLU* 4.5 15.7 - - - -
273A GLU 3.2 10.8 + - - +
274A GLU* 3.2 11.1 + - - +
276A TYR* 1.3 78.8 - - - +
278A LYS* 1.3 70.9 + - + +
280A ASP* 3.3 12.1 + - - +
311A LYS* 5.7 0.4 - - - +
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Residues in contact with LYS 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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81A LYS* 5.6 4.2 - - - +
82A GLU* 5.9 2.7 - - + +
248A ILE* 3.8 21.0 - - + +
249A GLY 3.7 21.9 + - - +
250A ARG* 5.5 8.6 - - + +
274A GLU* 3.1 20.2 + - + +
275A SER* 3.6 8.7 - - - +
277A TYR* 1.3 84.0 - - + +
279A LEU* 1.3 61.9 + - - +
280A ASP* 2.8 10.6 + - - +
282A ARG* 3.5 14.7 + - - -
6T G 4.1 12.1 + - - -
7T A 3.9 19.6 + - - -
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Residues in contact with LEU 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 ILE* 4.4 10.1 - - + -
275A SER 2.9 15.7 + - - +
276A TYR* 3.1 45.0 + - + +
278A LYS* 1.3 75.8 - - - +
280A ASP* 1.3 68.7 + - - +
282A ARG* 3.1 48.7 + - + +
284A PRO* 3.8 28.3 - - + -
340A PHE* 4.2 12.8 - - + -
343A PHE* 3.7 34.5 - - + -
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Residues in contact with ASP 280 (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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276A TYR 3.6 4.7 + - - +
277A TYR 3.3 13.2 + - - +
278A LYS 2.8 9.7 - - - +
279A LEU* 1.3 81.9 - - - +
281A LYS* 1.3 111.6 + - - +
282A ARG* 3.5 11.9 + - - +
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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
------------------------------------------------------------
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