Contacts of the helix formed by residues 247 - 259 (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 247 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D LYS* 5.1 10.5 - - - +
35D ARG* 5.4 0.7 + - - -
241D ASP* 3.2 8.1 - - - +
242D GLY* 4.0 15.9 - - - -
245D PHE 5.0 3.4 - - - +
246D VAL* 1.3 78.6 - - - +
248D LEU* 1.3 64.2 + - - +
249D GLN* 3.7 12.0 + - - +
250D ASP* 2.7 41.2 + - - +
251D ARG* 3.0 21.0 + - - +
297D LEU* 4.3 4.9 - - - -
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Residues in contact with LEU 248 (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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233D ARG* 3.9 46.0 - - + +
237D GLU* 3.8 47.8 - - + +
238D ARG* 4.5 6.5 - - + +
241D ASP* 2.8 32.8 + - + +
247D THR* 1.3 69.4 - - - +
249D GLN* 1.3 66.7 + - - +
251D ARG* 3.7 10.2 - - + +
252D ASP* 2.9 29.4 + - - +
297D LEU* 3.8 13.6 - - + +
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Residues in contact with GLN 249 (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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247D THR* 3.1 10.6 + - - +
248D LEU* 1.3 78.7 - - - +
250D ASP* 1.3 62.2 + - - +
252D ASP* 3.4 8.0 + - - +
253D TRP* 3.1 21.1 + - - +
601D NO3 3.0 30.2 + - - +
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Residues in contact with ASP 250 (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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35D ARG* 3.6 32.7 + - - +
245D PHE 4.4 3.3 - - - +
246D VAL* 3.7 6.5 - - - +
247D THR* 2.7 44.6 + - - +
249D GLN* 1.3 75.1 - - - +
251D ARG* 1.3 104.4 + - - +
253D TRP* 3.1 3.2 + - - +
254D TYR* 2.9 28.8 + - + -
401D GA4 3.9 11.5 - - - +
601D NO3 3.9 7.6 - - - +
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Residues in contact with ARG 251 (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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123D SER* 2.8 29.7 + - - -
227D MET* 3.8 26.4 - - - +
237D GLU* 5.9 1.3 - - - +
246D VAL* 3.3 20.8 - - + +
247D THR 3.0 18.7 + - - +
248D LEU* 3.2 16.1 + - + +
250D ASP* 1.3 103.2 + - - +
252D ASP* 1.3 65.0 + - - +
254D TYR* 3.3 20.4 + - - +
255D TRP* 3.2 37.3 + - + +
297D LEU* 4.0 18.4 - - + -
298D THR* 4.5 13.2 - - + -
401D GA4 3.7 22.0 + - - +
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Residues in contact with ASP 252 (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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233D ARG* 2.9 40.7 + - - -
248D LEU 2.9 20.4 + - - +
249D GLN* 3.7 6.3 - - - +
251D ARG* 1.3 78.2 - - - +
253D TRP* 1.3 63.8 + - - +
255D TRP* 3.4 5.4 + - - +
256D LYS* 3.0 26.0 + - - +
265D ARG* 3.3 30.9 + - - +
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Residues in contact with TRP 253 (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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35D ARG* 3.6 24.4 - - + +
36D ARG 2.9 22.0 + - - -
37D ALA* 5.2 4.9 - - - -
39D GLY* 3.7 23.8 - - - -
40D THR 3.2 23.8 - - - -
41D PHE* 3.7 28.7 - + + -
125D VAL* 4.1 6.1 - - + -
158D PRO* 5.0 1.3 - - + -
249D GLN 3.1 11.1 + - - +
250D ASP* 3.1 8.9 + - - +
252D ASP* 1.3 79.9 - - - +
254D TYR* 1.3 89.1 + + - +
256D LYS* 3.5 6.3 + - - +
257D ALA* 2.9 38.1 + - + +
601D NO3 3.7 22.9 - - - +
