Contacts of the helix formed by residues 218 - 235 (chain B) in PDB entry 5M4G
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 LYS 218 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU 3.6 18.6 - - - +
12A GLY* 3.8 15.0 - - - -
13A ASN* 3.7 20.6 - - - +
216B GLY 3.9 0.8 + - - +
217B MET* 1.3 74.1 - - - +
219B GLU* 1.3 65.4 + - - +
220B TYR* 3.6 30.1 - - + +
221B GLU* 2.8 32.3 + - + +
222B LEU* 3.6 7.0 - - - +
264B ASP 2.9 31.0 + - - +
265B ARG* 3.5 5.1 - - - +
266B THR* 3.0 29.5 + - - +
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Residues in contact with GLU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B MET 3.8 1.2 + - - -
218B LYS* 1.3 71.2 - - - +
220B TYR* 1.3 64.1 + - - +
222B LEU* 3.0 23.5 + - - +
223B GLU 3.3 7.6 + - - -
245B CYS* 3.0 35.0 - - + +
247B SER* 2.6 46.0 + - - +
250B ASN* 3.2 13.7 + - - -
256B TYR* 2.6 24.6 + - - -
263B ASN* 3.1 12.6 + - - +
265B ARG* 3.0 31.9 + - - +
267B ILE* 4.3 6.9 - - + +
275B PHE* 5.2 1.8 - - + -
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Residues in contact with TYR 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 2.7 53.9 + - + +
13A ASN* 4.2 9.5 + - - +
15A THR* 3.7 13.5 - - - +
231A TYR* 3.3 61.3 - + - +
232A SER 4.2 10.2 + - - -
235A GLY* 4.1 5.1 + - - -
218B LYS* 3.1 21.6 + - + -
219B GLU* 1.3 76.3 - - - +
221B GLU* 1.3 68.8 + - + +
222B LEU 3.1 0.2 - - - -
223B GLU* 3.3 11.4 + - - +
224B SER* 2.9 24.3 + - - -
262B PRO 4.5 1.8 - - - +
263B ASN* 2.9 30.4 + - + +
264B ASP* 4.2 5.2 - - - -
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Residues in contact with GLU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASN* 2.9 22.8 + - - +
228A HIS* 4.7 0.9 - - - -
232A SER* 3.9 30.5 - - - +
217B MET* 3.5 33.7 - - + +
218B LYS* 2.8 39.3 + - + +
220B TYR* 1.3 83.9 - - + +
222B LEU* 1.3 59.5 + - - +
224B SER* 3.6 6.0 + - - -
225B LEU* 3.1 25.5 + - - +
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Residues in contact with LEU 222 (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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209B VAL* 3.8 18.4 - - + +
212B ALA* 4.6 0.9 - - + -
213B VAL* 3.6 33.7 - - + +
217B MET* 3.7 29.8 - - + -
218B LYS 3.6 17.5 - - - +
219B GLU* 3.0 8.3 + - - +
221B GLU* 1.3 76.2 - - - +
223B GLU* 1.3 65.7 + - - +
224B SER 3.2 0.2 - - - -
225B LEU* 3.7 15.8 - - + +
226B PHE* 2.9 25.3 + - - +
245B CYS* 4.6 2.0 - - - -
267B ILE* 3.9 23.1 - - + -
275B PHE* 3.8 20.0 - - + -
277B MET* 4.8 0.9 - - - -
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Residues in contact with GLU 223 (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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231A TYR* 2.7 34.7 + - + -
237A ARG* 2.8 24.1 + - - -
219B GLU 3.3 3.2 + - - -
220B TYR* 3.3 9.7 + - - +
222B LEU* 1.3 76.5 - - - +
224B SER* 1.3 64.8 + - - +
226B PHE* 3.3 1.7 + - - +
227B GLU* 3.0 36.2 + - - +
242B THR* 4.4 1.0 - - - +
243B CYS* 3.6 24.9 + - + +
245B CYS* 3.8 21.9 - - - -
263B ASN* 3.0 24.4 + - - +
277B MET* 4.2 5.6 - - - -
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Residues in contact with SER 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A HIS* 2.8 33.0 + - - -
231A TYR* 3.5 14.7 - - - +
232A SER* 4.0 11.4 - - - -
220B TYR 2.9 17.2 + - - -
221B GLU 3.6 5.4 - - - -
223B GLU* 1.3 77.3 - - - +
225B LEU* 1.3 57.5 + - - +
227B GLU 3.4 1.0 + - - -
228B HIS* 2.9 26.7 + - - +
507B GOL 2.9 33.9 + - - -
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Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A HIS* 3.7 22.4 - - + +
208B GLU* 4.0 20.0 - - + +
209B VAL* 4.2 13.2 - - + -
212B ALA* 3.6 31.4 - - + -
217B MET* 6.2 0.4 - - + -
221B GLU 3.1 14.8 + - - +
222B LEU* 3.3 10.3 + - + +
224B SER* 1.3 78.6 - - - +
226B PHE* 1.3 63.9 + - - +
228B HIS* 3.3 9.2 + - + +
229B TYR* 2.9 25.2 + - + +
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Residues in contact with PHE 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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202B SER* 3.6 6.3 - - - -
205B ALA* 3.4 33.2 - - + +
206B HIS* 3.5 25.4 - + - -
209B VAL* 4.0 6.0 - - + +
222B LEU 2.9 17.5 + - - +
223B GLU 3.6 3.6 - - - +
225B LEU* 1.3 76.3 - - - +
227B GLU* 1.3 68.6 + - + +
229B TYR* 3.3 4.3 + - - +
230B CYS* 3.0 43.4 + - - -
239B SER* 5.1 2.9 - - - -
243B CYS* 4.1 9.2 - - - -
277B MET* 3.5 58.1 - - + -
278B GLY* 3.7 13.9 - - - -
279B GLY* 3.8 6.5 - - - -
