Contacts of the helix formed by residues 236 - 249 (chain L) in PDB entry 6AHU
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 ARG 236 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H TYR* 5.0 9.2 - - - +
139I ARG* 3.1 40.1 - - - +
222L LEU* 5.2 0.5 - - - +
227L LEU 3.5 11.0 - - - +
228L GLU* 3.0 33.8 + - - +
229L GLY* 3.9 1.4 + - - -
235L CYS* 1.3 79.3 - - - +
237L ALA* 1.3 68.5 + - - +
238L LEU* 3.5 36.8 - - + +
239L GLU* 3.1 36.5 + - + +
240L LEU* 3.5 9.7 + - - +
350L TRP* 5.1 1.2 - - - -
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Residues in contact with ALA 237 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H TYR* 6.5 0.2 - - + -
17L CYS* 3.8 21.1 - - + -
227L LEU* 3.1 20.5 + - + +
235L CYS 3.9 1.2 + - - -
236L ARG* 1.3 69.0 - - - +
238L LEU* 1.3 64.8 + - - +
239L GLU 3.6 0.2 + - - -
240L LEU* 3.6 3.0 + - - +
241L PHE* 3.6 9.7 + - - +
350L TRP* 3.7 29.9 - - + -
352L GLN* 2.7 37.3 + - - +
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Residues in contact with LEU 238 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H TYR* 5.5 17.3 + - + -
16H PRO* 3.5 43.3 - - + +
17H SER* 5.0 3.8 - - - +
110H PHE* 5.2 5.7 - - + -
139I ARG* 6.2 0.4 - - - +
15L LEU* 3.8 29.4 - - + -
236L ARG* 3.2 32.7 - - + +
237L ALA* 1.3 79.1 - - - +
239L GLU* 1.3 63.0 + - + +
241L PHE* 3.3 14.4 + - + +
242L ASP* 3.6 11.3 + - - +
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Residues in contact with GLU 239 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139I ARG* 3.2 33.6 + - - +
235L CYS* 4.0 10.1 - - + +
236L ARG* 3.1 36.1 + - + +
238L LEU* 1.3 79.1 - - + +
240L LEU* 1.3 61.0 + - - +
242L ASP* 3.7 7.2 + - - +
243L TRP* 3.3 21.1 + - - +
267L PRO* 3.7 35.5 - - + +
268L GLU 4.6 4.7 + - - +
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Residues in contact with LEU 240 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220L PRO* 5.1 9.0 - - + -
222L LEU* 3.7 40.6 - - + -
235L CYS* 6.4 0.7 - - + -
236L ARG 3.5 9.0 + - - +
237L ALA* 4.1 9.4 - - - +
238L LEU 3.3 1.0 - - - -
239L GLU* 1.3 75.9 - - - +
241L PHE* 1.3 60.8 + - - +
242L ASP 3.2 0.7 - - - -
243L TRP* 4.2 13.9 - - + -
244L LEU* 2.8 51.7 + - + +
267L PRO* 5.5 0.4 - - - -
309L TRP* 3.7 25.8 - - + -
340L ASN* 4.8 3.4 - - - +
342L VAL* 4.0 25.4 - - + -
350L TRP* 4.8 2.9 - - + -
352L GLN* 4.8 4.7 - - - +
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Residues in contact with PHE 241 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H PHE* 3.5 58.7 - + + +
111H LEU 5.6 0.3 + - - -
112H LEU* 3.8 29.4 + - + +
113H ALA* 6.0 0.9 - - + -
15L LEU* 4.1 16.8 - - + -
237L ALA 3.6 5.8 + - - +
238L LEU* 3.3 14.4 + - + +
240L LEU* 1.3 79.6 - - - +
242L ASP* 1.3 59.2 + - - +
244L LEU* 4.1 8.0 + - + +
245L GLY 4.4 5.4 + - - -
338L LEU* 3.8 16.6 - - + -
340L ASN* 4.0 10.8 - - - +
352L GLN* 3.2 37.7 - - + +
354L ALA* 4.0 21.3 - - + -
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Residues in contact with ASP 242 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H TYR* 4.3 20.2 - - - -
21H TYR* 2.6 42.7 + - - -
76H ARG* 4.5 3.3 + - - -
110H PHE* 4.6 15.8 - - + -
111H LEU* 4.9 5.6 + - - +
238L LEU 3.6 9.0 + - - +
239L GLU* 4.0 8.5 - - - +
240L LEU 3.2 0.4 - - - -
241L PHE* 1.3 79.4 - - - +
243L TRP* 1.3 63.1 + - - +
244L LEU 3.6 0.2 + - - -
245L GLY* 4.0 5.7 + - - -
246L ALA* 4.3 4.0 + - - +
264L TYR* 3.4 13.9 + - - -
