Contacts of the helix formed by residues 230 - 241 (chain C) in PDB entry 5T0I
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 MET 230 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256B ILE* 3.4 43.3 - - + +
217C SER 4.2 9.0 - - - +
220C VAL* 3.9 37.0 - - + +
221C GLN* 4.3 19.5 - - + +
224C ILE* 4.8 3.5 - - - +
225C GLY 4.5 12.6 - - - +
226C GLU* 5.1 4.5 - - - +
228C ALA* 3.2 9.3 - - - +
229C ARG* 1.3 74.7 - - - +
231C VAL* 1.3 60.2 + - + +
232C ARG 3.0 0.2 - - - -
233C GLU* 2.4 37.7 + - - +
234C LEU* 2.9 10.7 + - - -
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Residues in contact with VAL 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B ILE* 4.5 13.2 - - + -
229C ARG* 3.9 7.2 - - + +
230C MET* 1.3 79.1 - - + +
232C ARG* 1.3 57.6 + - + +
234C LEU* 3.6 13.4 - - + +
235C PHE* 2.7 32.7 + - - +
264C GLY 5.3 1.8 - - - +
268C GLU* 3.9 47.3 - - + +
269C VAL* 4.3 9.9 - - + +
271C ARG* 5.1 6.7 - - + -
272C THR* 3.4 19.2 + - - +
275C GLU* 3.5 8.0 - - - +
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Residues in contact with ARG 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B VAL* 3.5 9.7 - - + +
174B MET* 4.9 12.4 - - - +
249B ARG* 3.1 59.0 + - - +
250B VAL* 5.4 0.8 - - - +
251B VAL* 3.9 14.7 - - + +
229C ARG* 2.9 68.9 + - + +
230C MET 3.0 0.8 - - - -
231C VAL* 1.3 86.6 - - + +
233C GLU* 1.3 60.3 + - - +
235C PHE* 3.0 42.7 - - - +
236C VAL 3.4 2.3 + - - -
271C ARG* 6.0 0.2 - - + -
275C GLU* 2.4 39.7 + - - +
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Residues in contact with GLU 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B PRO* 2.8 40.7 - - - +
170B LEU* 3.2 15.8 - - - +
172B THR* 5.3 0.7 - - - -
173B VAL* 3.2 20.6 - - + +
224C ILE* 3.5 38.8 - - + +
228C ALA* 3.7 16.6 - - + +
229C ARG 4.0 2.9 + - - +
230C MET 2.4 31.3 + - - +
232C ARG* 1.3 67.3 - - - +
234C LEU* 1.3 58.1 + - - +
235C PHE 3.2 0.2 - - - -
236C VAL* 3.0 27.3 + - - +
237C MET* 3.3 11.1 + - - +
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Residues in contact with LEU 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C VAL* 5.6 3.4 - - - -
215C SER* 4.9 15.0 - - - +
217C SER* 4.7 19.3 - - - +
220C VAL* 5.7 8.1 - - + -
224C ILE* 4.3 5.0 - - + +
230C MET 2.9 9.2 + - - +
231C VAL* 3.7 13.7 - - + +
233C GLU* 1.3 72.9 - - - +
235C PHE* 1.3 60.3 + - - +
236C VAL 3.0 5.2 - - - -
237C MET* 3.1 22.4 + - + +
238C ALA* 3.2 13.5 + - + +
246C ILE* 5.5 11.4 - - + -
269C VAL* 5.3 8.3 - - + -
272C THR* 4.0 24.7 - - + +
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Residues in contact with PHE 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B VAL 3.2 26.5 - - - -
174B MET* 4.9 1.8 - - - -
231C VAL 2.7 14.8 + - - +
232C ARG* 3.0 36.6 - - - +
233C GLU 3.2 0.2 - - - -
234C LEU* 1.3 76.3 - - - +
236C VAL* 1.3 62.2 + - + +
238C ALA 4.2 0.2 - - - -
239C ARG* 3.7 14.3 + - - -
272C THR* 4.3 9.4 - - + -
275C GLU* 3.2 48.2 - - + +
276C LEU* 3.3 40.1 - - + +
279C GLN* 3.2 37.9 - - + -
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Residues in contact with VAL 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B THR* 3.6 23.8 - - + +
173B VAL* 3.5 35.7 - - + +
232C ARG 3.4 9.4 + - - +
233C GLU* 3.0 16.9 + - - +
235C PHE* 1.3 77.9 - - + +
237C MET* 1.3 55.0 + - - +
238C ALA 3.2 0.2 - - - -
239C ARG* 3.0 30.9 + - - +
240C GLU* 2.7 42.9 + - + +
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Residues in contact with MET 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C VAL* 5.0 7.2 - - + -
132C ASP* 5.1 0.4 - - - +
135C VAL* 3.7 32.3 - - + -
212C ILE* 5.3 0.2 - - - -
220C VAL* 6.6 0.4 - - + -
223C PHE* 4.1 27.8 - - + -
224C ILE* 4.3 12.1 - - + -
233C GLU 3.3 13.2 + - - +
234C LEU* 3.1 17.5 + - + +
236C VAL* 1.3 79.4 - - - +
238C ALA* 1.3 57.8 + - - +
240C GLU* 3.3 28.4 - - - +
241C HIS* 3.0 49.4 + - + +
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Residues in contact with ALA 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C ILE* 4.6 12.8 - - + -
234C LEU* 3.2 14.8 + - + +
236C VAL 3.2 0.2 - - - -
237C MET* 1.3 76.6 - - - +
239C ARG* 1.3 60.1 + - - +
241C HIS* 3.2 16.5 + - - +
242C ALA 4.1 4.9 - - - +
243C PRO* 5.0 0.3 - - - +
244C SER* 4.6 5.3 + - - +
246C ILE* 4.7 10.8 - - + -
276C LEU* 3.9 29.8 - - + -
289C ILE* 4.1 19.3 - - + +
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Residues in contact with ARG 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B THR* 3.5 21.4 + - - +
175B LYS* 4.3 7.9 - - - +
235C PHE* 3.7 21.4 + - - +
236C VAL* 3.0 41.0 + - - +
238C ALA* 1.3 77.7 - - - +
240C GLU* 1.3 61.8 + - - +
241C HIS 2.9 12.3 - - - +
276C LEU* 4.5 6.5 - - + +
279C GLN* 3.3 34.4 + - - +
280C LEU* 6.0 5.4 - - + -
284C GLU* 3.7 30.4 + - + +
285C ALA 4.7 13.0 - - - +
289C ILE* 5.6 2.2 - - - -
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Residues in contact with GLU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C VAL* 4.0 20.2 - - - +
132C ASP* 4.4 13.1 - - - +
223C PHE* 5.7 0.5 - - - -
236C VAL* 2.7 26.1 + - + +
237C MET* 3.3 35.8 - - - +
239C ARG* 1.3 75.9 - - - +
241C HIS* 1.3 60.4 + - + +
242C ALA 4.0 0.3 + - - -
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Residues in contact with HIS 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C ASP* 3.0 54.2 + - + +
135C VAL* 3.8 27.5 - - + +
136C SER* 5.0 7.0 - - - -
210C THR* 6.1 0.9 - - + -
212C ILE* 3.6 31.0 - - + +
237C MET* 3.0 39.2 + - + +
238C ALA 3.2 6.4 - - - +
239C ARG* 2.9 17.2 - - - +
240C GLU* 1.3 78.2 - - + +
242C ALA* 1.3 68.9 + - - +
243C PRO* 3.7 1.6 - - - +
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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