Contacts of the helix formed by residues 220 - 242 (chain B) in PDB entry 2WMZ
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 ASN 220 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B ALA 2.8 18.8 + - - +
219B ARG* 1.3 74.4 - - - +
221B LEU* 1.3 61.6 + - - +
222B SER* 3.4 18.2 + - - -
223B LEU* 3.0 27.7 + - + +
224B LEU* 2.9 25.1 + - - +
319B ALA 4.8 1.2 + - - -
323B VAL* 3.2 34.1 - - + +
402B SER 4.1 4.9 - - - +
403B ALA* 3.3 22.2 - - - +
404B LEU 3.0 11.9 + - - -
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B VAL* 3.4 15.0 - - + +
99B GLN* 3.5 34.5 - - + +
100B THR* 3.3 48.9 + - + +
103B GLN* 4.1 21.3 - - + +
219B ARG 2.9 13.8 + - - +
220B ASN* 1.3 73.3 + - - +
222B SER* 1.3 62.1 + - - +
224B LEU* 3.5 19.6 - - + +
225B GLN* 3.2 18.0 + - - +
405B GLY* 4.1 13.4 - - - +
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Residues in contact with SER 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B THR* 5.3 8.3 - - - +
220B ASN* 3.1 18.1 + - - -
221B LEU* 1.3 76.7 - - - +
223B LEU* 1.3 66.1 + - - +
225B GLN* 3.3 7.9 + - - +
226B ALA* 3.2 19.8 + - - +
319B ALA* 4.4 7.7 - - - +
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Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ALA 4.8 0.2 - - - +
217B GLU* 3.6 24.0 - - - +
220B ASN* 3.0 26.9 + - + +
222B SER* 1.3 75.8 - - - +
224B LEU* 1.3 63.4 + - - +
226B ALA* 3.2 11.8 + - - +
227B ARG* 3.2 47.6 + - - +
316B LEU* 4.0 12.1 - - + -
319B ALA* 3.7 10.7 - - + +
320B HIS* 3.5 54.7 - - + +
323B VAL* 4.2 6.3 - - + -
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Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B VAL* 3.5 32.1 - - + -
99B GLN* 5.5 3.4 - - - +
219B ARG 5.2 3.1 - - - +
220B ASN 2.9 13.6 + - - +
221B LEU* 3.5 23.3 - - + +
222B SER 3.2 0.2 - - - -
223B LEU* 1.3 76.7 - - - +
225B GLN* 1.3 57.2 + - - +
227B ARG* 3.1 24.7 + - + +
228B LEU* 3.0 34.7 + - + +
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Residues in contact with GLN 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 3.8 23.2 - - + +
96B VAL* 3.1 28.5 - - + +
97B THR* 2.9 45.0 + - - +
100B THR* 4.2 7.3 + - - +
221B LEU 3.2 6.9 + - - +
222B SER* 3.3 8.7 + - - +
224B LEU* 1.3 75.1 - - - +
226B ALA* 1.3 60.2 + - - +
227B ARG 2.9 1.8 - - - -
228B LEU* 4.2 4.9 - - - +
229B SER* 2.7 40.0 + - - +
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Residues in contact with ALA 226 (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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222B SER 3.2 3.9 + - - +
223B LEU 3.2 5.3 + - - +
225B GLN* 1.3 78.7 - - - +
227B ARG* 1.3 56.1 + - - +
229B SER* 4.0 5.4 - - - -
230B GLN* 3.0 28.2 + - - +
312B ALA 4.4 2.8 - - - +
315B GLN* 4.1 5.6 - - + +
316B LEU* 3.4 27.7 - - + +
319B ALA* 3.4 33.0 - - + -
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Residues in contact with ARG 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLU* 3.4 25.3 + - - +
218B LYS* 6.0 1.2 - - - +
223B LEU* 3.2 35.9 + - - +
224B LEU* 3.1 22.1 + - + +
225B GLN 2.9 0.2 - - - -
226B ALA* 1.3 75.1 - - - +
228B LEU* 1.3 68.4 + - + +
230B GLN* 3.0 18.3 + - - +
231B ASP* 3.0 13.7 + - - +
316B LEU* 3.9 24.1 - - + +
320B HIS* 5.3 3.2 - - - -
