Contacts of the helix formed by residues 226 - 235 (chain C) in PDB entry 1M54
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 ALA 226 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C HIS* 4.6 7.4 - - + +
129C ASP* 6.0 0.2 - - - +
224C ARG 3.6 4.0 + - - -
225C ASN* 1.3 77.8 + - - +
227C SER* 1.3 63.2 + - - +
228C ASN 3.2 1.2 + - - -
229C PRO* 3.3 15.6 - - - +
230C LEU* 3.3 25.3 + - + +
1320C HEM 3.2 38.3 - - + +
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Residues in contact with SER 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C ILE* 5.1 1.1 - - - -
125C ARG* 3.6 13.7 - - - +
126C MET* 4.0 23.3 - - - +
129C ASP* 3.5 33.9 + - - +
225C ASN* 2.5 25.6 + - - -
226C ALA* 1.3 72.7 - - - +
228C ASN* 1.3 66.3 + - - +
230C LEU* 4.2 4.0 - - - -
231C ALA* 3.0 25.3 + - - +
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Residues in contact with ASN 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LYS* 5.6 0.2 - - - +
122C ILE* 2.8 48.0 - - + +
126C MET* 4.4 7.3 - - + +
222C GLN 3.1 23.6 + - - +
225C ASN 3.3 5.9 + - - +
226C ALA 3.2 1.6 + - - -
227C SER* 1.3 80.5 - - - +
229C PRO* 1.3 76.2 - - + +
231C ALA 3.3 5.0 + - - -
232C HIS* 3.5 9.9 + - - -
257C THR* 2.7 32.1 + - - +
259C GLY* 3.5 17.6 - - - +
314C VAL* 4.4 0.6 - - - +
1310C PLP 4.7 1.0 + - - -
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Residues in contact with PRO 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C ASN 4.0 4.9 - - - +
226C ALA 3.5 8.5 - - - +
228C ASN* 1.3 102.8 - - + +
230C LEU* 1.3 67.5 - - - +
232C HIS* 3.1 4.3 + - - +
233C TYR* 3.0 17.3 + - - +
259C GLY* 4.5 12.6 - - - +
262C THR* 4.6 4.3 - - + -
263C GLY* 3.4 10.2 - - - -
314C VAL* 3.7 35.7 - - + +
1320C HEM 3.1 38.1 - - + -
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Residues in contact with LEU 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C HIS* 3.7 34.1 - - + +
66C HIS* 4.5 3.8 - - + +
67C HIS* 3.7 24.2 - - + +
125C ARG* 3.5 21.3 - - - +
129C ASP* 5.0 4.0 - - - +
226C ALA* 3.4 23.6 - - + +
227C SER* 3.8 5.6 - - - +
229C PRO* 1.3 84.3 - - - +
231C ALA* 1.3 57.5 + - - +
233C TYR* 3.0 4.0 + - + +
234C ASP* 2.8 33.6 + - - +
1320C HEM 3.4 39.5 - - + -
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Residues in contact with ALA 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ARG* 4.2 18.4 - - + +
122C ILE* 4.6 3.1 - - + +
125C ARG* 3.2 35.6 - - + +
227C SER 3.0 18.4 + - - +
228C ASN 3.8 4.3 - - - +
229C PRO 3.2 0.4 - - - -
230C LEU* 1.3 75.6 - - - +
232C HIS* 1.3 55.4 + - - +
235C THR* 2.7 37.1 + - - -
236C THR* 3.5 5.0 + - - -
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Residues in contact with HIS 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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118C VAL* 3.8 11.5 + - + +
119C LYS* 5.7 1.2 - - - +
121C ARG* 3.8 29.8 - - + +
122C ILE* 3.5 14.8 - - + +
228C ASN* 3.5 22.8 + - - -
229C PRO 3.1 7.0 + - - +
231C ALA* 1.3 77.5 - - - +
233C TYR* 1.3 55.3 + - - +
236C THR* 3.1 29.6 + - + +
237C ALA* 2.8 32.1 + - - +
259C GLY 3.6 0.2 - - - -
260C THR* 2.9 64.5 + - + +
263C GLY* 4.1 4.9 - - - -
264C ILE* 3.6 4.3 - - + +
1310C PLP 4.3 0.6 + - - -
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Residues in contact with TYR 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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54C TRP* 4.7 1.0 + - - -
60C ALA* 5.9 3.1 - - - +
67C HIS* 3.4 38.4 - + - -
229C PRO 3.0 12.1 + - - +
230C LEU* 3.0 13.2 + - + +
232C HIS* 1.3 75.3 - - - +
234C ASP* 1.3 69.5 + - - +
237C ALA* 3.0 20.0 - - - +
263C GLY* 3.3 23.3 - - - +
266C ARG* 3.7 8.3 - - + -
267C LYS* 3.2 60.7 + - + -
270C GLU* 2.7 25.2 + - - -
1320C HEM 3.6 27.0 - - + +
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Residues in contact with ASP 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C HIS* 2.6 34.9 + - - +
68C THR* 3.0 35.8 + - - +
70C PRO* 3.8 15.9 - - - +
125C ARG* 2.7 40.5 + - - +
230C LEU* 2.8 15.0 + - - +
231C ALA 3.9 0.4 - - - +
233C TYR* 1.3 83.7 - - - +
235C THR* 1.3 60.4 + - - +
238C ASP* 3.8 10.7 - - - +
267C LYS* 4.6 4.0 + - - +
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Residues in contact with THR 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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68C THR* 4.8 2.9 + - - +
69C ALA 4.3 4.7 + - - -
70C PRO* 4.1 21.2 - - + +
71C ALA 5.3 1.3 - - - +
85C GLY* 4.6 3.6 - - - -
121C ARG* 2.9 16.6 - - - +
125C ARG* 5.9 0.3 + - - -
231C ALA* 2.7 18.9 + - - -
234C ASP* 1.3 79.6 - - - +
236C THR* 1.3 54.6 + - - +
237C ALA 3.3 1.8 - - - -
238C ASP 4.3 2.2 - - - -
239C GLU* 2.6 51.0 + - + +
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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