Contacts of the helix formed by residues 235 - 249 (chain A) in PDB entry 3MY0
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 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A ARG 4.5 1.6 - - - +
213A TYR* 3.8 26.1 - - - +
229A LYS* 5.0 0.5 + - - -
231A PHE* 3.7 12.2 - - + -
232A SER* 3.0 22.3 + - - +
234A ARG* 1.3 79.6 - - - +
236A GLU* 1.3 64.5 + - - +
237A GLN* 3.2 3.4 - - - +
238A SER* 2.7 42.5 + - - -
239A TRP 3.5 3.6 + - - -
367A ASN* 4.5 3.9 + - - +
369A ARG* 3.2 32.7 + - - +
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Residues in contact with GLU 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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231A PHE* 5.2 0.7 - - - -
232A SER 3.4 5.1 + - - +
233A SER* 3.4 29.4 + - - +
234A ARG 3.7 0.6 - - - -
235A ASP* 1.3 77.3 - - - +
237A GLN* 1.3 64.4 + - + +
239A TRP* 3.2 16.2 + - + +
240A PHE* 3.1 20.4 + - - +
271A THR* 4.2 13.9 - - - +
273A LEU* 3.8 34.2 - - + +
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Residues in contact with GLN 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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235A ASP* 3.2 1.6 - - - +
236A GLU* 1.3 77.4 - - + +
238A SER* 1.3 59.6 + - - +
240A PHE* 3.7 14.0 - - + +
241A ARG* 3.1 28.1 + - - +
366A ASN* 3.3 44.1 + - - +
367A ASN* 3.5 25.9 + - + +
368A PRO* 4.4 11.8 - - + +
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Residues in contact with SER 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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231A PHE* 4.0 9.2 - - - -
235A ASP* 2.7 38.8 + - - -
237A GLN* 1.3 75.0 - - - +
239A TRP* 1.3 60.2 + - - +
241A ARG 3.5 0.2 + - - -
242A GLU* 3.0 32.3 + - - +
348A ASP* 5.4 1.6 - - - -
350A GLY* 3.6 17.4 + - - -
367A ASN* 3.0 20.2 + - - +
369A ARG* 3.4 17.7 + - - -
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Residues in contact with TRP 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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231A PHE* 3.6 41.8 - + + -
235A ASP 3.5 2.2 + - - -
236A GLU* 3.2 14.7 + - + +
238A SER* 1.3 80.9 - - - +
240A PHE* 1.3 87.2 + + + +
242A GLU* 3.9 1.8 - - - +
243A THR* 2.7 51.0 + - + -
262A SER* 3.2 15.8 + - - -
263A ASP* 4.0 16.6 - - - -
264A MET* 3.9 28.9 - - + -
273A LEU* 3.7 31.9 - - + -
274A TRP 3.0 30.4 + - - +
275A LEU* 4.5 3.4 - - + -
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Residues in contact with PHE 240 (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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236A GLU 3.1 10.0 + - - +
237A GLN* 3.7 17.0 - - + +
238A SER 3.3 0.4 - - - -
239A TRP* 1.3 101.2 - + + +
241A ARG* 1.3 56.5 + - + +
243A THR* 3.2 3.9 + - + -
244A GLU* 2.8 72.3 + - + +
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Residues in contact with ARG 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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237A GLN 3.1 12.0 + - - +
238A SER 4.0 0.2 - - - +
240A PHE* 1.3 83.2 - - + +
242A GLU* 1.3 58.2 + - - +
244A GLU* 3.4 12.1 + - - +
245A ILE* 3.0 47.0 + - + +
349A LEU 4.2 5.4 - - - +
350A GLY 3.3 31.2 - - - +
351A LEU 5.1 0.4 - - - -
352A ALA 3.3 24.4 + - - +
353A VAL* 4.2 1.6 - - - +
354A MET* 4.2 12.7 - - - +
363A ASP* 2.8 57.0 + - - -
364A ILE* 3.6 0.2 - - - +
365A GLY* 3.4 28.9 - - - +
367A ASN* 6.1 1.3 - - + -
