Contacts of the helix formed by residues 214 - 229 (chain A) in PDB entry 3MYV
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 214 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A MSE 3.4 13.9 - - - +
205A SER 3.5 7.0 - - - +
206A GLU 3.0 22.8 + - - -
207A GLU 3.1 24.3 + - - +
208A LYS* 3.9 7.0 - - - +
209A ASN* 5.0 4.3 - - + +
212A ARG 3.8 1.6 + - - +
213A MSE 1.3 72.7 - - - +
215A LYS* 1.3 66.4 + - - +
216A TYR* 3.3 8.7 + - - +
217A ALA* 3.1 20.7 + - - +
218A ALA 3.0 18.4 + - - -
252A TYR* 3.0 24.9 + - - -
275A PHE 4.2 4.8 - - - +
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Residues in contact with LYS 215 (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 VAL* 3.5 42.4 + - + +
202A THR* 5.1 5.5 + - - +
204A MSE 3.6 28.1 + - + +
205A SER 2.9 24.6 + - - +
206A GLU* 3.8 30.9 + - + +
214A ASN* 1.3 71.5 - - - +
216A TYR* 1.3 62.7 + - + +
218A ALA* 3.3 4.0 + - - +
219A ARG* 3.0 41.2 + - - +
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Residues in contact with TYR 216 (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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206A GLU* 4.0 43.4 + - + -
214A ASN* 3.2 17.8 + - - +
215A LYS* 1.3 77.8 - - - +
217A ALA* 1.3 56.0 + - - +
219A ARG* 3.3 9.6 + - - +
220A ALA* 2.9 28.8 + - - +
242A LEU* 3.5 26.3 - - + +
245A ASP* 3.9 15.8 + - + +
246A ALA* 4.1 20.4 - - - -
249A SER* 3.3 26.7 + - - -
251A SER* 4.5 5.7 + - - -
252A TYR* 3.5 31.2 - + + -
275A PHE* 3.7 17.6 - + + -
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Residues in contact with ALA 217 (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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213A MSE 3.7 22.2 - - + -
214A ASN* 3.1 26.6 + - - +
216A TYR* 1.3 76.8 - - - +
218A ALA* 1.3 59.3 + - - +
220A ALA* 3.1 2.1 + - - +
221A LEU 2.9 25.3 + - - -
275A PHE* 3.6 29.9 - - + +
276A PHE* 4.1 0.4 - - + -
358A LEU* 3.4 18.1 - - + +
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Residues in contact with ALA 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ALA* 4.4 2.9 - - + -
197A LEU* 3.8 20.0 - - + +
201A VAL* 3.9 13.9 - - + -
204A MSE 3.5 33.9 - - + -
213A MSE 4.9 5.1 - - - +
214A ASN 3.0 6.9 + - - +
215A LYS 3.7 6.3 - - - +
217A ALA* 1.3 78.0 - - - +
219A ARG* 1.3 56.2 + - - +
221A LEU* 3.5 5.8 + - - +
222A LEU* 3.0 28.1 + - - +
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Residues in contact with ARG 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A VAL* 3.6 32.4 - - + +
206A GLU* 4.8 8.9 + - - -
215A LYS* 3.0 36.5 + - - +
216A TYR* 3.7 11.1 - - - +
218A ALA* 1.3 72.2 - - - +
220A ALA* 1.3 65.8 + - - +
222A LEU* 3.3 4.6 + - - -
223A ALA* 2.9 21.5 + - - +
238A LEU* 3.5 31.9 - - + +
241A GLN* 3.8 19.6 - - - +
242A LEU* 3.7 36.4 - - + +
245A ASP* 2.9 34.7 + - - +
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Residues in contact with ALA 220 (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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216A TYR 2.9 15.1 + - - +
217A ALA 3.1 7.8 + - - +
219A ARG* 1.3 74.4 - - - +
221A LEU* 1.3 62.7 + - - +
223A ALA* 3.3 5.6 + - - +
224A ARG* 3.1 21.0 + - - +
242A LEU* 3.4 12.7 - - + +
275A PHE* 3.6 32.5 - - + -
358A LEU* 4.2 12.3 - - + +
359A ARG 5.6 0.2 - - - +
362A GLU* 5.6 0.7 - - - -
363A VAL* 3.9 9.0 - - + -
366A ILE* 4.3 4.9 - - - +
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Residues in contact with LEU 221 (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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141A ALA 4.4 4.0 - - - +
145A LEU* 3.8 50.3 - - + +
148A PHE* 4.6 2.2 - - + -
197A LEU* 3.8 21.8 - - + -
213A MSE 4.3 15.3 - - - -
217A ALA 2.9 15.7 + - - +
218A ALA* 3.7 5.6 - - - +
220A ALA* 1.3 75.0 - - - +
222A LEU* 1.3 57.7 + - - +
224A ARG* 3.1 28.4 + - - +
225A ILE* 2.9 41.2 + - + +
358A LEU* 3.8 16.5 - - + +
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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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194A ILE* 4.3 19.5 - - + +
197A LEU* 3.7 30.0 - - + +