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Residues in contact with TYR 254 (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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31D TYR* 4.0 0.2 - - - +
35D ARG* 3.0 34.7 + - - -
123D SER* 3.5 34.5 - - - +
124D PHE* 5.1 0.2 - - - -
125D VAL* 3.5 17.0 - - + +
126D HIS* 2.5 42.6 + + - -
227D MET* 4.0 8.5 - - + -
250D ASP* 2.9 30.8 + - - -
251D ARG* 3.3 20.6 + - - +
253D TRP* 1.3 88.3 - + - +
255D TRP* 1.3 65.3 + - - +
257D ALA* 3.2 4.1 + - - +
258D TYR* 3.0 23.9 + - - +
401D GA4 3.6 24.0 - - + +
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Residues in contact with TRP 255 (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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124D PHE* 3.7 28.5 - + - -
202D ASN* 4.0 5.4 - - - -
227D MET* 3.5 40.9 - - + +
228D PHE* 3.4 25.9 + - - -
229D GLY* 3.5 10.6 - - - -
251D ARG* 3.2 32.4 + - + +
252D ASP 3.8 4.9 - - - +
253D TRP 3.4 0.2 - - - -
254D TYR* 1.3 75.9 - - - +
256D LYS* 1.3 57.6 + - - +
258D TYR* 3.0 8.6 + + - -
259D LEU* 2.8 48.1 + - + +
265D ARG* 3.7 36.1 - - + -
269D ALA 4.6 0.7 - - - -
270D CYS* 3.6 41.5 - - + -
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Residues in contact with LYS 256 (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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39D GLY* 6.1 6.5 - - - -
161D ARG* 2.9 23.7 + - - +
252D ASP 3.0 17.2 + - - +
253D TRP* 3.9 5.8 - - - +
255D TRP* 1.3 77.1 - - - +
257D ALA* 1.3 59.7 + - - +
258D TYR 3.4 0.2 + - - -
259D LEU* 3.6 7.2 - - - +
260D PRO 5.3 0.5 - - - +
261D GLU* 5.8 0.2 - - - -
265D ARG* 5.7 0.2 - - - +
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Residues in contact with ALA 257 (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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39D GLY 4.9 4.3 - - - +
125D VAL* 4.2 10.3 - - + -
157D ALA* 3.4 12.1 - - - +
158D PRO* 3.5 17.2 - - + +
161D ARG* 3.3 28.7 - - - +
253D TRP* 2.9 41.7 + - + +
254D TYR 3.5 5.2 - - - +
255D TRP 3.2 0.4 - - - -
256D LYS* 1.3 78.4 - - - +
258D TYR* 1.3 57.2 + - - +
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Residues in contact with TYR 258 (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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124D PHE* 3.7 56.8 - + + -
155D ARG 5.9 0.2 - - - -
157D ALA* 3.8 10.3 - - + -
160D HIS 4.4 2.9 - - - -
161D ARG* 3.3 9.8 - - - +
162D TYR* 2.8 64.6 + + + -
163D PRO* 3.9 2.1 - - - +
165D ALA* 3.9 16.3 - - + +
166D TYR* 3.3 51.3 - + - -
254D TYR 3.0 14.8 + - - +
255D TRP* 3.0 7.2 + + + +
257D ALA* 1.3 75.0 - - - +
259D LEU* 1.3 79.6 + - + +
269D ALA* 4.5 3.6 - - + -
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Residues in contact with LEU 259 (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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161D ARG* 2.9 21.9 + - - -
162D TYR* 4.5 0.7 - - + -
255D TRP* 2.8 32.2 + - + +
256D LYS* 3.6 5.1 - - - +
258D TYR* 1.3 89.0 - - + +
260D PRO* 1.4 75.2 - - + +
263D ALA* 4.2 8.3 - - + +
264D ASP* 3.3 32.3 - - - +
265D ARG* 4.0 5.4 - - + -
267D HIS* 4.1 20.9 - - - +
269D ALA* 4.1 11.9 - - + -
270D CYS* 3.9 28.9 - - + +
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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
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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