Contacts of the helix formed by residues 225 - 233 (chain C) in PDB entry 3LL8
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 GLY 225 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205C GLU* 3.7 11.2 - - - -
224C TYR* 1.3 85.0 - - - +
226C PRO* 1.3 72.3 - - - +
227C MET 3.3 2.5 - - - -
228C CYS* 3.3 3.3 + - - +
229C ASP* 2.9 37.6 + - - +
258C TYR* 6.2 0.4 - - - -
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Residues in contact with PRO 226 (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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359A GLU* 5.0 6.1 - - - +
203C SER* 3.8 12.3 - - - +
205C GLU* 3.5 35.0 - - + +
206C ILE* 4.0 23.5 - - + +
211C ASP 5.5 0.4 - - - +
215C LEU* 4.0 23.1 - - + -
225C GLY* 1.3 84.0 - - - +
227C MET* 1.3 58.2 + - - +
229C ASP* 3.3 1.8 + - - +
230C ILE* 2.9 35.5 + - - +
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Residues in contact with MET 227 (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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148C ARG* 3.3 30.3 - - - +
187C LEU* 3.8 27.6 - - + -
215C LEU* 4.1 15.7 - - + +
216C ASP 4.1 9.4 - - - +
217C ARG* 3.4 20.2 - - - +
219C LYS* 3.7 35.4 - - - +
221C PRO* 4.1 13.2 - - + -
222C PRO* 4.0 13.9 - - + -
225C GLY 3.3 0.4 - - - -
226C PRO* 1.3 78.9 - - - +
228C CYS* 1.3 66.9 + - - +
230C ILE* 3.5 5.8 + - - +
231C LEU* 3.4 25.0 + - + +
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Residues in contact with CYS 228 (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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221C PRO* 5.3 1.6 - - - -
222C PRO* 3.4 24.2 - - - +
223C ALA* 3.6 24.0 - - - -
224C TYR* 3.7 14.3 + - - +
225C GLY 3.3 9.5 + - - +
227C MET* 1.3 78.0 - - - +
229C ASP* 1.3 60.4 + - - +
231C LEU* 3.1 6.2 + - - -
232C TRP* 2.9 49.9 + - - +
256C CYS* 4.0 14.6 - - - -
257C SER* 4.2 10.1 - - - -
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Residues in contact with ASP 229 (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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202C LEU 3.8 8.7 - - - +
203C SER* 2.9 36.9 + - - -
204C PRO* 3.7 0.9 - - - +
205C GLU* 4.5 2.8 - - - +
224C TYR* 5.3 0.3 - - - -
225C GLY* 2.9 30.1 + - - +
226C PRO 3.7 0.7 - - - +
227C MET 3.3 0.2 - - - -
228C CYS* 1.3 75.4 - - - +
230C ILE* 1.3 62.0 + - - +
233C SER* 2.8 31.0 + - - -
257C SER* 2.7 38.1 + - - +
258C TYR* 3.6 23.3 - - + -
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Residues in contact with ILE 230 (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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187C LEU* 3.7 40.4 - - + +
188C ALA* 5.6 0.2 - - + -
198C VAL* 4.0 16.3 - - + +
199C HIS 4.1 1.6 + - - +
200C GLY 2.9 24.4 + - - -
201C GLY 3.2 18.3 + - - +
203C SER* 5.1 0.4 - - - -
206C ILE* 3.7 25.6 - - + -
212C ILE* 4.5 13.5 - - + -
215C LEU* 3.8 20.0 - - + -
226C PRO 2.9 23.1 + - - +
227C MET 3.7 4.7 - - - +
228C CYS 3.3 0.2 - - - -
229C ASP* 1.3 77.0 - - - +
231C LEU* 1.3 66.3 + - + +
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Residues in contact with LEU 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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148C ARG* 3.2 49.6 - - + +
149C GLY 4.2 7.0 - - - +
150C ASN* 3.5 17.0 - - - +
187C LEU* 4.4 11.4 - - + +
199C HIS* 3.4 24.8 - - + -
200C GLY* 4.1 4.9 - - - +
221C PRO* 3.7 35.7 - - + -
227C MET* 3.4 20.4 - - + +
228C CYS 3.1 6.1 + - - +
230C ILE* 1.3 84.1 - - + +
232C TRP* 1.3 67.7 + - + +
233C SER 3.9 0.2 - - - -
281C HIS* 3.8 2.6 + - - -
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Residues in contact with TRP 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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159A TYR* 4.5 7.0 - - - -
150C ASN* 3.3 41.2 + - + +
153C CYS* 5.9 0.7 - - - -
156C LEU* 3.8 33.2 - - + -
221C PRO* 5.4 6.6 - - + +
228C CYS* 2.9 38.7 + - - +
231C LEU* 1.3 89.5 - - + +
233C SER* 1.3 65.0 + - - +
234C ASP* 4.0 0.2 - - - +
251C ASN* 4.1 0.7 + - - -
254C ARG* 3.8 63.4 - - + +
256C CYS* 3.5 14.1 - - - -
257C SER* 3.8 17.1 - - - -
281C HIS* 2.9 19.3 + + - -
507C PO4 5.4 1.6 - - - -
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Residues in contact with SER 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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200C GLY* 3.1 19.7 - - - +
201C GLY* 3.2 16.3 - - - -
202C LEU 3.2 21.9 + - - -
229C ASP 2.8 22.3 + - - -
231C LEU 3.9 0.4 - - - -
232C TRP* 1.3 82.4 - - - +
234C ASP* 1.3 59.0 + - - +
257C SER* 3.7 10.9 + - - -
258C TYR* 3.3 19.7 - - - +
260C TYR* 3.7 7.6 - - - -
279C ARG* 3.2 6.4 + - - -
281C HIS* 3.4 2.1 - - - -
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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