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Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LYS* 5.2 1.5 - - - +
92B GLY* 3.9 5.8 - - - -
93B ILE* 3.5 36.8 - - + +
96B VAL* 3.5 31.9 - - + -
224B LEU* 3.0 27.6 + - + +
225B GLN* 3.1 6.7 + - - +
227B ARG* 1.3 75.9 - - + +
229B SER* 1.3 57.2 + - - +
231B ASP* 3.1 13.3 + - + +
232B LEU* 2.9 26.3 + - - +
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Residues in contact with SER 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 3.4 25.5 - - - +
225B GLN* 2.7 27.2 + - - +
226B ALA* 4.0 6.1 - - - -
228B LEU* 1.3 71.6 - - - +
230B GLN* 1.3 63.5 + - - +
232B LEU* 3.4 6.3 + - - +
233B ALA* 3.1 20.4 + - - +
312B ALA* 4.0 5.6 - - - +
315B GLN* 5.9 3.6 - - - -
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Residues in contact with GLN 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ALA 3.0 18.4 + - - +
227B ARG* 3.0 8.2 + - - +
229B SER* 1.3 73.4 - - - +
231B ASP* 1.3 66.2 + - - +
233B ALA* 3.1 12.3 + - - +
234B ARG* 3.2 24.6 + - - +
309B PHE* 3.4 18.8 - - + -
312B ALA* 3.7 20.4 - - + +
313B SER* 2.8 34.7 + - - +
316B LEU* 3.5 23.6 - - + +
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Residues in contact with ASP 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LYS* 2.9 46.1 + - - +
227B ARG 3.0 11.1 + - - +
228B LEU* 3.2 15.5 - - + +
230B GLN* 1.3 77.9 + - - +
232B LEU* 1.3 56.7 + - - +
234B ARG* 2.8 45.1 + - - +
235B GLU* 2.8 12.3 + - - +
238B ARG* 5.8 2.1 + - - -
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 3.4 37.5 - - + +
89B LYS* 3.8 23.6 - - + -
90B ALA* 5.2 9.4 - - + -
93B ILE* 4.1 19.7 - - + -
228B LEU 2.9 13.1 + - - +
229B SER* 3.5 11.4 - - - +
230B GLN 3.3 0.2 - - - -
231B ASP* 1.3 81.7 + - - +
233B ALA* 1.3 56.1 + - - +
235B GLU* 3.3 4.5 + - - +
236B GLN* 2.9 50.1 + - + +
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Residues in contact with ALA 233 (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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229B SER 3.1 7.5 + - - +
230B GLN 3.1 10.5 + - - +
232B LEU* 1.3 76.0 - - - +
234B ARG* 1.3 61.6 + - - +
236B GLN* 3.5 15.7 + - - +
237B ILE* 3.3 23.0 + - - +
305B ALA 3.9 4.5 - - - +
308B ASN* 3.6 14.8 - - - +
309B PHE* 3.7 12.8 - - + -
312B ALA* 3.4 29.2 - - + -
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Residues in contact with ARG 234 (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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230B GLN* 3.2 20.8 + - - -
231B ASP* 2.8 41.2 + - - +
233B ALA* 1.3 73.8 - - - +
235B GLU* 1.3 67.0 + - - +
236B GLN 3.0 1.3 - - - -
237B ILE* 2.8 28.4 + - + +
238B ARG* 3.2 38.8 + - + +
309B PHE* 3.4 40.4 - - + -
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Residues in contact with GLU 235 (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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82B ARG* 3.0 31.4 + - - -
85B THR* 3.2 24.4 + - + +
86B LEU* 3.2 28.7 - - + -
89B LYS* 3.5 27.8 - - + -
231B ASP* 2.8 9.9 + - - +
232B LEU 3.6 4.7 - - - +
234B ARG* 1.3 75.8 - - - +
236B GLN* 1.3 56.5 + - - +
238B ARG* 2.7 39.1 + - - +
239B GLN 3.1 20.6 + - - -
