Contacts of the helix formed by residues 236 - 248 (chain H) in PDB entry 4PIW
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 SER 236 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186G GLY 3.7 12.8 + - - -
188G GLU* 3.7 31.6 - - - +
239G GLN* 3.3 8.4 + - - -
26H LEU 3.3 15.5 - - - -
28H GLY 4.0 1.1 - - - +
235H MSE 1.3 79.4 - - - +
237H ASP* 1.3 59.8 + - - +
238H LEU* 3.0 3.0 + - - +
239H GLN* 3.1 48.2 + - - +
240H ALA 3.2 7.3 + - - -
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Residues in contact with ASP 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H ALA* 4.3 7.0 - - + +
23H SER* 5.3 1.4 + - - -
25H LYS* 4.1 14.3 - - - +
26H LEU 3.1 12.9 + - - +
27H CYS 3.1 19.0 + - - +
30H GLY* 4.0 2.6 - - - -
31H GLY* 3.2 22.4 + - - -
32H PHE* 2.9 22.3 + - - +
33H THR* 2.7 40.2 + - - +
235H MSE 3.6 0.4 + - - -
236H SER* 1.3 69.8 - - - +
238H LEU* 1.3 60.0 + - - +
240H ALA* 3.4 1.9 - - - +
241H ALA* 3.0 27.7 + - - +
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Residues in contact with LEU 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G MSE 4.2 9.9 - - - -
186G GLY* 3.5 37.5 - - - +
238G LEU* 3.7 33.7 - - + -
239G GLN* 4.7 10.5 - - + +
242G TYR* 3.8 24.7 - - + -
17H MSE 3.9 20.1 - - + +
20H ALA* 4.8 6.3 - - + -
21H MSE 5.0 5.8 - - + -
26H LEU* 3.9 17.2 + - + +
236H SER* 3.0 3.8 - - - +
237H ASP* 1.3 79.3 - - - +
239H GLN* 1.3 62.0 + - - +
241H ALA* 3.5 7.0 + - - +
242H TYR* 3.4 15.2 + - - +
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Residues in contact with GLN 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G GLU* 5.5 0.2 - - - +
236G SER* 4.2 4.4 + - - +
238G LEU* 5.3 0.9 - - + -
239G GLN* 2.9 37.2 + - + +
53H PRO* 4.7 3.6 + - - +
185H ALA* 3.4 16.1 + - - +
186H GLY* 5.0 4.0 - - - +
188H GLU* 2.5 42.8 + - - +
189H GLY* 4.6 0.2 - - - -
235H MSE 3.5 27.0 - - + +
236H SER* 3.1 26.2 + - - +
238H LEU* 1.3 76.8 - - + +
240H ALA* 1.3 59.5 + - - +
242H TYR* 3.2 7.9 + - - +
243H LEU* 2.9 27.7 + - - +
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Residues in contact with ALA 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H PHE* 3.5 6.3 - - - +
33H THR* 3.5 16.4 - - - +
36H CYS* 3.4 5.8 - - - -
235H MSE 3.6 24.4 - - + +
236H SER 3.2 2.4 + - - -
237H ASP* 3.3 27.8 + - - +
239H GLN* 1.3 77.1 - - - +
241H ALA* 1.3 55.0 + - - +
243H LEU* 3.1 6.0 + - - -
244H TRP* 2.6 37.2 + - - +
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Residues in contact with ALA 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H TYR* 3.3 39.2 - - - +
17H MSE 4.0 7.2 - - - -
20H ALA* 4.1 4.0 - - + -
32H PHE* 3.6 22.8 - - + +
237H ASP 3.0 15.9 + - - +
238H LEU 3.7 6.1 - - - +
240H ALA* 1.3 76.0 - - - +
242H TYR* 1.3 63.3 + - - +
244H TRP* 3.9 0.3 - - - +
245H ALA* 3.1 24.1 + - - +
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Residues in contact with TYR 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G MSE 4.2 18.1 - - - +
26G LEU* 3.8 31.2 - - + +
238G LEU* 3.9 7.6 - - + -
7H PRO* 5.7 0.2 - - - +
8H PRO 3.9 10.0 + - - -
9H VAL* 4.7 8.0 - - - +
13H GLU* 3.5 28.0 - - + +
