Contacts of the helix formed by residues 193 - 214 (chain B) in PDB entry 1JW9
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 MET 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ARG 3.1 8.7 + - - +
157B MET* 3.5 37.0 - - + -
192B VAL* 1.3 76.9 - - - +
194B ALA* 1.3 72.0 + - - +
195B PRO* 4.0 15.9 - - + -
196B LEU* 3.0 23.3 + - + +
197B ILE 4.1 0.5 + - - -
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Residues in contact with ALA 194 (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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72B GLN* 3.2 44.2 - - + +
73B ARG* 3.9 12.2 - - + +
193B MET* 1.3 74.3 - - - +
195B PRO* 1.3 72.7 - - + +
196B LEU 3.1 1.4 + - - -
197B ILE* 3.2 22.2 + - - +
198B GLY 4.0 1.4 + - - -
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Residues in contact with PRO 195 (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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193B MET* 3.7 18.2 - - + -
194B ALA* 1.3 91.3 - - + +
196B LEU* 1.3 64.1 + - - +
197B ILE 3.2 0.2 - - - -
198B GLY* 3.0 14.3 + - - +
199B VAL* 3.0 19.5 + - + +
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Residues in contact with LEU 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ALA* 3.8 16.6 - - + -
155B ILE 3.6 6.5 - - - +
156B ARG 3.5 23.8 - - - +
157B MET* 4.0 4.7 - - - -
158B GLU 3.4 28.5 - - - +
159B GLY* 3.9 14.6 - - - +
192B VAL* 4.0 4.5 - - + -
193B MET* 3.0 18.7 + - + +
195B PRO* 1.3 77.5 - - - +
197B ILE* 1.3 62.1 + - + +
199B VAL* 3.2 6.5 + - - +
200B ILE* 3.1 23.6 + - + +
226B TYR* 3.4 36.1 - - + -
228B ALA* 4.6 4.0 - - + -
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Residues in contact with ILE 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLY* 3.2 39.7 - - - +
42B LEU* 3.7 10.7 - - + +
45B ALA* 3.4 7.7 - - + +
73B ARG* 3.6 22.2 - - + +
154B ALA* 3.5 28.3 - - + -
192B VAL* 4.0 17.3 - - + -
194B ALA 3.2 11.1 + - - +
195B PRO 3.2 0.4 - - - -
196B LEU* 1.3 76.3 - - - +
198B GLY* 1.3 61.8 + - - +
201B GLY* 2.8 28.6 + - - -
82D SO4 3.4 26.2 - - - +
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Residues in contact with GLY 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ALA* 4.1 11.0 - - - -
194B ALA 4.0 1.2 + - - -
195B PRO* 3.0 12.0 + - - -
197B ILE* 1.3 79.6 - - - +
199B VAL* 1.3 63.9 + - - +
202B SER* 2.6 33.3 + - - -
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Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B PRO* 3.0 16.4 + - + +
196B LEU 3.2 6.0 + - - +
198B GLY* 1.3 77.8 - - - +
200B ILE* 1.3 64.9 + - + +
202B SER* 3.8 3.3 - - - -
203B LEU* 3.0 43.9 + - + +
226B TYR* 3.9 43.5 - - + +
233B PHE* 4.8 7.2 - - + -
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Residues in contact with ILE 200 (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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42B LEU* 3.7 23.8 - - + -
152B GLY* 3.9 14.4 - - - -
153B ALA 3.9 5.8 - - - +
154B ALA* 4.6 2.5 - - + -
159B GLY* 3.8 36.1 - - - -
160B GLN* 3.8 22.4 - - - +
161B ILE* 5.1 4.5 - - + +
196B LEU* 3.1 17.9 + - + +
199B VAL* 1.3 77.5 - - + +
201B GLY* 1.3 63.6 + - - +
203B LEU* 3.2 21.2 + - + +
204B GLN* 2.9 22.4 + - + +
224B VAL 5.6 0.4 - - - +
226B TYR* 4.4 13.7 - - + -
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Residues in contact with GLY 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.8 13.4 - - - +
45B ALA* 3.9 10.8 - - - -
46B ALA* 3.4 16.8 - - - -
197B ILE 2.8 19.6 + - - -
200B ILE* 1.3 79.6 - - - +
202B SER* 1.3 55.3 + - - +
204B GLN* 3.2 12.1 + - - +
205B ALA 3.0 23.0 + - - -
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Residues in contact with SER 202 (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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45B ALA* 4.5 2.3 + - - +
49B TYR* 3.6 30.8 - - - -
198B GLY* 2.6 25.2 + - - -
199B VAL* 3.8 3.6 - - - -
201B GLY* 1.3 76.5 - - - +
203B LEU* 1.3 59.4 + - - +
205B ALA* 3.3 8.5 + - - +
206B MET* 2.9 28.4 + - - +
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Residues in contact with LEU 203 (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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161B ILE* 3.6 26.5 - - + -
199B VAL* 3.0 37.3 + - + +
200B ILE* 3.5 19.1 - - + +
202B SER* 1.3 76.4 - - - +
204B GLN* 1.3 57.4 + - - +
206B MET* 3.3 10.9 + - + +
207B GLU* 2.9 36.1 + - + +
224B VAL* 5.6 5.2 - - + -
226B TYR* 5.9 0.4 - - + -
233B PHE* 5.0 11.9 - - + -
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Residues in contact with GLN 204 (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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42B LEU* 3.8 18.2 - - - +
46B ALA* 4.4 0.4 - - + -
126B LEU* 3.9 13.9 - - + +
127B ASP 3.2 14.6 + - - +
128B CYS* 3.6 23.6 - - - -
150B VAL* 3.2 24.7 + - + +
152B GLY* 3.2 34.8 - - - +
