Contacts of the helix formed by residues 236 - 248 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A GLY 3.3 22.7 + - - -
188A GLU* 3.8 19.8 - - - +
239A GLN* 3.5 17.4 + - - +
26B LEU 3.4 6.1 - - - -
27B CYS 4.2 1.3 - - - -
33B THR* 4.6 0.2 - - - -
235B MSE 1.3 79.8 - - - +
237B ASP* 1.3 62.5 + - - +
238B LEU* 3.6 3.1 + - - +
239B GLN* 3.2 33.9 + - - +
240B ALA* 3.2 16.6 + - - +
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Residues in contact with ASP 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ALA* 4.0 8.2 - - + +
23B SER* 5.0 2.1 + - - -
25B LYS* 3.6 24.7 - - - +
26B LEU 2.8 9.2 + - - +
27B CYS 3.3 16.0 + - - +
30B GLY* 3.6 4.1 - - - -
31B GLY* 3.4 20.9 + - - -
32B PHE* 3.2 18.2 + - - +
33B THR* 3.0 34.9 + - - -
236B SER* 1.3 69.4 - - - +
238B LEU* 1.3 59.1 + - - +
239B GLN 3.3 0.2 - - - -
240B ALA* 3.6 3.9 - - - +
241B ALA* 3.0 28.1 + - - +
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A MSE 3.8 28.0 - - - -
186A GLY* 3.7 24.2 - - - +
238A LEU* 4.2 22.9 - - + +
239A GLN* 5.0 4.3 - - + +
242A TYR* 4.2 13.2 - - + -
17B MSE 3.8 46.6 - - + +
20B ALA* 4.8 4.7 - - + -
21B MSE 4.5 12.3 - - + -
26B LEU* 4.0 11.4 + - + +
236B SER* 3.8 3.4 - - - +
237B ASP* 1.3 79.1 - - - +
239B GLN* 1.3 62.3 + - + +
241B ALA* 3.4 5.4 + - - +
242B TYR* 3.3 16.8 + - - +
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Residues in contact with GLN 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A SER* 3.8 12.2 + - - +
238A LEU* 5.4 5.2 - - + -
239A GLN* 2.8 36.5 + - + +
53B PRO* 5.0 3.1 + - - +
185B ALA* 3.2 19.3 + - - +
186B GLY* 4.9 4.3 - - - +
188B GLU* 2.5 44.1 + - - +
235B MSE 3.7 20.7 - - + +
236B SER* 3.2 23.0 + - - +
238B LEU* 1.3 76.0 - - + +
240B ALA* 1.3 65.7 + - - +
242B TYR* 3.1 8.0 + - - +
243B LEU* 3.0 21.3 + - - +
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Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B PHE* 3.5 7.4 - - + +
33B THR* 3.5 41.1 - - - +
36B CYS* 3.4 9.6 - - - -
235B MSE 3.6 17.4 - - + +
236B SER 3.2 4.9 + - - -
237B ASP* 3.4 13.0 - - - +
238B LEU 3.2 0.4 - - - -
239B GLN* 1.3 76.5 - - - +
241B ALA* 1.3 51.2 + - - +
243B LEU* 3.0 4.5 + - - -
244B TRP* 2.8 32.2 + - - +
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Residues in contact with ALA 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLU 4.8 0.2 - - - +
16B TYR* 3.4 39.1 - - + +
17B MSE 3.9 8.5 - - - -
20B ALA* 4.3 3.1 - - + -
32B PHE* 3.7 23.3 - - + +
237B ASP 3.0 15.6 + - - +
238B LEU 3.8 5.4 - - - +
239B GLN 3.3 0.2 - - - -
240B ALA* 1.3 77.5 - - - +
242B TYR* 1.3 59.8 + - - +
244B TRP* 4.0 0.7 - - - +
245B ALA* 3.2 23.9 + - - +
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Residues in contact with TYR 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A MSE 4.2 11.4 - - - +
26A LEU* 3.9 32.4 - - + +
238A LEU* 3.7 9.0 - - + -
7B PRO* 5.6 0.5 - - - +
8B PRO 4.1 8.1 + - - -
9B VAL* 5.0 7.4 - - - +
13B GLU* 3.6 30.8 - - + +
17B MSE 3.6 30.0 - - + +
184B THR* 3.6 14.9 - - + +
