Contacts of the helix formed by residues 298 - 312 (chain D) in PDB entry 3EBL
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 THR 298 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225D ASN 5.6 0.2 + - - -
226D ALA 4.7 2.9 + - - -
227D MET* 5.6 3.7 - - + -
228D PHE 4.2 22.1 + - - +
236D SER* 4.2 0.4 - - - -
237D GLU* 4.3 14.4 - - - +
251D ARG* 4.5 14.6 - - + -
255D TRP* 6.3 0.4 - - - +
296D ASP* 2.8 19.4 + - - +
297D LEU* 1.3 95.3 - - + +
299D CYS* 1.3 64.6 + - - +
300D ASP 3.2 3.4 - - - -
301D ARG* 3.1 22.8 + - - +
302D GLN* 3.1 25.5 + - - +
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Residues in contact with CYS 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D SER* 3.5 18.8 - - - -
239D ARG* 4.7 5.4 - - - -
240D LEU* 4.6 1.6 - - - -
292D VAL* 3.6 17.0 - - + +
293D SER 3.5 17.7 - - - +
294D GLY* 3.9 16.2 - - - -
296D ASP 2.9 18.9 + - - +
297D LEU 3.3 0.6 - - - -
298D THR* 1.3 79.0 + - - +
300D ASP* 1.3 77.3 + - - +
302D GLN* 3.0 8.6 + - - +
303D LEU* 3.0 32.1 + - + +
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Residues in contact with ASP 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D THR* 3.6 16.6 - - + +
235D GLU* 3.4 18.0 + - - +
236D SER* 2.9 42.2 + - - +
239D ARG* 5.1 2.1 + - - -
299D CYS* 1.3 81.6 - - - +
301D ARG* 1.3 57.1 + - - +
303D LEU* 3.4 11.6 + - - +
304D ALA* 3.0 29.0 + - - +
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Residues in contact with ARG 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D PHE* 3.3 39.2 - - + +
229D GLY* 3.5 21.5 + - - +
230D GLY* 3.6 20.6 + - - +
232D GLU 2.4 31.9 + - - -
233D ARG* 5.6 0.2 - - - +
234D THR* 3.6 22.1 - - + +
237D GLU* 2.9 32.9 + - - -
271D ASN* 5.1 4.0 + - - +
298D THR* 3.1 18.1 + - - +
300D ASP* 1.3 75.3 - - - +
302D GLN* 1.3 57.5 + - + +
304D ALA* 3.5 7.2 + - - +
305D TYR* 3.0 28.8 + - - +
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Residues in contact with GLN 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D ASN* 3.2 29.2 + - - +
226D ALA* 3.5 26.3 + - + +
228D PHE* 4.8 6.3 - - + +
290D ILE* 4.5 7.5 - - + +
291D ILE 3.6 9.2 - - - +
292D VAL* 3.7 22.3 - - + +
296D ASP* 3.0 31.1 + - - +
298D THR* 3.1 22.8 + - - +
299D CYS* 3.0 9.2 + - - +
301D ARG* 1.3 79.3 - - + +
303D LEU* 1.3 62.6 + - - +
305D TYR* 3.3 12.1 + - - +
306D ALA* 3.1 21.3 + - - +
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Residues in contact with LEU 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D VAL* 4.0 13.7 - - + -
299D CYS* 3.0 26.4 + - + +
300D ASP* 3.9 11.2 - - - +
302D GLN* 1.3 76.1 - - - +
304D ALA* 1.3 57.4 + - - +
306D ALA* 3.4 5.0 + - + +
307D ASP* 3.0 38.0 + - - +
318D VAL* 3.7 30.1 - - + -
320D GLN* 3.6 35.2 - - + +
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Residues in contact with ALA 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D ASP 3.0 17.9 + - - +
301D ARG* 3.7 9.0 - - - +
302D GLN 3.2 0.2 - - - -
303D LEU* 1.3 75.0 - - - +
305D TYR* 1.3 54.5 + - - +
307D ASP* 3.3 7.3 + - - +
308D ALA* 2.8 37.2 + - - +
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Residues in contact with TYR 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D HIS* 2.5 48.5 + + - +
