Contacts of the helix formed by residues 247 - 259 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C LYS* 5.0 13.2 - - - +
35C ARG* 5.4 0.9 + - - -
241C ASP* 3.3 8.5 - - - -
242C GLY* 4.1 12.8 - - - -
245C PHE 4.9 3.6 - - - +
246C VAL* 1.3 79.9 - - - +
248C LEU* 1.3 60.3 + - - +
249C GLN* 3.8 9.9 + - - +
250C ASP* 2.7 40.7 + - - +
251C ARG* 3.0 28.0 + - - +
297C LEU* 4.3 1.8 - - - -
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Residues in contact with LEU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C ARG* 3.9 41.7 - - + +
237C GLU* 3.8 39.9 - - + +
238C ARG* 4.7 5.2 - - + +
241C ASP* 2.8 36.2 + - + +
247C THR* 1.3 68.8 - - - +
249C GLN* 1.3 67.3 + - - +
251C ARG* 3.6 10.3 - - + +
252C ASP* 2.8 31.7 + - - +
297C LEU* 3.7 19.7 - - + +
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Residues in contact with GLN 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C ASP* 5.6 0.2 - - - -
247C THR* 3.8 9.6 - - - +
248C LEU* 1.3 78.6 - - - +
250C ASP* 1.3 57.3 + - - +
252C ASP* 3.6 7.5 + - - +
253C TRP* 3.0 26.2 + - - +
601C NO3 3.8 23.3 + - - +
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Residues in contact with ASP 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ARG* 3.6 32.8 + - - +
245C PHE 4.5 2.1 - - - +
246C VAL* 3.8 5.1 - - - +
247C THR* 2.7 48.1 + - - +
249C GLN* 1.3 72.6 - - - +
251C ARG* 1.3 107.9 + - - +
253C TRP* 3.0 7.3 + - - +
254C TYR* 2.9 29.5 + - + -
401C GA4 3.7 11.9 - - - +
601C NO3 4.1 2.6 + - - +
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Residues in contact with ARG 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C SER* 3.0 28.9 + - - -
227C MET* 3.8 24.9 - - - +
237C GLU* 6.0 0.7 - - - +
246C VAL* 3.3 21.2 - - + +
247C THR 3.0 18.6 + - - +
248C LEU* 3.6 15.5 - - + +
250C ASP* 1.3 104.0 + - - +
252C ASP* 1.3 65.7 + - - +
254C TYR* 3.1 15.9 + - - +
255C TRP* 3.1 36.4 + - + +
297C LEU* 4.2 17.3 - - + -
298C THR* 4.5 13.9 - - + -
401C GA4 3.5 27.9 + - - +
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Residues in contact with ASP 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C ARG* 2.6 46.8 + - - -
248C LEU 2.8 19.3 + - - +
249C GLN* 3.7 7.3 - - - +
251C ARG* 1.3 78.8 - - - +
253C TRP* 1.3 62.9 - - - +
255C TRP* 3.4 5.3 + - - +
256C LYS* 3.0 24.7 + - - +
265C ARG* 3.3 26.4 + - - +
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Residues in contact with TRP 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ARG* 3.6 27.3 - - + +
36C ARG 3.0 26.7 + - - -
37C ALA* 4.8 3.1 - - - +
39C GLY* 3.8 25.0 - - - +
40C THR 3.3 27.8 - - - -
41C PHE* 4.0 19.3 - + + -
125C VAL* 4.3 6.7 - - + -
158C PRO* 4.6 1.3 - - + -
249C GLN 3.0 14.4 + - - +
250C ASP* 3.0 14.2 + - - +
252C ASP* 1.3 76.7 - - - +
254C TYR* 1.3 82.2 + + - +
256C LYS* 3.4 7.4 + - + +
257C ALA* 2.9 37.8 + - + +
601C NO3 3.6 21.5 + - - +
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Residues in contact with TYR 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ARG* 2.9 34.3 + - - -
123C SER* 3.5 27.2 - - - +
124C PHE* 5.2 0.2 - - - -
125C VAL* 3.6 26.6 - - + +
126C HIS* 2.5 42.9 + + - -
227C MET* 4.0 9.0 - - + -
250C ASP* 2.9 35.1 + - + +
251C ARG* 3.1 19.7 + - - +
253C TRP* 1.3 86.7 - + - +
255C TRP* 1.3 63.5 + - - +
257C ALA* 3.1 5.3 + - - +
258C TYR* 3.1 22.7 + - - +
401C GA4 3.5 25.7 - - + +
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Residues in contact with TRP 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C PHE* 3.6 31.6 - + - -
202C ASN* 3.8 3.6 - - - -
227C MET* 3.5 46.0 - - + +
228C PHE 3.6 20.5 + - - -
229C GLY* 3.7 9.1 - - - -
251C ARG* 3.1 34.7 + - + +
252C ASP 3.8 3.8 - - - +
254C TYR* 1.3 71.4 - - - +
256C LYS* 1.3 61.6 + - - +
258C TYR* 4.5 8.5 - + - +
259C LEU* 2.9 50.3 + - + +
265C ARG* 3.8 35.9 - - + -
269C ALA 4.6 0.9 - - - -
270C CYS* 3.6 41.9 - - + -
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Residues in contact with LYS 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C GLY* 6.1 6.2 - - - -
161C ARG* 2.7 30.7 + - - +
252C ASP 3.0 19.0 + - - +
253C TRP* 3.6 7.2 - - + +
255C TRP* 1.3 76.2 - - - +
257C ALA* 1.3 51.7 + - - +
258C TYR 3.5 0.2 + - - -
259C LEU* 3.7 5.0 - - - +
260C PRO 5.2 0.7 - - - +
261C GLU* 5.7 1.4 - - - -
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Residues in contact with ALA 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C GLY* 4.9 3.8 - - - +
125C VAL* 4.0 11.7 - - + -
157C ALA* 3.3 11.0 - - - +
158C PRO* 3.5 23.8 - - + +
161C ARG* 3.2 23.4 + - - +
253C TRP* 2.9 36.0 + - + +
254C TYR 3.1 9.8 + - - +
256C LYS* 1.3 77.1 - - - +
258C TYR* 1.3 57.5 + - - +
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Residues in contact with TYR 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C PHE* 3.7 55.2 - + + -
155C ARG 5.7 0.7 - - - -
157C ALA* 3.6 10.5 - - + -
160C HIS 4.3 2.9 - - - -
161C ARG* 3.2 9.7 - - - +
162C TYR* 2.7 59.5 + + + +
163C PRO* 3.8 8.5 - - - +
165C ALA* 3.9 16.8 - - + +
166C TYR* 3.3 52.6 - + - -
254C TYR 3.1 14.6 + - - +
255C TRP* 4.2 6.1 - + - +
257C ALA* 1.3 75.2 - - - +
259C LEU* 1.3 76.6 + - + +
269C ALA* 4.5 2.0 - - + -
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Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ARG* 2.9 22.9 + - - -
162C TYR* 4.4 0.7 - - + -
255C TRP* 2.9 35.3 + - + +
256C LYS* 3.7 2.8 - - - +
258C TYR* 1.3 89.5 - - + +
260C PRO* 1.3 87.4 - - + +
263C ALA* 4.3 5.2 - - + -
264C ASP* 3.5 30.1 - - - +
265C ARG* 4.2 4.7 - - + -
267C HIS* 4.1 8.3 - - + +
269C ALA* 4.1 26.5 - - + -
270C CYS* 3.9 21.8 - - + -
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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