Contacts of the helix formed by residues 218 - 235 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A GLY 3.9 0.6 + - - +
217A MET* 1.3 74.2 - - - +
219A GLU* 1.3 66.5 + - - +
220A TYR* 3.1 32.3 - - + -
221A GLU* 2.8 32.3 + - + +
222A LEU* 3.6 6.1 - - - +
264A ASP 3.0 30.3 + - - +
265A ARG* 3.5 6.5 - - - +
266A THR* 2.9 29.5 + - - +
267A ILE* 4.5 1.3 - - - -
10B TRP 5.9 0.4 + - - -
11B LEU* 3.6 22.9 - - - +
12B GLY* 3.9 13.6 - - - +
13B ASN* 3.9 15.9 - - - +
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Residues in contact with GLU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A MET 3.9 0.8 + - - -
218A LYS* 1.3 71.3 - - - +
220A TYR* 1.3 57.1 + - - +
222A LEU* 3.0 24.4 + - - +
223A GLU 3.4 6.6 + - - -
245A CYS* 3.0 34.5 - - + +
247A SER* 2.7 44.3 + - - +
250A ASN* 3.2 14.2 + - - -
256A TYR* 2.5 23.7 + - - -
263A ASN* 3.2 13.2 + - - +
265A ARG* 3.0 33.8 + - - +
267A ILE* 4.2 12.3 - - + +
275A PHE* 5.3 1.3 - - + -
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Residues in contact with TYR 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LYS* 3.4 25.1 - - + +
219A GLU* 1.3 72.9 - - - +
221A GLU* 1.3 72.7 + - + +
222A LEU 3.1 0.4 - - - -
223A GLU* 3.5 10.7 - - - +
224A SER* 3.0 24.4 + - - -
262A PRO 4.7 1.8 - - - +
263A ASN* 2.9 29.7 + - + +
264A ASP* 4.3 4.9 - - + -
11B LEU* 2.7 47.3 + - + -
13B ASN* 4.2 6.6 + - - -
15B THR* 3.6 17.5 - - - +
231B TYR* 3.3 60.5 - + - +
232B SER 4.1 11.5 + - - -
235B GLY* 4.0 5.4 - - - -
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Residues in contact with GLU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A MET* 3.3 35.8 - - + +
218A LYS* 2.8 38.7 + - + +
220A TYR* 1.3 84.4 - - + +
222A LEU* 1.3 60.8 + - - +
224A SER* 3.6 6.7 + - - -
225A LEU* 3.2 24.6 + - - +
13B ASN* 2.9 24.1 + - - +
228B HIS* 4.7 0.7 - - - -
232B SER* 3.9 30.4 - - - +
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Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A VAL* 3.8 20.2 - - + +
212A ALA* 4.4 8.1 - - + -
213A VAL* 3.6 32.5 - - + +
217A MET* 3.9 28.3 - - + -
218A LYS 3.6 16.8 - - - +
219A GLU 3.0 8.3 + - - +
221A GLU* 1.3 77.0 - - - +
223A GLU* 1.3 65.6 + - - +
224A SER 3.2 0.2 - - - -
225A LEU* 4.4 7.0 - - + -
226A PHE* 2.9 25.1 + - - +
245A CYS* 4.5 2.9 - - - -
267A ILE* 3.8 23.6 - - + -
275A PHE* 3.7 19.3 - - + -
277A MET* 4.7 0.7 - - - -
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Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A GLU 3.4 3.4 + - - -
220A TYR* 3.3 10.3 + - - +
222A LEU* 1.3 78.2 - - - +
224A SER* 1.3 61.5 + - - +
226A PHE* 3.3 1.6 + - - +
227A GLU* 3.0 37.7 + - - +
242A THR* 4.6 1.2 - - - +
243A CYS* 3.6 25.5 + - + +
245A CYS* 3.8 20.3 - - - -
263A ASN* 3.0 20.8 + - - +
277A MET* 4.1 5.6 - - - -
231B TYR* 2.6 35.7 + - + -
237B ARG* 2.9 25.4 + - - +
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Residues in contact with SER 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR 3.0 16.6 + - - -
221A GLU 3.6 5.8 - - - -
223A GLU* 1.3 76.4 - - - +
225A LEU* 1.3 57.5 + - - +
227A GLU* 3.4 5.8 + - - +
228A HIS* 2.9 30.8 + - - +
228B HIS* 2.8 37.8 + - - -
231B TYR* 3.4 29.0 - - - +
232B SER* 4.0 9.2 - - - -
506B GOL 5.1 1.8 + - - -
507B GOL 4.4 2.3 + - - -
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A GLU* 4.0 20.0 - - + +
209A VAL* 4.2 11.9 - - + -
212A ALA* 3.5 32.3 - - + -
221A GLU 3.2 14.6 + - - +
222A LEU* 3.8 9.2 - - + +
223A GLU 3.3 0.2 - - - -
224A SER* 1.3 76.9 - - - +
226A PHE* 1.3 64.7 + - - +
228A HIS* 3.2 10.5 + - + +
229A TYR* 2.9 27.3 + - + +
228B HIS* 3.7 22.8 - - + +
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Residues in contact with PHE 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A SER* 3.6 6.1 - - - -
205A ALA* 3.5 34.7 - - + +
206A HIS* 3.6 23.8 - + - -
209A VAL* 4.0 6.0 - - + +
222A LEU 2.9 17.6 + - - +
223A GLU 3.5 4.0 - - - +
225A LEU* 1.3 79.2 - - - +
227A GLU* 1.3 63.6 + - + +
229A TYR* 3.3 2.6 + - - +