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Residues in contact with GLU 227 (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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231A TYR* 5.4 0.2 - - - -
223B GLU* 3.0 23.0 + - - +
226B PHE* 1.3 78.4 - - + +
228B HIS* 1.3 57.7 + - - +
230B CYS* 3.4 5.9 + - - +
231B TYR* 2.9 31.4 + - - +
236B MET 4.7 0.9 - - - +
239B SER* 2.6 28.1 + - - +
242B THR* 5.7 0.7 - - - -
243B CYS* 3.7 21.4 + - - -
506B GOL 2.8 41.2 + - - +
507B GOL 2.5 38.5 + - - +
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Residues in contact with HIS 228 (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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221A GLU 4.7 1.1 - - - -
224A SER* 2.8 30.3 + - - -
225A LEU* 3.7 35.4 - - + +
228A HIS* 3.6 38.4 - + + +
224B SER 2.9 17.7 + - - +
225B LEU* 3.6 11.0 - - + +
227B GLU* 1.3 73.5 - - - +
229B TYR* 1.3 56.5 + - - +
232B SER* 2.7 60.5 + - - -
507B GOL 3.7 3.9 + - - +
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Residues in contact with TYR 229 (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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201B ILE* 3.9 12.3 - - + -
204B GLU* 2.7 49.4 + - + +
205B ALA* 3.7 24.5 - - + -
208B GLU* 3.8 31.5 + - + -
225B LEU* 2.9 19.9 + - + +
226B PHE* 3.7 4.3 - - - +
228B HIS* 1.3 77.1 - - - +
230B CYS* 1.3 58.7 + - - +
232B SER* 4.1 3.4 - - - -
233B ARG* 2.8 90.1 + - + +
234B GLY 3.5 0.3 + - - -
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Residues in contact with CYS 230 (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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201B ILE* 3.9 13.2 - - - -
202B SER* 4.2 5.6 - - - -
205B ALA* 3.9 10.8 - - - -
226B PHE* 3.0 50.2 + - + +
227B GLU* 3.8 7.2 - - - +
228B HIS 3.3 0.2 - - - -
229B TYR* 1.3 78.2 - - - +
231B TYR* 1.3 55.8 + - - +
234B GLY* 3.0 21.5 + - - -
236B MET* 3.0 44.1 + - + +
238B HIS 5.9 0.2 - - - +
279B GLY* 4.2 4.3 - - - -
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Residues in contact with TYR 231 (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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220A TYR* 3.3 37.4 - + + +
223A GLU* 2.6 42.7 + - + -
224A SER* 3.4 26.9 - - - +
227A GLU* 5.4 2.7 - - - -
262A PRO 4.6 3.5 + - - -
11B LEU* 5.7 1.8 - - + -
227B GLU 2.9 14.2 + - - +
230B CYS* 1.3 75.7 - - - +
232B SER* 1.3 63.7 + - - +
235B GLY* 2.9 31.5 + - - -
236B MET 3.3 24.9 + - - +
237B ARG* 3.2 42.4 + - + -
506B GOL 3.9 15.9 - - - +
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Residues in contact with SER 232 (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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220A TYR* 4.1 11.2 + - - -
221A GLU* 3.9 33.5 - - - +
224A SER* 3.5 10.7 + - - -
13B ASN* 4.9 3.6 + - - -
228B HIS* 2.7 52.6 + - - -
229B TYR* 4.1 0.9 - - - -
231B TYR* 1.3 75.3 - - - +
233B ARG* 1.3 71.2 + - - +
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Residues in contact with ARG 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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13B ASN* 5.9 1.2 - - - +
14B GLU* 4.9 12.0 + - - +
15B THR* 4.3 10.0 + - - +
197B TYR* 4.3 0.7 + - - -
201B ILE* 4.3 9.4 - - + +
204B GLU* 5.1 0.4 + - - +
208B GLU* 5.2 4.6 + - - -
229B TYR* 2.8 76.8 + - + +
232B SER* 1.3 85.1 - - - +
234B GLY* 1.3 59.0 + - - +
235B GLY 3.7 0.4 - - - -
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Residues in contact with GLY 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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15B THR* 3.6 4.0 - - - +
197B TYR* 2.7 27.2 + - - -
201B ILE* 3.9 18.3 - - - +
229B TYR 3.5 1.2 + - - -
230B CYS 3.0 13.4 + - - -
233B ARG* 1.3 78.8 - - - +
235B GLY* 1.3 63.9 + - - +
236B MET* 3.2 5.1 + - - +
281B TYR* 3.3 14.7 - - - -
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Residues in contact with GLY 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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220A TYR* 4.0 19.8 + - - -
11B LEU* 3.2 30.9 - - - +
15B THR* 3.9 4.1 - - - +
231B TYR* 2.9 20.6 + - - -
233B ARG 3.7 1.2 - - - -
234B GLY* 1.3 77.0 - - - +
236B MET* 1.3 59.0 + - - +
237B ARG* 3.3 7.1 + - - +
281B TYR* 3.8 5.7 - - - -
282B TYR 5.6 0.3 + - - -
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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