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Residues in contact with TRP 243 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45L LEU* 6.1 2.9 - - + -
217L LEU* 3.8 21.6 - - + +
218L GLN 3.2 25.9 + - - -
219L CYS* 3.6 26.2 - - - -
220L PRO* 3.6 20.6 - - + -
239L GLU 3.3 17.2 + - - +
240L LEU* 3.2 14.9 + - + +
242L ASP* 1.3 77.0 - - - +
244L LEU* 1.3 76.7 + - + +
246L ALA* 3.3 10.5 + - + +
247L VAL* 3.7 29.6 + - + +
252L ASP* 5.1 4.8 + - - -
264L TYR* 3.3 23.7 + + - +
266L CYS* 4.3 5.7 - - - +
267L PRO* 3.8 27.6 - - + -
309L TRP* 4.0 19.3 - + - -
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Residues in contact with LEU 244 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H LEU* 4.1 11.0 - - + -
45L LEU* 4.9 9.4 - - + -
240L LEU* 2.8 27.8 + - + +
241L PHE* 4.6 4.9 - - + +
242L ASP 3.4 0.6 - - - -
243L TRP* 1.3 93.9 - - + +
245L GLY* 1.3 61.6 + - - +
246L ALA 3.5 0.3 + - - -
247L VAL* 3.5 12.0 + - + +
248L PHE* 3.6 28.2 + - + -
309L TRP* 5.3 1.8 - - + -
311L THR* 3.7 29.4 - - + +
313L SER* 3.3 26.2 - - - +
340L ASN* 3.5 20.2 - - - +
342L VAL* 5.8 0.4 - - + -
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Residues in contact with GLY 245 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H LEU* 3.5 10.8 - - - +
112H LEU* 3.5 38.1 - - - +
115H SER* 3.6 6.5 + - - -
241L PHE 4.4 2.6 + - - -
242L ASP 4.0 3.6 + - - -
243L TRP 3.3 0.8 - - - -
244L LEU* 1.3 78.9 - - - +
246L ALA* 1.3 57.4 + - - +
248L PHE* 3.6 2.2 + - - +
249L SER* 3.1 29.1 + - - -
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Residues in contact with ALA 246 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H LEU* 3.8 21.0 - - + +
242L ASP 4.3 1.0 + - - +
243L TRP* 3.3 4.5 + - + +
244L LEU 3.3 0.8 - - - -
245L GLY* 1.3 75.3 - - - +
247L VAL* 1.3 61.4 + - + +
249L SER* 3.5 1.3 + - - +
250L ASN 3.4 2.8 + - - -
251L VAL* 2.7 55.7 + - + +
264L TYR* 3.3 33.7 - - + +
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Residues in contact with VAL 247 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45L LEU* 3.8 28.3 - - + -
214L LEU* 3.8 26.8 - - + +
217L LEU* 3.8 14.4 - - + -
243L TRP* 3.7 49.6 - - + +
244L LEU* 3.5 8.7 + - + +
245L GLY 3.3 0.4 - - - -
246L ALA* 1.3 79.4 - - + +
248L PHE* 1.3 61.5 + - + +
250L ASN* 3.5 11.8 + - - +
251L VAL 4.5 4.9 - - - +
252L ASP* 5.6 1.3 - - + +
278L LEU* 4.2 15.9 - - + +
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Residues in contact with PHE 248 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H LEU* 3.6 24.0 - - + -
115H SER* 4.5 4.5 - - - +
41L ARG* 3.4 31.1 + - - +
43L SER* 3.7 35.9 - - - -
44L PHE 4.5 3.6 - - - -
45L LEU* 3.6 37.5 - - + -
244L LEU* 3.6 17.4 + - + +
245L GLY* 3.6 8.1 + - - +
246L ALA 3.4 0.2 - - - -
247L VAL* 1.3 78.3 - - - +
249L SER* 1.3 56.6 + - - +
250L ASN* 3.3 9.6 + - - +
278L LEU* 3.7 22.7 - - + +
279L CYS 5.1 3.8 - - - -
280L THR* 6.0 2.0 - - - +
311L THR* 4.6 7.2 - - + -
313L SER* 4.6 4.3 - - - -
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Residues in contact with SER 249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H THR* 3.8 9.7 + - - +
74H ILE* 3.5 27.0 - - - +
111H LEU* 5.1 3.8 - - - -
114H LEU* 5.7 1.1 - - - +
115H SER* 3.5 17.3 - - - -
245L GLY 3.1 18.6 + - - -
246L ALA* 3.5 3.3 + - - -
247L VAL 3.3 0.6 - - - -
248L PHE* 1.3 74.3 - - - +
250L ASN* 1.3 70.3 + - - +
251L VAL* 3.3 13.4 + - - +
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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