17H MSE 3.6 22.8 - - - +
184H THR* 3.5 13.4 - - + +
185H ALA* 4.3 0.7 - - - -
186H GLY* 3.2 24.5 - - - +
238H LEU 3.4 9.8 + - - +
239H GLN* 3.2 10.2 + - - +
241H ALA* 1.3 78.2 - - - +
243H LEU* 1.3 62.3 + - - +
245H ALA* 3.5 13.4 + - - +
246H GLN* 3.4 36.2 + - - +
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Residues in contact with LEU 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H CYS* 3.8 23.6 - - + -
40H LEU* 5.6 0.4 - - + -
51H LEU* 4.4 11.9 - - + -
177H PHE* 3.7 50.7 - - + -
183H TYR* 4.2 12.1 - - + -
184H THR 5.1 0.2 - - - +
185H ALA* 3.6 25.3 - - + +
235H MSE 5.1 4.3 - - - -
239H GLN 2.9 13.2 + - - +
240H ALA* 3.4 8.3 - - - +
242H TYR* 1.3 76.2 - - - +
244H TRP* 1.3 59.7 + - - +
245H ALA 3.1 0.2 - - - -
246H GLN* 3.0 6.2 + - + -
247H LEU* 2.9 37.2 + - + +
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Residues in contact with TRP 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H TYR* 3.3 43.2 + + - -
32H PHE* 3.6 22.6 - + + -
35H ARG* 3.2 51.1 - - + -
36H CYS* 3.5 15.2 - - - -
39H TRP* 3.9 28.3 - + + -
240H ALA 2.6 20.8 + - - +
241H ALA 3.9 1.3 - - - +
243H LEU* 1.3 72.9 - - - +
245H ALA* 1.3 61.1 + - - +
247H LEU* 3.4 5.4 + - + +
248H GLU* 3.3 25.4 + - + +
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Residues in contact with ALA 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H VAL* 4.1 8.5 - - - +
12H THR* 3.6 19.5 + - - +
13H GLU* 3.8 20.4 - - + +
16H TYR* 3.6 29.4 - - + -
241H ALA 3.1 18.0 + - - +
242H TYR 3.6 7.4 - - - +
243H LEU 3.1 0.4 - - - -
244H TRP* 1.3 77.5 - - - +
246H GLN* 1.3 59.8 + - - +
248H GLU* 3.9 13.1 - - - +
249H ALA 4.2 2.4 + - - -
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Residues in contact with GLN 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H PRO* 2.6 45.2 + - - +
10H VAL* 3.7 13.0 - - + -
13H GLU* 3.3 21.7 + - - +
182H ASN 4.0 0.9 - - - +
183H TYR* 3.6 26.8 - - + -
184H THR* 3.3 37.1 + - - +
185H ALA 5.0 0.7 - - - -
242H TYR* 3.4 19.6 - - - +
243H LEU* 3.0 8.5 + - - +
245H ALA* 1.3 75.6 - - - +
247H LEU* 1.3 63.7 + - - +
248H GLU 3.2 1.8 - - - -
249H ALA 3.3 12.4 + - - +
250H ALA 3.4 8.7 + - - -
253H ILE* 3.9 2.3 - - + +
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Residues in contact with LEU 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H CYS* 4.0 41.1 - - + +
39H TRP* 3.3 71.6 + - + +
40H LEU* 4.6 10.8 - - + -
157H VAL* 5.9 2.7 - - + -
177H PHE* 5.3 2.9 - - + -
183H TYR* 4.8 15.9 - - + -
243H LEU* 2.9 31.8 + - + +
244H TRP* 3.4 7.8 + - + +
246H GLN* 1.3 77.4 - - - +
248H GLU* 1.3 64.9 + - - +
250H ALA* 3.3 10.3 - - + +
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Residues in contact with GLU 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H THR* 4.6 7.1 + - - +
16H TYR* 2.9 36.2 + - - +
39H TRP* 5.2 2.9 - - - +
244H TRP* 3.3 21.2 + - + +
245H ALA 3.9 8.1 - - - +
246H GLN 3.2 0.2 - - - -
247H LEU* 1.3 79.9 - - - +
249H ALA* 1.3 55.9 + - + +
250H ALA 3.4 1.8 + - - -
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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