Contacts of the helix formed by residues 226 - 235 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65D HIS* 4.7 9.0 - - + +
224D ARG 3.2 5.3 + - - -
225D ASN* 1.3 74.2 + - - +
227D SER* 1.3 65.9 + - - +
228D ASN 2.6 2.8 + - - -
229D PRO* 2.9 17.0 - - - +
230D LEU* 3.5 15.4 + - + +
1420D HEM 3.3 48.6 - - + +
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Residues in contact with SER 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D ARG* 3.6 14.3 - - - +
126D MET* 3.6 15.7 - - - -
129D ASP* 3.0 32.5 + - - +
225D ASN* 3.1 26.7 + - - -
226D ALA* 1.3 75.9 - - - +
228D ASN* 1.3 61.7 + - - +
230D LEU* 4.2 10.6 - - - +
231D ALA* 3.1 21.1 + - - +
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Residues in contact with ASN 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D LYS* 5.2 1.8 - - - +
122D ILE* 3.1 49.5 - - + +
126D MET* 4.7 2.8 - - + +
222D GLN* 4.0 19.6 + - - +
225D ASN* 3.2 7.2 + - - +
226D ALA 2.6 7.1 + - - -
227D SER* 1.3 75.4 - - - +
229D PRO* 1.3 73.0 - - + +
231D ALA 3.7 0.2 + - - -
232D HIS* 3.4 18.4 + - - -
257D THR* 3.4 19.9 + - - +
259D GLY* 2.7 28.2 - - - -
1410D PLP 4.4 3.4 + - - -
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Residues in contact with PRO 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D ALA 3.2 10.5 - - - +
228D ASN* 1.3 97.8 - - + +
230D LEU* 1.3 52.6 + - - +
232D HIS* 3.0 5.5 + - - +
233D TYR 2.7 28.9 + - - -
259D GLY* 3.3 13.7 - - - +
262D THR* 4.7 1.3 - - + -
263D GLY* 3.3 15.0 - - - +
314D VAL* 3.3 45.5 - - + +
1420D HEM 3.2 34.1 - - + -
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Residues in contact with LEU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D HIS* 3.7 30.1 - - + +
66D HIS 5.1 0.2 - - - +
67D HIS* 3.6 30.3 - - + +
125D ARG* 3.1 31.0 - - - +
129D ASP* 5.3 1.6 - - - +
226D ALA* 3.5 17.2 + - + +
227D SER* 3.8 9.9 - - - +
228D ASN 3.3 0.4 - - - -
229D PRO* 1.3 76.6 - - - +
231D ALA* 1.3 54.5 + - - +
233D TYR* 2.6 10.1 + - + -
234D ASP* 2.5 38.8 + - - +
1420D HEM 3.4 28.9 - - + -
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Residues in contact with ALA 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ARG* 3.6 22.2 - - + +
122D ILE* 4.6 2.2 - - + -
125D ARG* 3.3 37.8 - - + +
227D SER 3.1 9.1 + - - +
228D ASN 4.1 3.8 - - - +
229D PRO 3.4 0.2 - - - -
230D LEU* 1.3 76.4 - - - +
232D HIS* 1.3 58.7 + - - +
234D ASP* 4.8 1.6 - - - -
235D THR* 2.2 45.0 + - + +
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Residues in contact with HIS 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D VAL* 3.6 35.0 + - + +
119D LYS* 5.6 2.0 - - - +
121D ARG* 3.6 17.1 - - + -
122D ILE* 3.6 14.7 - - + +
228D ASN* 3.4 14.2 + - - -
229D PRO 3.0 8.3 + - - +
231D ALA* 1.3 76.9 - - - +
233D TYR* 1.3 58.3 + - - +
236D THR* 3.0 28.1 + - - +
237D ALA* 2.8 32.5 + - - +
259D GLY 3.0 27.1 - - - +
260D THR* 3.1 35.9 + - + +
264D ILE* 3.5 4.5 - - + +
1410D PLP 4.4 1.0 + - - -
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Residues in contact with TYR 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D TRP* 5.0 0.5 + - - -
60D ALA* 6.1 1.4 - - - +
67D HIS* 4.0 23.7 + + - -
229D PRO 2.7 12.2 + - - +
230D LEU* 2.6 25.8 + - + +
232D HIS* 1.3 72.9 - - - +
234D ASP* 1.3 68.3 + - - +
237D ALA* 3.7 6.7 - - - +
263D GLY 2.9 26.7 - - - +
266D ARG* 3.6 12.6 - - + -
267D LYS* 2.4 82.8 + - + -
270D GLU* 2.6 23.2 + - - -
1420D HEM 3.5 24.1 - - + +
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Residues in contact with ASP 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D HIS* 3.3 23.3 + - - +
68D THR* 2.9 45.0 + - - +
70D PRO* 3.8 4.7 - - - +
125D ARG* 2.6 34.3 + - - +
230D LEU* 2.5 17.4 + - - +
231D ALA* 4.3 1.3 - - - +
233D TYR* 1.3 80.7 - - - +
235D THR* 1.3 61.6 + - + +
238D ASP* 2.7 31.0 - - - +
267D LYS* 4.3 2.7 - - - +
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Residues in contact with THR 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D THR* 5.6 3.1 - - + -
69D ALA 4.4 6.1 - - - +
70D PRO* 4.2 22.9 - - + -
71D ALA 5.3 1.1 - - - +
121D ARG* 3.2 20.2 + - - +
231D ALA* 2.2 35.1 + - - +
234D ASP* 1.3 83.7 - - + +
236D THR* 1.3 61.1 + - - +
237D ALA 3.3 0.9 - - - -
238D ASP* 3.1 3.2 + - - +
239D GLU* 2.8 41.4 + - - +
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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