Contacts of the helix formed by residues 226 - 240 (chain Y) in PDB entry 5MG3
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 LEU 226 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202Y ALA* 4.4 4.9 - - - -
222Y LEU 5.0 1.3 - - - +
223Y VAL* 3.6 33.6 + - + +
224Y ALA 3.0 4.4 + - - -
225Y VAL* 1.3 94.7 - - + +
227Y VAL* 1.4 54.2 + - - +
228Y PHE* 3.1 27.1 - - + -
229Y ALA* 2.8 35.2 + - + +
230Y VAL* 3.6 4.0 + - - +
398Y PRO* 4.0 21.4 - - + +
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Residues in contact with VAL 227 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199Y LEU 4.2 10.3 - - - +
200Y PRO* 3.4 26.9 - - + +
201Y PRO* 4.1 2.0 - - + -
202Y ALA* 4.0 14.3 - - - +
224Y ALA 3.5 19.1 - - - +
225Y VAL* 3.4 7.8 + - - +
226Y LEU* 1.4 77.7 - - - +
228Y PHE* 1.3 57.1 + - + +
230Y VAL* 3.4 3.6 + - + +
231Y THR* 2.8 44.6 + - + +
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Residues in contact with PHE 228 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225Y VAL 3.5 20.4 - - - -
226Y LEU* 3.7 25.6 - - + -
227Y VAL* 1.3 78.7 - - + +
229Y ALA* 1.4 72.7 + - + -
231Y THR* 3.7 7.6 + - - -
232Y PHE* 2.9 30.0 + - - +
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Residues in contact with ALA 229 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226Y LEU* 2.8 19.5 + - + +
228Y PHE* 1.4 81.1 - - + +
230Y VAL* 1.3 58.0 + - - +
232Y PHE* 3.4 7.6 + - + +
233Y PHE* 2.9 46.9 + - + -
398Y PRO* 4.3 18.6 - - + -
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Residues in contact with VAL 230 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199Y LEU* 4.1 29.4 - - + +
202Y ALA* 3.8 36.8 - - + +
226Y LEU 3.6 1.6 + - - +
227Y VAL* 3.4 8.4 + - - +
229Y ALA* 1.3 74.9 - - - +
231Y THR* 1.4 60.4 + - + +
233Y PHE* 3.5 3.4 + - - +
234Y VAL* 3.1 28.3 + - + +
397Y VAL* 3.6 27.6 - - + -
398Y PRO* 3.9 15.0 - - + +
399Y PHE* 4.2 13.5 - - + +
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Residues in contact with THR 231 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482E THR* 4.7 16.2 - - + -
483E ALA* 6.2 2.7 - - - -
486E SER* 5.6 5.4 - - - +
199Y LEU* 5.5 7.9 - - + +
227Y VAL* 2.8 41.1 + - + +
228Y PHE* 3.7 9.2 + - - -
230Y VAL* 1.4 76.0 - - + +
232Y PHE* 1.4 53.5 + - - +
234Y VAL* 3.7 5.5 - - + +
235Y VAL* 2.7 46.9 + - - +
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Residues in contact with PHE 232 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228Y PHE 2.9 22.1 + - - +
229Y ALA* 3.6 8.5 - - - +
230Y VAL 3.4 0.2 - - - -
231Y THR* 1.4 73.4 + - - +
233Y PHE* 1.4 78.3 + + - +
235Y VAL* 3.9 9.1 - - + -
236Y PHE* 2.9 46.0 + + - +
391Y MET* 3.8 29.8 - - + -
395Y MET* 6.1 0.2 - - + -
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Residues in contact with PHE 233 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229Y ALA* 2.9 36.6 + - + +
230Y VAL* 3.5 4.9 + - - +
231Y THR 3.4 0.4 - - - -
232Y PHE* 1.4 75.2 - + - +
234Y VAL* 1.4 61.2 + - + +
236Y PHE* 3.1 25.0 + + + +
237Y VAL* 3.3 12.7 - - - +
388Y PRO* 5.4 0.6 - - - +
391Y MET* 3.7 24.2 - - + -
392Y ARG* 3.5 47.1 - - + +
395Y MET* 4.5 15.0 - - + -
396Y LYS 3.3 24.9 - - - -
397Y VAL* 3.9 21.1 - - + -
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Residues in contact with VAL 234 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482E THR* 4.0 26.9 - - + +