185B ALA* 4.0 0.7 - - - -
186B GLY* 3.2 25.6 - - - +
238B LEU 3.3 9.8 + - - +
239B GLN* 3.1 10.5 + - - +
240B ALA 3.1 0.6 - - - -
241B ALA* 1.3 80.2 - - - +
243B LEU* 1.3 60.7 + - - +
245B ALA* 3.7 3.8 + - - +
246B GLN* 3.4 39.6 + - - +
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B CYS* 4.1 22.0 - - + -
40B LEU* 5.5 0.7 - - + -
51B LEU* 4.6 10.1 - - + -
177B PHE* 3.6 51.8 - - + -
183B TYR* 3.9 16.8 - - + -
185B ALA* 3.6 28.9 - - + +
235B MSE 5.1 4.7 - - - -
239B GLN 3.0 7.7 + - - +
240B ALA* 3.0 8.3 + - - +
242B TYR* 1.3 73.8 - - - +
244B TRP* 1.3 60.4 + - - +
245B ALA 3.1 1.8 - - - -
246B GLN* 2.9 6.2 + - + -
247B LEU* 2.9 42.4 + - + +
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Residues in contact with TRP 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B TYR* 3.4 41.0 + + - -
32B PHE* 3.8 20.5 - + + -
35B ARG* 3.3 52.0 - - + -
36B CYS* 3.6 16.1 - - - -
39B TRP* 3.9 26.0 - + + -
240B ALA 2.8 19.9 + - - +
241B ALA 4.0 2.7 - - - +
243B LEU* 1.3 72.9 - - - +
245B ALA* 1.3 61.0 + - - +
247B LEU* 4.0 6.1 - - + +
248B GLU* 3.3 23.4 + - + +
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Residues in contact with ALA 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 4.2 7.4 - - - +
12B THR* 3.4 27.9 + - - +
13B GLU* 3.7 20.2 - - + +
16B TYR* 3.6 22.2 - - + -
241B ALA 3.2 18.7 + - - +
242B TYR 3.7 5.2 - - - +
243B LEU 3.1 0.4 - - - -
244B TRP* 1.3 80.0 - - - +
246B GLN* 1.3 58.5 + - - +
248B GLU* 3.6 14.4 - - - +
249B ALA 3.9 2.9 + - - -
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Residues in contact with GLN 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PRO* 2.4 46.2 + - - +
10B VAL* 3.7 12.8 - - + -
13B GLU* 3.2 19.7 + - - +
182B ASN 4.1 0.7 - - - +
183B TYR* 3.4 23.8 - - + -
184B THR* 3.2 39.0 + - - +
185B ALA 4.5 1.1 + - - -
242B TYR* 3.4 18.6 - - - +
243B LEU* 2.9 7.9 + - - +
245B ALA* 1.3 74.5 - - - +
247B LEU* 1.3 64.1 + - - +
248B GLU 3.2 2.0 - - - -
249B ALA 3.3 5.6 + - - -
250B ALA* 3.2 18.2 + - - -
253B ILE* 4.0 2.4 - - + +
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Residues in contact with LEU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B CYS* 4.0 37.2 - - + +
39B TRP* 3.3 66.1 + - + +
40B LEU* 4.6 10.3 - - + -
157B VAL* 5.9 1.3 - - + -
177B PHE* 5.3 2.7 - - + -
183B TYR* 4.7 16.6 - - + -
243B LEU* 2.9 35.2 + - + +
244B TRP* 4.0 8.1 - - + +
245B ALA 3.4 0.2 - - - -
246B GLN* 1.3 75.4 - - - +
248B GLU* 1.3 63.5 + - - +
249B ALA 3.2 0.2 - - - -
250B ALA* 3.3 19.2 - - + +
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Residues in contact with GLU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 6.0 0.3 - - - +
12B THR* 4.4 9.2 + - - +
16B TYR* 2.9 36.9 + - - -
39B TRP* 5.3 1.8 - - - +
244B TRP* 3.3 15.1 + - + +
245B ALA* 3.6 12.0 - - - +
247B LEU* 1.3 80.7 - - - +
249B ALA* 1.3 56.4 + - + +
250B ALA 3.4 0.7 + - - -
251B ASP 5.3 0.5 + - - -
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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