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Residues in contact with GLN 236 (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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86B LEU* 4.0 15.2 - - + +
232B LEU* 2.9 35.5 + - - +
233B ALA* 3.6 11.8 - - - +
235B GLU* 1.3 75.6 - - - +
237B ILE* 1.3 65.4 + - - +
239B GLN* 3.3 21.3 + - - +
240B ALA* 3.0 21.7 + - - +
305B ALA* 3.9 5.4 - - + +
308B ASN* 3.6 20.1 + - - +
1432B PGE 3.7 30.3 - - - +
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Residues in contact with ILE 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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233B ALA 3.3 10.1 + - - +
234B ARG* 2.8 14.2 + - + +
236B GLN* 1.3 74.5 - - - +
238B ARG* 1.3 65.7 + - + +
240B ALA* 3.1 13.7 + - - +
241B GLN* 3.2 31.0 + - - +
302B VAL* 4.5 3.6 - - + -
305B ALA* 3.1 30.7 - - + +
306B GLN* 3.7 33.2 - - + +
309B PHE* 3.5 35.2 - - + -
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Residues in contact with ARG 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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82B ARG* 3.0 32.1 - - - +
89B LYS* 5.7 0.6 - - - +
231B ASP* 5.8 2.0 + - - -
234B ARG* 3.2 38.1 + - + +
235B GLU* 2.7 33.6 + - - +
237B ILE* 1.3 76.1 - - + +
239B GLN* 1.3 65.4 + - - +
241B GLN* 3.0 29.8 + - - +
242B ASP* 3.0 19.2 + - - +
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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
----------------------------------------------------------
79B SER* 5.5 6.6 + - - -
82B ARG* 3.2 31.6 - - + +
83B ALA* 4.8 7.5 - - - +
86B LEU* 3.1 27.7 - - + +
235B GLU 3.1 7.2 + - - +
236B GLN* 3.4 21.2 + - - +
238B ARG* 1.3 80.0 - - - +
240B ALA* 1.3 64.7 + - - +
242B ASP* 3.0 19.7 + - + +
243B GLY 3.9 1.4 + - - -
1432B PGE 5.3 6.8 - - - +
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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
----------------------------------------------------------
236B GLN 3.0 12.0 + - - +
237B ILE 3.1 9.6 + - - +
239B GLN* 1.3 77.2 - - - +
241B GLN* 1.3 61.4 + - - +
243B GLY* 3.2 11.6 + - - -
298B VAL* 3.4 16.1 - - - +
301B GLN* 3.8 20.4 + - + +
302B VAL* 3.6 32.0 - - + +
305B ALA* 3.9 5.2 - - + -
1432B PGE 4.4 5.8 - - - +
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Residues in contact with GLN 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ILE* 3.2 20.6 - - - +
238B ARG* 3.0 29.1 + - - +
240B ALA* 1.3 72.5 - - - +
242B ASP* 1.3 62.3 + - - +
243B GLY 2.9 7.8 + - - -
244B HIS* 3.1 27.0 + - - +
245B LEU* 4.2 3.5 + - - +
302B VAL* 3.7 30.7 - - + +
306B GLN* 5.6 2.2 - - - +
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Residues in contact with ASP 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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78B MET* 3.7 23.5 - - + +
79B SER* 4.3 13.0 - - - +
82B ARG* 2.8 49.7 + - - +
238B ARG* 3.0 15.6 + - - +
239B GLN 3.0 10.2 + - - +
241B GLN* 1.3 72.2 - - - +
243B GLY* 1.3 56.0 + - - +
244B HIS 2.8 12.2 + - - -
245B LEU* 2.9 35.7 + - - +
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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
------------------------------------------------------------
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