Contacts of the helix formed by residues 232 - 241 (chain F) in PDB entry 4RYD
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 THR 232 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453E ASP* 3.8 16.0 + - - +
565E LYS* 6.5 1.3 - - - -
230F GLU* 3.2 40.1 + - + +
231F VAL* 1.3 75.3 - - - +
233F ASP* 1.3 66.1 + - - +
234F ALA* 3.4 8.6 + - - +
235F VAL* 3.0 27.3 + - + +
236F GLU* 3.0 23.2 + - - +
1N 2UE 3.5 10.5 - - - -
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Residues in contact with ASP 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530E ASP* 4.4 8.0 - - - +
565E LYS* 6.1 6.2 - - + -
232F THR* 1.3 73.1 - - - +
234F ALA* 1.3 58.6 + - - +
236F GLU* 3.2 5.3 + - - +
237F ALA* 2.8 27.8 + - - +
267F ALA* 3.1 33.0 + - + +
268F ARG* 3.5 1.4 + - - -
269F LEU* 2.9 32.4 + - + +
270F ALA* 2.9 30.1 + - - +
1N 2UE 3.7 15.6 + - - +
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Residues in contact with ALA 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451E ILE* 4.0 20.9 - - + -
453E ASP* 3.7 34.3 - - + +
567E THR* 4.5 3.1 - - + +
232F THR* 3.2 2.3 + - - +
233F ASP* 1.3 79.8 - - - +
235F VAL* 1.3 56.7 + - + +
237F ALA* 3.3 2.0 + - - +
238F ARG* 2.9 40.3 + - - +
269F LEU* 4.1 16.0 - - + +
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Residues in contact with VAL 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F VAL* 3.8 29.2 - - + +
176F ASN* 4.4 5.2 - - - +
178F GLN* 5.6 2.0 - - - +
226F MET* 3.6 40.8 - - + +
230F GLU 3.6 15.0 - - - +
231F VAL* 4.4 6.7 - - + -
232F THR* 3.0 28.7 + - + +
234F ALA* 1.3 76.8 - - + +
236F GLU* 1.3 62.5 + - - +
238F ARG* 3.5 0.6 + - - +
239F SER* 2.8 29.1 + - - -
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Residues in contact with GLU 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226F MET* 4.4 5.2 - - + -
231F VAL* 3.8 14.0 - - + +
232F THR 3.0 11.8 + - - +
233F ASP* 3.5 6.5 - - - +
235F VAL* 1.3 78.2 - - - +
237F ALA* 1.3 57.3 + - - +
239F SER* 3.1 4.2 + - - -
240F LEU* 2.9 38.2 + - + +
254F TRP* 3.9 20.0 - - + -
270F ALA* 3.8 14.6 - - + +
308F TYR* 2.5 30.9 + - - -
1N 2UE 2.7 31.8 + - - -
2N ARG* 3.0 20.6 + - - +
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Residues in contact with ALA 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451E ILE* 3.9 16.4 - - + +
233F ASP 2.8 19.9 + - - +
234F ALA 3.8 4.3 - - - +
236F GLU* 1.3 73.4 - - - +
238F ARG* 1.3 57.2 - - - +
241F GLY* 2.9 27.5 + - - -
269F LEU* 3.5 37.5 - - + +
270F ALA* 4.2 2.6 - - - +
273F ALA* 3.8 15.4 - - + +
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Residues in contact with ARG 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451E ILE* 3.7 43.2 + - + +
453E ASP 6.0 1.1 - - - +
474E CYS* 5.9 6.7 - - - -
477E GLU* 6.1 2.0 - - - +
173F PHE* 3.7 24.6 - - - -
175F VAL* 3.4 27.5 - - + +
178F GLN* 2.7 42.7 + - - +
234F ALA* 2.9 24.3 + - - +
235F VAL* 4.0 3.8 - - - +
236F GLU 3.3 0.2 - - - -
237F ALA* 1.3 76.4 - - - +
239F SER* 1.3 61.3 + - - +
241F GLY* 3.8 1.8 - - - -
242F LEU* 3.2 24.4 + - - +
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Residues in contact with SER 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F LEU* 3.8 20.9 - - - +
175F VAL* 3.7 3.5 - - - +
224F VAL* 3.5 22.9 - - - +
226F MET* 3.3 33.7 - - - +
235F VAL 2.8 14.5 + - - -
236F GLU 3.1 8.6 + - - -
238F ARG* 1.3 75.2 - - - +
240F LEU* 1.3 64.5 + - - +
241F GLY 3.1 1.6 - - - -
242F LEU* 3.2 17.9 + - - +
250F TYR* 3.8 8.0 - - - -
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Residues in contact with LEU 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F LEU* 3.5 21.1 - - + -
236F GLU* 2.9 23.2 + - + +
239F SER* 1.3 74.2 - - - +
241F GLY* 1.3 57.3 + - - +
242F LEU 3.4 0.4 - - - -
244F PRO* 5.4 0.3 - - - +
250F TYR* 3.5 21.0 + - + -
254F TRP* 5.3 3.1 - - + -
270F ALA* 4.1 22.7 - - + +
273F ALA* 4.0 14.1 - - + +
274F PHE* 3.6 29.4 - - + -
277F GLY* 5.8 1.0 - - - -
287F SER* 5.4 0.3 + - - -
289F PHE* 3.7 36.9 - - + -
291F TRP* 3.9 26.9 - - + -
308F TYR* 5.3 2.0 - - + -
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Residues in contact with GLY 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237F ALA 2.9 16.9 + - - -
238F ARG* 3.8 4.3 - - - -
240F LEU* 1.3 78.3 - - - +
242F LEU* 1.3 62.2 + - - +
243F ASN 3.3 0.7 + - - -
244F PRO* 3.2 23.9 - - - +
273F ALA* 4.4 9.2 - - - +
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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