199Y LEU* 4.1 23.6 - - + -
230Y VAL* 3.1 19.7 + - + +
231Y THR* 3.3 6.0 + - - +
233Y PHE* 1.4 75.9 - - + +
235Y VAL* 1.3 60.9 + - - +
237Y VAL* 3.6 14.3 - - + +
238Y GLU* 3.5 21.1 + - + +
399Y PHE* 6.3 0.2 - - + -
406Y LEU* 5.5 7.0 - - + +
410Y VAL* 3.8 32.9 - - + +
413Y ILE* 6.4 1.1 - - + -
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Residues in contact with VAL 235 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475E THR* 4.7 19.3 - - + +
478E VAL* 4.5 14.4 - - + -
479E ALA* 4.0 32.5 - - + +
482E THR* 4.7 13.5 - - + +
231Y THR* 2.7 29.5 + - - +
232Y PHE* 4.0 10.5 - - + +
234Y VAL* 1.3 73.4 - - - +
236Y PHE* 1.3 51.6 + - - +
238Y GLU* 2.9 8.4 + - + +
239Y ARG* 2.7 37.5 + - + +
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Residues in contact with PHE 236 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232Y PHE* 2.9 39.0 + + + +
233Y PHE* 3.1 13.6 + + + +
235Y VAL* 1.3 75.2 - - - +
237Y VAL* 1.3 58.0 + - - +
239Y ARG* 3.7 14.8 - - + +
240Y GLY* 3.5 15.6 + - - -
387Y ILE* 4.1 15.0 - - + -
388Y PRO* 3.8 30.1 - - + +
391Y MET* 3.6 50.0 - - + -
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Residues in contact with VAL 237 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233Y PHE 3.3 16.8 - - - +
234Y VAL* 3.6 15.3 - - + +
236Y PHE* 1.3 75.6 - - - +
238Y GLU* 1.3 61.1 - - - +
240Y GLY* 3.5 10.0 + - - -
241Y GLN* 3.9 15.6 + - - +
270Y ASN* 5.2 1.4 + - - -
388Y PRO* 4.2 23.1 - - + +
392Y ARG* 5.8 2.5 - - - +
406Y LEU 5.0 9.0 - - - +
407Y LEU* 4.1 25.1 - - + -
410Y VAL* 4.1 23.8 - - + -
411Y VAL* 5.4 4.0 - - + -
414Y MET* 4.6 7.4 - - + -
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Residues in contact with GLU 238 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478E VAL* 3.9 35.9 - - + +
481E VAL* 6.0 2.8 - - - +
482E THR* 4.4 15.6 + - - +
234Y VAL* 3.5 13.0 + - + +
235Y VAL* 2.9 13.7 + - - +
237Y VAL* 1.3 73.8 - - - +
239Y ARG* 1.3 63.8 + - - +
241Y GLN* 3.3 23.6 - - - +
268Y LYS* 2.7 37.0 + - - +
410Y VAL* 5.2 2.9 - - + +
413Y ILE* 5.7 3.1 - - - +
414Y MET* 3.4 32.4 - - + +
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Residues in contact with ARG 239 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469E GLN 3.4 20.4 + - - +
470E GLU* 2.7 60.0 + - - +
471E THR* 3.4 4.4 + - - +
474E THR* 3.0 30.2 + - - -
475E THR* 3.1 16.6 + - - +
478E VAL* 4.9 4.6 - - + +
235Y VAL* 2.7 24.2 + - + +
236Y PHE* 3.7 18.2 - - + +
237Y VAL 3.4 0.2 - - - -
238Y GLU* 1.3 72.9 + - - +
240Y GLY* 1.3 60.2 + - - +
241Y GLN 3.2 13.2 + - - +
243Y ARG* 4.2 18.8 - - - +
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Residues in contact with GLY 240 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469E GLN* 5.7 3.4 - - - +
236Y PHE 3.5 6.5 + - - -
237Y VAL 3.5 8.4 + - - -
238Y GLU 3.3 1.2 - - - -
239Y ARG* 1.3 73.7 - - - +
241Y GLN* 1.3 62.8 + - - +
242Y ARG* 3.7 3.3 + - - +
269Y VAL* 5.2 0.3 - - - +
270Y ASN* 3.0 21.3 + - - +
380Y TYR* 4.8 3.6 + - - -
384Y ILE* 5.0 8.6 - - - +
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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
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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