161B ILE* 3.7 17.7 - - + -
200B ILE* 2.9 16.0 + - + +
201B GLY* 3.4 15.0 - - - +
203B LEU* 1.3 76.1 - - - +
205B ALA* 1.3 61.9 + - - +
207B GLU 3.3 0.7 + - - -
208B ALA* 2.9 24.8 + - - +
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Residues in contact with ALA 205 (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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46B ALA* 3.6 24.8 - - - +
49B TYR* 4.0 20.2 - - + -
50B LEU* 3.7 17.8 - - + +
201B GLY 3.0 11.5 + - - +
202B SER* 3.3 8.3 + - - +
204B GLN* 1.3 77.4 - - - +
206B MET* 1.3 62.1 + - - +
208B ALA* 3.3 2.4 + - - +
209B ILE* 2.9 32.8 + - + +
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Residues in contact with MET 206 (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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202B SER 2.9 14.4 + - - +
203B LEU* 3.6 16.2 - - + +
205B ALA* 1.3 76.5 - - - +
207B GLU* 1.3 67.9 + - - +
209B ILE* 3.2 16.4 + - - +
210B LYS* 3.0 43.7 + - + +
215B TYR* 6.5 0.7 - - - -
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Residues in contact with GLU 207 (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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150B VAL* 4.0 8.3 - - + -
161B ILE* 4.0 11.2 - - + -
163B VAL* 3.6 23.4 - - + +
203B LEU* 2.9 22.7 + - + +
204B GLN 3.9 3.4 - - - +
206B MET* 1.3 78.8 - - - +
208B ALA* 1.3 57.8 + - - +
210B LYS* 2.8 30.9 + - - +
211B MET* 3.0 32.9 + - - +
218B PRO* 3.4 10.9 - - - +
219B ALA* 2.8 38.7 + - + +
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Residues in contact with ALA 208 (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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34B VAL* 5.5 0.7 - - + -
50B LEU* 4.0 13.9 - - + -
124B LEU* 3.9 31.4 - - + -
126B LEU* 3.9 11.7 - - + -
150B VAL* 4.2 2.8 - - + +
204B GLN 2.9 17.4 + - - +
205B ALA* 3.6 5.2 - - - +
207B GLU* 1.3 71.9 - - - +
209B ILE* 1.3 64.7 + - - +
211B MET* 3.1 3.1 + - - +
212B LEU* 2.9 33.7 + - + +
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Residues in contact with ILE 209 (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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15B GLN* 5.2 3.8 - - - +
21B PHE* 4.1 16.6 - - + -
29B LEU* 4.1 31.6 - - + +
49B TYR* 4.7 3.1 - - + +
50B LEU* 4.1 14.8 - - + -
53B ALA* 3.6 29.4 - - + -
55B VAL* 4.6 1.8 - - + -
205B ALA* 2.9 24.9 + - + +
206B MET* 3.2 14.1 + - - +
208B ALA* 1.3 73.5 - - - +
210B LYS* 1.3 66.4 + - + +
212B LEU* 3.3 2.2 + - - +
213B ALA* 3.0 24.1 + - - +
215B TYR* 5.6 3.4 - - + -
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Residues in contact with LYS 210 (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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206B MET* 3.0 35.8 + - + +
207B GLU* 2.8 36.4 + - - +
209B ILE* 1.3 75.9 - - + +
211B MET* 1.3 59.8 + - + +
214B GLY* 2.9 25.1 + - - -
215B TYR* 2.9 47.8 + - + +
216B GLY* 4.3 2.2 - - - -
217B LYS 2.8 38.7 + - - +
218B PRO* 5.6 1.8 - - + -
219B ALA* 4.7 0.4 - - - +
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Residues in contact with MET 211 (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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124B LEU* 3.7 21.8 - - + -
148B PRO* 3.8 26.9 - - + -
150B VAL* 5.0 0.7 - - + -
163B VAL* 4.3 13.2 - - + -
165B THR* 3.9 19.5 - - + -
207B GLU 3.0 21.1 + - - +
210B LYS* 1.3 78.0 - - + +
212B LEU* 1.3 63.3 + - - +
214B GLY* 3.4 10.8 + - - -
218B PRO* 3.4 38.8 - - + -
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Residues in contact with LEU 212 (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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28B ALA* 4.0 12.1 - - - +
29B LEU* 3.9 18.6 - - + -
32B SER* 3.5 34.0 + - - +
34B VAL* 3.7 24.2 - - + -
55B VAL* 4.1 10.8 - - + -
123B ASP* 3.9 23.8 - - + -
124B LEU* 4.0 18.8 - - + -
208B ALA* 2.9 28.2 + - + +
209B ILE 3.9 3.1 - - - +
211B MET* 1.3 78.4 - - - +
213B ALA* 1.3 60.1 + - - +
214B GLY 3.7 0.2 + - - -
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Residues in contact with ALA 213 (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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21B PHE* 3.5 33.4 - - + -
25B GLY* 4.2 17.6 - - - +
28B ALA* 4.2 9.5 - - + +
29B LEU* 4.6 2.7 - - + -
209B ILE 3.0 15.8 + - - +
212B LEU* 1.3 77.3 - - - +
214B GLY* 1.3 63.1 - - - +
215B TYR* 4.2 6.6 - - + +
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Residues in contact with GLY 214 (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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210B LYS 2.9 8.5 + - - -
211B MET 3.4 7.8 + - - -
212B LEU 3.3 3.8 + - - -
213B ALA* 1.3 78.9 - - - +
215B TYR* 1.3 58.8 + - - +
216B GLY 4.1 5.0 + - - +
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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