221D ASN* 5.1 1.4 + - - -
223D LEU* 3.7 24.1 - - + +
228D PHE* 3.6 38.6 - + + -
272D PRO* 4.5 4.7 - - + -
273D PHE* 3.7 24.4 - + - -
285D PHE* 4.2 4.9 - - - -
288D SER* 5.1 0.7 + - - -
290D ILE* 3.9 12.8 - - + -
301D ARG 3.0 14.9 + - - +
302D GLN* 3.4 11.9 - - - +
304D ALA* 1.3 75.1 - - - +
306D ALA* 1.3 65.8 + - - +
308D ALA* 3.6 2.8 + - - +
309D LEU* 3.1 47.1 + - + +
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Residues in contact with ALA 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D ILE* 4.5 8.7 - - + -
302D GLN 3.1 10.3 + - - +
303D LEU* 3.6 10.8 - - - +
304D ALA 3.1 0.4 - - - -
305D TYR* 1.3 83.1 - - - +
307D ASP* 1.3 66.8 + - - +
309D LEU* 3.1 7.8 + - - +
310D ARG* 3.1 26.9 + - - +
316D VAL* 3.9 11.9 - - + +
318D VAL* 3.6 31.0 - - + -
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Residues in contact with ASP 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D LEU* 3.0 27.3 + - - +
304D ALA* 3.8 5.9 - - - +
306D ALA* 1.3 76.9 - - - +
308D ALA* 1.3 55.1 + - - +
310D ARG* 3.2 24.1 + - - +
311D GLU* 2.9 37.0 + - + +
318D VAL* 6.0 0.7 - - - +
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Residues in contact with ALA 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D PHE* 3.2 43.5 - - + -
279D ARG* 3.1 28.6 + - - +
304D ALA 2.8 20.3 + - - +
305D TYR 3.6 0.4 - - - +
307D ASP* 1.3 72.8 - - - +
309D LEU* 1.3 53.9 + - - +
311D GLU* 3.3 2.2 + - - -
312D ASP* 3.0 26.2 + - - +
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Residues in contact with LEU 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D PHE* 3.6 23.1 - - + -
280D LEU* 4.2 9.0 - - + -
285D PHE* 3.7 26.9 - - + -
288D SER* 3.7 22.7 - - - +
290D ILE* 4.9 1.1 - - + -
305D TYR* 3.1 47.8 + - + +
306D ALA* 3.1 9.0 + - - +
308D ALA* 1.3 73.0 - - - +
310D ARG* 1.3 67.0 + - - +
312D ASP* 3.1 10.2 + - - +
313D GLY 3.4 0.2 + - - -
314D HIS* 2.9 32.9 + - + +
316D VAL* 3.7 15.9 - - + -
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Residues in contact with ARG 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D ALA 3.1 14.9 + - - +
307D ASP* 3.4 23.7 + - - +
309D LEU* 1.3 74.3 - - - +
311D GLU* 1.3 64.0 + - - +
313D GLY* 2.9 22.5 + - - -
314D HIS 3.5 12.3 + - - +
316D VAL* 4.2 30.6 + - + +
318D VAL* 5.0 7.1 - - - +
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Residues in contact with GLU 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D ARG* 3.1 29.4 - - - +
307D ASP* 2.9 25.1 + - + +
308D ALA* 3.4 2.7 - - - +
309D LEU 3.2 0.2 - - - -
310D ARG* 1.3 76.4 - - - +
312D ASP* 1.3 58.2 + - - +
313D GLY* 2.9 9.8 + - - -
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Residues in contact with ASP 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D PHE* 3.5 7.8 - - - -
279D ARG* 2.7 41.2 + - - +
280D LEU* 2.4 35.4 + - + +
281D GLY* 3.2 32.6 - - - +
282D GLY 4.2 1.7 + - - -
308D ALA 3.0 10.8 + - - +
309D LEU* 3.1 8.8 + - - +
311D GLU* 1.3 74.8 - - - +
313D GLY* 1.3 58.5 + - - +
314D HIS* 3.3 19.6 + - + -
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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