Contacts of the helix formed by residues 267 - 282 (chain A) in PDB entry 2JDQ
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 ASP 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LEU* 3.8 24.5 - - + +
230A ARG* 2.7 48.1 + - - -
265A VAL* 3.5 7.2 - - + +
266A SER* 1.3 80.2 + - - +
268A THR* 1.3 66.2 + - - +
269A ASP* 3.4 5.5 + - - +
270A VAL* 3.2 29.4 + - + +
271A LEU* 3.1 23.4 + - - +
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Residues in contact with THR 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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266A SER 3.1 5.6 + - - -
267A ASP* 1.3 75.7 + - - +
269A ASP* 1.3 62.9 + - - +
271A LEU* 4.5 2.9 - - - -
272A ALA* 2.9 28.4 + - - +
307A HIS* 3.9 15.1 + - - -
309A ASP* 3.3 29.2 + - + +
311A LYS* 4.7 9.0 - - + -
312A VAL* 3.6 23.8 - - + +
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Residues in contact with ASP 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ARG* 3.4 36.9 + - + -
267A ASP* 3.3 13.8 + - - +
268A THR* 1.3 83.2 - - - +
270A VAL* 1.3 61.9 + - - +
272A ALA* 3.9 4.7 - - - +
273A ASP* 3.2 33.0 + - - +
311A LYS* 5.5 6.1 - - - +
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Residues in contact with VAL 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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226A LEU* 4.7 3.8 - - + -
229A THR* 3.9 20.4 - - + -
230A ARG* 3.5 24.2 - - + +
233A VAL* 3.8 21.6 - - + +
262A LEU* 4.0 32.3 - - + +
265A VAL* 4.5 9.4 - - + -
267A ASP* 3.2 28.5 + - + +
268A THR 3.4 0.4 - - - -
269A ASP* 1.3 74.5 - - - +
271A LEU* 1.3 65.9 + - - +
273A ASP* 3.3 2.9 + - - +
274A ALA* 3.0 22.3 + - - +
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Residues in contact with LEU 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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262A LEU 3.9 3.4 - - - +
263A LEU* 3.6 32.8 - - - +
265A VAL 3.1 28.7 - - - +
266A SER* 3.7 17.3 - - - +
267A ASP 3.1 13.6 + - - +
268A THR* 3.9 4.3 - - - +
270A VAL* 1.3 76.7 - - - +
272A ALA* 1.3 64.3 + - - +
274A ALA* 3.3 5.6 + - - +
275A CYS* 3.0 28.6 + - - -
300A ARG* 4.5 2.0 - - - +
304A LEU* 4.1 17.7 - - + -
307A HIS* 3.9 28.5 - - + +
312A VAL* 4.2 10.8 - - + -
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Residues in contact with ALA 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 THR 2.9 19.6 + - - +
269A ASP* 3.9 6.3 - - - +
271A LEU* 1.3 77.3 - - - +
273A ASP* 1.3 59.6 + - - +
275A CYS* 3.4 4.3 + - - +
276A TRP* 3.0 36.1 + - + +
311A LYS* 3.3 35.0 - - + +
312A VAL* 4.1 5.5 - - + +
315A PRO* 3.7 4.2 - - + +
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Residues in contact with ASP 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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230A ARG* 4.3 5.0 - - - +
233A VAL* 4.0 23.1 - - + +
234A TRP* 3.7 33.6 + - - +
237A SER* 3.7 9.2 + - - +
269A ASP* 3.2 19.6 + - - +
270A VAL 4.1 2.2 - - - +
272A ALA* 1.3 77.5 - - - +
274A ALA* 1.3 59.8 + - - +
276A TRP* 3.7 17.4 - - - +
277A ALA* 3.0 27.9 + - - +
749E THR* 5.8 1.7 - - - +
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Residues in contact with ALA 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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233A VAL* 3.8 15.3 - - + +
259A LEU* 4.1 12.3 - - + +
262A LEU* 4.4 17.7 - - + +
263A LEU* 4.0 18.2 - - + -
270A VAL 3.0 17.8 + - - +
271A LEU* 3.5 5.6 - - - +
273A ASP* 1.3 74.7 - - - +
275A CYS* 1.3 62.6 + - - +
277A ALA* 3.4 4.2 + - - +
278A LEU* 3.1 30.1 + - - +
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Residues in contact with CYS 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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263A LEU* 3.9 3.8 - - - -
271A LEU 3.0 18.7 + - - +
272A ALA 3.5 8.3 - - - +
274A ALA* 1.3 72.8 - - - +
276A TRP* 1.3 64.7 + - - +