198A GLU* 3.8 22.4 - - + +
201A VAL* 4.5 10.3 - - + -
218A ALA 3.0 17.7 + - - +
219A ARG 3.3 5.6 + - - +
221A LEU* 1.3 74.2 - - - +
223A ALA* 1.3 58.8 + - - +
225A ILE* 4.4 2.5 - - + +
226A TYR* 2.8 72.1 + - + +
238A LEU* 3.7 12.8 - - + -
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Residues in contact with ALA 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 ARG 2.9 14.3 + - - +
220A ALA* 3.3 10.1 + - - +
222A LEU* 1.3 75.6 - - - +
224A ARG* 1.3 63.8 + - - +
226A TYR* 3.5 7.5 + - - +
227A LEU* 3.1 22.3 + - - +
235A ALA* 3.7 13.3 - - - +
238A LEU* 3.6 19.0 - - + +
239A ALA* 4.3 9.0 - - + +
242A LEU* 5.5 0.4 - - + -
363A VAL* 5.4 2.9 - - + -
366A ILE* 3.9 20.9 - - + +
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Residues in contact with ARG 224 (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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145A LEU* 4.9 1.4 - - - +
148A PHE* 3.9 19.0 - - - -
152A ARG* 3.7 11.9 - - - +
220A ALA 3.1 10.1 + - - +
221A LEU* 3.1 25.9 + - - +
223A ALA* 1.3 76.8 - - - +
225A ILE* 1.3 56.4 + - - +
227A LEU* 3.1 6.9 + - + +
228A TYR* 2.9 55.2 + - + -
357A VAL* 3.0 24.4 + - - +
358A LEU* 3.4 11.6 - - - +
362A GLU* 2.8 42.5 + - - +
366A ILE* 3.6 12.7 - - + +
413A ARG* 6.3 0.2 - - - +
422A HIS* 3.7 10.8 - - - -
516A EDO 2.7 31.5 + - - -
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Residues in contact with ILE 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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144A ALA 4.8 1.1 - - - +
148A PHE* 3.7 33.7 - - + -
190A TYR* 3.9 18.1 - - + -
193A ILE* 3.5 27.8 - - + -
194A ILE* 3.6 26.9 - - + -
197A LEU* 3.7 22.7 - - + -
221A LEU* 2.9 29.9 + - + +
222A LEU* 3.2 6.3 + - + +
224A ARG* 1.3 72.1 - - + +
226A TYR* 1.3 66.4 + - - +
228A TYR* 3.3 7.6 + - - +
229A HIS* 2.8 22.7 + - - +
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Residues in contact with TYR 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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194A ILE* 3.7 18.6 - - + -
198A GLU* 2.6 37.2 + - - +
222A LEU* 2.8 43.3 + - + +
223A ALA* 3.6 6.3 - - - +
225A ILE* 1.3 75.8 - - - +
227A LEU* 1.3 60.4 + - - +
229A HIS* 3.0 8.6 + - - +
231A ASP* 2.9 47.4 + - - +
234A LYS* 3.7 45.9 - - + +
235A ALA 3.8 12.6 - - - +
238A LEU* 3.7 17.3 - - + -
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Residues in contact with LEU 227 (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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159A THR* 5.1 2.8 - - - +
223A ALA 3.1 9.4 + - - +
224A ARG* 3.1 11.3 + - + +
226A TYR* 1.3 79.7 - - - +
228A TYR* 1.3 65.3 + - + +
230A ASP* 3.0 14.9 + - - +
232A ASN* 3.7 25.8 + - - +
235A ALA* 3.8 7.8 - - + +
366A ILE* 4.2 15.5 - - + +
369A GLU* 3.5 20.2 - - + +
370A ALA* 3.9 27.8 - - + +
373A LYS* 4.7 4.1 + - - +
413A ARG* 3.3 30.5 - - - +
429A ARG* 3.6 19.2 + - - +
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Residues in contact with TYR 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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148A PHE* 3.6 22.9 - + + -
152A ARG* 3.2 36.9 + - + -
158A TYR* 3.9 12.3 + - - +
159A THR* 3.8 17.1 + - - +
190A TYR* 3.3 22.3 + - + +
224A ARG* 2.9 46.1 + - + +
225A ILE 3.6 7.0 - - - +
227A LEU* 1.3 78.8 - - + +
229A HIS* 1.3 58.4 + - - +
230A ASP 3.3 1.3 + - - -
413A ARG* 6.2 0.4 - - - -
422A HIS* 4.9 6.0 + - - -
425A PHE* 3.2 23.1 - + + +
426A ASP* 3.8 9.3 + - - -
429A ARG* 3.5 45.3 - - + +
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Residues in contact with HIS 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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158A TYR* 3.3 52.1 + + - -
162A LYS* 5.3 0.2 + - - -
187A ALA 5.1 0.2 + - - -
190A TYR* 3.4 36.4 - + + +
191A ASP* 4.3 14.2 + - - -
194A ILE* 3.5 17.1 - - + +
225A ILE 2.8 16.7 + - - +
226A TYR 3.0 6.2 + - - +
228A TYR* 1.3 76.3 - - - +
230A ASP* 1.3 68.0 + - - +
231A ASP* 2.7 30.4 + - - +
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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