Contacts of the helix formed by residues 231 - 250 (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 ASP 231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ILE* 4.0 3.5 - - - +
226A TYR* 2.9 28.0 + - + +
229A HIS* 2.7 39.6 + - - +
230A ASP* 1.3 75.2 - - - +
232A ASN* 1.3 58.4 + - - +
233A ARG 3.4 2.2 - - - -
234A LYS* 3.2 32.1 + - + +
235A ALA* 2.9 28.1 + - - +
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Residues in contact with ASN 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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227A LEU* 3.7 22.6 + - - +
230A ASP* 3.1 32.6 + - - +
231A ASP* 1.3 75.7 - - - +
233A ARG* 1.3 56.8 + - - +
235A ALA* 4.3 1.1 - - - -
236A PHE* 2.9 31.7 + - - +
370A ALA* 3.5 11.6 - - + +
373A LYS* 3.6 36.2 - - + +
374A LEU* 3.7 22.4 - - + -
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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
----------------------------------------------------------
231A ASP 3.4 0.2 - - - -
232A ASN* 1.3 76.7 - - - +
234A LYS* 1.3 62.1 + - + +
236A PHE* 3.4 12.6 + - - -
237A ASP* 2.9 72.8 + - - +
374A LEU* 3.8 33.9 - - + +
375A GLY 5.2 1.4 + - - -
378A ALA* 3.8 22.4 - - - +
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Residues in contact with LYS 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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194A ILE* 5.8 1.8 - - - +
198A GLU* 4.7 8.2 + - - +
226A TYR* 3.7 42.2 - - + +
231A ASP* 3.2 26.5 + - + +
233A ARG* 1.3 79.8 - - + +
235A ALA* 1.3 62.5 + - - +
237A ASP* 4.0 3.9 - - - +
238A LEU* 3.0 27.7 + - - +
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Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ALA* 3.7 22.6 - - - +
226A TYR* 3.8 9.3 - - - +
227A LEU* 3.8 22.9 - - + +
231A ASP 2.9 17.1 + - - +
232A ASN 3.7 4.5 - - - +
234A LYS* 1.3 73.6 - - - +
236A PHE* 1.3 61.0 + - - +
238A LEU* 3.9 0.9 - - - +
239A ALA* 2.9 33.8 + - - +
366A ILE* 4.1 5.5 - - + +
370A ALA* 4.1 10.3 - - + -
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Residues in contact with PHE 236 (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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232A ASN 2.9 21.6 + - - +
233A ARG* 3.9 11.4 - - - +
235A ALA* 1.3 74.4 - - - +
237A ASP* 1.3 73.6 + - - +
239A ALA* 3.2 4.4 + - - +
240A ASP* 2.8 50.9 + - + +
367A ALA* 3.5 32.8 - - + +
370A ALA* 3.8 8.7 - - + +
371A GLY* 4.0 7.6 - - - -
374A LEU* 3.8 11.4 - - + -
378A ALA* 3.4 30.3 - - + -
381A GLN* 3.4 37.0 - - + -
382A GLY* 4.1 8.1 - - - -
385A TYR* 4.8 1.8 - + - -
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Residues in contact with ASP 237 (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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233A ARG* 2.9 60.0 + - - +
234A LYS* 4.0 4.3 - - - +
236A PHE* 1.3 85.7 - - - +
238A LEU* 1.3 57.3 + - - +
240A ASP* 3.7 5.4 + - - +
241A GLN* 3.1 29.3 + - - +
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Residues in contact with LEU 238 (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* 3.5 61.0 - - + +
222A LEU* 3.7 14.1 - - + -
223A ALA* 3.6 17.7 - - + +
226A TYR* 3.7 20.9 - - + -
234A LYS 3.0 18.2 + - - +
235A ALA 4.1 2.0 - - - +
237A ASP* 1.3 74.7 - - - +
239A ALA* 1.3 59.6 + - - +
241A GLN* 3.2 3.6 + - + -
242A LEU* 2.9 32.8 + - + +
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Residues in contact with ALA 239 (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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223A ALA* 4.3 6.5 - - + +
235A ALA 2.9 19.0 + - - +
236A PHE 3.8 1.6 - - - +
238A LEU* 1.3 76.7 - - - +
240A ASP* 1.3 63.5 + - - +
242A LEU* 3.4 1.7 + - - -
243A ILE* 3.0 31.1 + - - +
363A VAL* 3.5 35.0 - - + +
366A ILE* 4.0 8.1 - - + -
367A ALA* 3.8 16.6 - - + +
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Residues in contact with ASP 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A PHE* 2.8 39.3 + - + +
237A ASP* 3.7 5.5 - - - +
239A ALA* 1.3 78.3 - - - +
241A GLN* 1.3 59.9 + - - +
243A ILE* 3.4 3.3 + - - +
244A LYS* 2.8 62.0 + - - +
367A ALA* 4.6 0.8 - - - +
381A GLN* 4.3 9.2 - - - +