278A LEU* 3.3 7.8 + - - +
279A SER* 2.9 24.9 + - - -
301A LEU* 3.9 17.7 - - + -
304A LEU* 3.8 28.5 - - - -
312A VAL* 4.7 4.0 - - - -
315A PRO* 3.6 20.4 - - + +
316A ALA* 3.7 18.2 - - - +
319A ALA* 4.3 0.9 - - - +
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Residues in contact with TRP 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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237A SER* 4.7 4.5 - - - -
272A ALA* 3.0 32.1 + - + +
273A ASP* 3.7 18.8 - - - +
274A ALA 3.4 0.2 - - - -
275A CYS* 1.3 73.9 - - - +
277A ALA* 1.3 64.5 + - - +
279A SER* 2.8 30.2 + - - -
280A TYR* 3.0 44.5 + + + +
311A LYS 4.7 2.8 + - - -
314A SER* 5.0 7.0 - - - -
315A PRO* 3.7 30.1 - - + +
318A ARG* 3.4 42.6 - - - -
749E THR* 3.1 41.5 - - + +
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Residues in contact with ALA 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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233A VAL 5.3 0.9 - - - +
236A LEU* 4.9 0.7 - - + -
237A SER* 3.9 22.1 - - - +
240A CYS* 4.0 8.0 - - - +
259A LEU* 4.1 24.5 - - + -
273A ASP 3.0 14.2 + - - +
274A ALA 3.5 9.4 - - - +
275A CYS 3.3 0.2 - - - -
276A TRP* 1.3 75.7 - - - +
278A LEU* 1.3 57.1 + - - +
280A TYR* 3.2 16.0 + - - +
281A LEU* 3.1 30.7 + - - +
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Residues in contact with LEU 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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256A LEU* 3.5 31.6 - - + -
259A LEU* 3.9 21.3 - - + -
263A LEU* 3.8 31.6 - - + -
274A ALA 3.1 14.7 + - - +
275A CYS 3.3 6.7 + - - +
277A ALA* 1.3 75.7 - - - +
279A SER* 1.3 59.0 + - - +
281A LEU* 3.9 4.0 - - + +
282A SER* 2.7 35.8 + - - -
292A VAL* 4.2 15.4 - - + +
297A VAL* 4.0 15.5 - - + -
301A LEU* 4.0 15.0 - - + -
319A ALA* 4.3 10.8 - - + -
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Residues in contact with SER 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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275A CYS 2.9 18.1 + - - -
276A TRP* 2.8 29.7 + - - -
278A LEU* 1.3 73.1 - - - +
280A TYR* 1.3 66.4 + - - +
282A SER* 3.5 5.0 + - - -
283A ASP* 3.5 9.2 + - - +
315A PRO 4.1 2.0 - - - -
318A ARG* 3.9 20.0 + - - -
319A ALA* 3.7 27.3 - - - +
322A ASN* 3.0 21.8 + - - -
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Residues in contact with TYR 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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237A SER* 3.6 28.9 - - - -
240A CYS 3.3 23.3 - - - +
241A ARG* 3.6 48.0 + - + -
242A GLY 5.0 2.5 - - - -
276A TRP* 3.0 53.9 + + + +
277A ALA* 3.4 9.4 - - - +
278A LEU 3.1 0.6 - - - -
279A SER* 1.3 84.7 - - - +
281A LEU* 1.3 64.2 + - - +
283A ASP* 3.3 20.8 + - - +
318A ARG* 5.4 4.3 - - - -
749E THR* 3.9 4.5 + - - -
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Residues in contact with LEU 281 (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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240A CYS* 3.8 14.6 - - + +
247A PRO* 5.4 3.6 - - + -
249A PHE* 3.8 26.0 - - + -
252A VAL* 3.6 29.4 - - + +
255A CYS* 3.9 28.0 - - - -
256A LEU* 3.9 25.4 - - + -
259A LEU* 4.0 7.6 - - + -
277A ALA 3.1 16.4 + - - +
278A LEU* 3.3 4.7 + - - +
280A TYR* 1.3 77.3 - - - +
282A SER* 1.3 59.2 + - - +
283A ASP 3.3 1.1 + - - -
288A LYS* 3.5 26.7 - - - +
292A VAL* 3.9 16.6 - - + +
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Residues in contact with SER 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU 2.7 22.7 + - - -
279A SER* 3.5 9.1 + - - -
281A LEU* 1.3 77.1 - - - +
283A ASP* 1.3 56.2 + - - -
284A GLY 3.5 5.2 + - - -
288A LYS* 5.0 0.7 - - - -
289A ILE* 3.6 25.4 - - - +
292A VAL* 4.0 15.7 - - - +
319A ALA* 3.9 6.4 + - - +
322A ASN* 3.5 23.7 - - - +
323A ILE* 4.0 24.3 - - - +
740E ASP* 4.3 0.9 - - - +
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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