230A CYS* 3.0 49.5 + - - -
239A SER* 4.9 2.9 - - - -
243A CYS* 4.1 9.6 - - - -
277A MET* 3.6 57.0 - - + -
278A GLY* 3.6 13.7 - - - -
279A GLY* 3.8 7.4 - - - -
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Residues in contact with GLU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A GLU* 3.0 28.9 + - - +
224A SER* 3.9 4.5 - - - +
226A PHE* 1.3 83.5 - - + +
228A HIS* 1.3 57.5 + - - +
230A CYS* 3.4 5.6 + - - +
231A TYR* 2.9 31.2 + - - +
236A MET 4.6 0.5 - - - +
239A SER* 2.6 33.2 + - - +
242A THR* 5.8 0.5 - - - -
243A CYS* 3.7 21.4 + - - -
231B TYR* 5.4 2.8 - - - -
506B GOL 4.1 12.6 + - - -
507B GOL 3.5 30.1 + - - +
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Residues in contact with HIS 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A SER 2.9 18.6 + - - +
225A LEU* 3.6 12.6 - - + +
227A GLU* 1.3 73.2 - - - +
229A TYR* 1.3 66.3 + - - +
232A SER* 2.7 49.8 + - - -
221B GLU 4.7 1.1 - - - -
224B SER* 2.8 28.6 + - - -
225B LEU* 3.7 34.7 - - + +
228B HIS* 3.6 30.8 - + + +
507B GOL 3.5 13.2 - - - +
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Residues in contact with TYR 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ILE* 3.9 14.4 - - + -
204A GLU* 2.6 48.5 + - + +
205A ALA* 3.7 22.0 - - + -
208A GLU* 3.8 30.9 + - + -
225A LEU* 2.9 17.1 + - + +
226A PHE 3.6 7.2 - - - +
228A HIS* 1.3 80.4 - - - +
230A CYS* 1.3 57.5 + - - +
232A SER* 4.0 4.3 - - - -
233A ARG* 2.9 89.0 + - + +
234A GLY 3.6 0.2 + - - -
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Residues in contact with CYS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ILE* 3.9 13.5 - - - -
202A SER* 4.2 3.1 - - - -
205A ALA* 3.9 10.5 - - - -
226A PHE* 3.0 51.0 + - + +
227A GLU* 3.8 6.7 - - - +
229A TYR* 1.3 77.0 - - - +
231A TYR* 1.3 57.2 + - - +
234A GLY* 3.0 21.1 + - - -
236A MET* 3.0 44.0 + - + +
238A HIS 5.9 0.2 - - - +
279A GLY* 4.2 6.7 - - - -
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Residues in contact with TYR 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 5.7 2.2 - - + -
227A GLU 2.9 16.9 + - - +
230A CYS* 1.3 74.8 - - - +
232A SER* 1.3 63.6 + - - +
235A GLY* 2.8 28.0 + - - -
236A MET 3.3 25.3 + - - +
237A ARG* 3.2 41.3 + - + -
220B TYR* 3.3 37.2 - + + +
223B GLU* 2.7 40.6 + - + -
224B SER* 3.5 17.0 - - - +
262B PRO 4.5 3.8 + - - -
507B GOL 3.4 27.4 - - - +
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Residues in contact with SER 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ASN* 4.8 4.0 + - - +
228A HIS* 2.7 52.3 + - - -
229A TYR* 4.0 1.2 - - - -
231A TYR* 1.3 76.1 - - - +
233A ARG* 1.3 71.8 + - - +
220B TYR* 4.2 10.0 + - - -
221B GLU* 3.9 32.2 - - - +
224B SER* 3.6 10.7 + - - -
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Residues in contact with ARG 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ASN* 6.0 1.0 - - - +
14A GLU* 4.9 12.3 + - - +
15A THR* 4.4 7.9 - - - +
197A TYR* 4.3 2.8 + - - -
201A ILE* 4.3 7.6 - - + +
204A GLU* 5.0 1.0 + - - +
208A GLU* 5.4 4.0 + - - -
229A TYR* 2.9 75.4 + - + +
232A SER* 1.3 84.6 - - - +
234A GLY* 1.3 58.0 + - - +
235A GLY 3.7 0.7 - - - -
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Residues in contact with GLY 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A THR* 3.6 3.7 - - - +
197A TYR* 2.7 27.6 + - - -
201A ILE* 3.9 18.1 - - - +
229A TYR 3.6 1.2 + - - -
230A CYS 3.0 12.9 + - - -
233A ARG* 1.3 79.3 - - - +
235A GLY* 1.3 63.9 + - - +
236A MET* 3.2 4.7 + - - +
281A TYR* 3.4 14.6 - - - -
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Residues in contact with GLY 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.1 31.2 - - - +
15A THR* 3.9 12.8 - - - +
231A TYR* 2.8 19.1 + - - -
233A ARG 3.7 1.2 - - - -
234A GLY* 1.3 78.8 - - - +
236A MET* 1.3 59.8 + - - +
237A ARG* 3.5 5.9 + - - +
281A TYR* 3.7 7.0 - - - -
282A TYR 5.7 0.2 + - - -
220B TYR* 4.1 11.6 + - - -
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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