385A TYR* 2.6 40.3 + - + -
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Residues in contact with GLN 241 (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* 3.8 16.6 - - - +
237A ASP 3.1 18.9 + - - +
238A LEU* 3.2 4.9 + - + +
240A ASP* 1.3 78.7 - - - +
242A LEU* 1.3 53.1 + - - +
244A LYS* 3.3 23.3 + - - +
245A ASP* 2.8 64.3 + - - +
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Residues in contact with LEU 242 (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* 3.5 41.7 - - + +
219A ARG* 3.7 31.5 - - + +
220A ALA* 3.4 42.8 - - + +
223A ALA* 5.5 1.1 - - + -
238A LEU* 2.9 17.4 + - + +
239A ALA* 3.7 5.4 - - - +
241A GLN* 1.3 74.1 - - - +
243A ILE* 1.3 61.7 + - - +
245A ASP* 3.3 0.7 + - - +
246A ALA* 2.9 28.6 + - - +
275A PHE* 4.3 9.9 - - + -
360A LEU* 5.6 0.4 - - + -
363A VAL* 3.9 18.8 - - + -
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Residues in contact with ILE 243 (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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239A ALA 3.0 24.1 + - - +
240A ASP 3.7 3.6 - - - +
242A LEU* 1.3 76.8 - - - +
244A LYS* 1.3 63.2 + - - +
246A ALA* 3.3 7.8 + - - +
247A ASP* 3.0 30.6 + - - +
360A LEU* 4.5 4.7 - - + -
363A VAL* 3.7 17.0 - - + +
364A TYR* 3.4 64.2 - - + +
367A ALA* 4.4 0.7 - - + -
385A TYR* 3.8 40.6 - - + +
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Residues in contact with LYS 244 (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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240A ASP* 2.8 49.0 + - - +
241A GLN* 3.3 28.3 + - - +
243A ILE* 1.3 76.6 - - + +
245A ASP* 1.3 57.7 + - - +
247A ASP* 3.2 8.6 + - - +
248A THR* 2.9 35.7 + - - +
381A GLN* 5.2 3.8 + - - -
385A TYR* 4.3 7.4 - - - +
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Residues in contact with ASP 245 (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* 5.6 1.5 - - - +
216A TYR* 3.9 11.6 + - + +
219A ARG* 2.9 40.5 + - - +
241A GLN* 2.8 47.2 + - - +
242A LEU 3.8 4.3 - - - +
244A LYS* 1.3 71.8 - - - +
246A ALA* 1.3 62.4 + - - +
248A THR* 4.0 5.8 + - - +
249A SER* 2.8 32.0 + - - -
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Residues in contact with ALA 246 (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* 4.1 9.0 - - + -
242A LEU 2.9 17.3 + - - +
243A ILE* 3.6 5.8 - - + +
245A ASP* 1.3 75.2 - - - +
247A ASP* 1.3 59.4 + - - +
249A SER* 3.3 5.3 + - - -
250A GLY* 2.9 28.6 + - - -
251A SER 3.4 3.3 + - - -
252A TYR* 3.4 39.4 - - + +
275A PHE* 5.4 1.3 - - + -
360A LEU* 4.4 15.0 - - + -
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Residues in contact with ASP 247 (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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243A ILE* 3.0 27.9 + - - +
244A LYS* 3.2 10.5 + - - +
246A ALA* 1.3 77.4 - - - +
248A THR* 1.3 64.6 + - - +
250A GLY* 3.4 9.9 + - - -
252A TYR 4.5 6.2 - - - +
253A ALA* 5.5 3.1 - - - +
360A LEU* 5.6 2.1 - - - +
364A TYR* 4.1 10.5 + - - -
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Residues in contact with THR 248 (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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244A LYS* 2.9 24.4 + - - +
245A ASP* 4.0 7.1 + - - -
247A ASP* 1.3 74.5 - - - +
249A SER* 1.3 63.5 + - - +
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Residues in contact with SER 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A TYR* 3.3 18.0 + - - -
245A ASP 2.8 21.9 + - - -
246A ALA* 3.3 2.3 + - - -
248A THR* 1.3 78.3 - - - +
250A GLY* 1.3 59.9 + - - +
251A SER* 3.1 30.7 + - - -
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Residues in contact with GLY 250 (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 LYS* 5.3 0.2 + - - -
246A ALA 2.9 11.4 + - - -
247A ASP* 3.4 6.8 + - - -
248A THR 3.4 3.4 + - - -
249A SER* 1.3 77.1 - - - +
251A SER* 1.3 60.6 + - - +
252A TYR* 3.3 8.2 + - - +
253A ALA* 5.5 1.7 - - - +
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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
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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