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Residues in contact with GLU 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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229A LYS* 4.7 3.3 + - - +
231A PHE* 3.7 21.5 - - + -
238A SER 3.0 16.7 + - - +
239A TRP* 3.9 4.0 - - - +
241A ARG* 1.3 73.7 - - - +
243A THR* 1.3 64.4 + - - +
245A ILE* 4.1 2.6 - - - +
246A TYR* 3.1 58.8 + - + -
257A LEU* 5.8 1.6 - - - +
275A LEU* 3.9 23.0 - - + +
348A ASP* 3.3 19.2 + - - +
349A LEU* 3.1 36.4 + - + +
350A GLY* 4.1 7.0 + - - +
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Residues in contact with THR 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 TRP* 2.7 42.7 + - + -
240A PHE* 3.6 6.3 - - - -
242A GLU* 1.3 74.4 - - - +
244A GLU* 1.3 73.5 + - - +
246A TYR* 4.0 3.3 - - - +
247A ASN* 3.1 47.6 + - - +
259A PHE* 5.4 0.9 - - - -
262A SER* 2.7 35.7 + - - +
275A LEU* 5.0 4.7 - - - +
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Residues in contact with GLU 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 PHE* 2.8 64.5 + - + +
241A ARG* 3.7 15.0 - - - +
243A THR* 1.3 82.1 - - - +
245A ILE* 1.3 62.2 + - + +
247A ASN* 3.3 3.6 + - - +
248A THR* 2.9 38.2 + - - +
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Residues in contact with ILE 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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241A ARG* 3.0 41.6 + - + +
242A GLU* 4.1 3.8 - - - +
244A GLU* 1.3 76.4 - - - +
246A TYR* 1.3 58.8 + - - +
248A THR* 4.5 1.3 - - - -
249A VAL* 2.9 43.7 + - + +
251A LEU* 4.2 11.1 - - + +
326A ILE* 5.0 3.4 - - + -
349A LEU* 3.6 37.7 - - + +
352A ALA* 3.5 33.2 - - + +
354A MET* 4.4 20.6 - - + -
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Residues in contact with TYR 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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242A GLU* 3.1 52.1 + - + +
243A THR 4.2 1.1 - - - +
245A ILE* 1.3 79.9 - - - +
247A ASN* 1.3 61.1 + - - +
248A THR 3.7 0.3 + - - -
249A VAL 4.1 8.8 - - - +
251A LEU* 4.6 17.5 - - + -
256A ILE* 4.6 4.1 - - + +
257A LEU* 3.1 41.1 + - - +
258A GLY 5.3 0.2 - - - -
259A PHE* 3.4 59.3 - + + -
275A LEU* 4.2 9.2 - - + -
277A THR* 5.4 2.2 - - + -
347A ALA* 5.0 0.9 - - - -
349A LEU* 3.9 29.8 - - + +
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Residues in contact with ASN 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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195A GLN* 2.6 33.8 + - - +
243A THR* 3.1 41.7 + - - +
244A GLU* 3.9 4.6 - - - +
246A TYR* 1.3 76.3 - - - +
248A THR* 1.3 60.8 + - - +
249A VAL 3.8 0.7 - - - -
259A PHE* 3.7 9.7 - - - -
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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 GLU* 2.9 28.0 + - - +
245A ILE* 4.2 1.3 - - - -
247A ASN* 1.3 81.1 - - - +
249A VAL* 1.3 73.8 + - + +
250A LEU* 4.1 1.6 + - - +
354A MET* 5.4 5.8 - - + -
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Residues in contact with VAL 249 (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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245A ILE* 2.9 26.9 + - + +
246A TYR 4.1 9.4 - - - +
247A ASN 5.2 0.4 - - - -
248A THR* 1.3 93.2 - - + +
250A LEU* 1.3 63.3 + - - +
251A LEU* 3.0 21.2 + - + +
323A LYS* 3.9 12.3 - - + -
324A PRO* 3.8 26.9 - - + -
326A ILE* 4.1 16.4 - - + -
354A MET* 3.8 29.4 - - + -
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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