Contacts of the helix formed by residues 235 - 244 (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 THR 235 (chain D).
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Specific contacts
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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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Residues in contact with THR 236 (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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108D LYS* 5.1 2.2 - - + -
110D GLU* 5.0 8.3 - - - +
118D VAL* 5.9 1.1 - - + -
121D ARG* 2.6 49.1 + - - +
231D ALA 3.4 1.4 + - - -
232D HIS* 3.0 24.0 + - + +
235D THR* 1.3 81.7 + - - +
237D ALA* 1.3 57.1 + - - +
239D GLU* 3.4 2.8 + - - +
240D ILE* 2.9 40.4 + - + +
260D THR* 5.4 1.1 - - + -
264D ILE* 3.3 29.8 - - + -
373D ILE* 5.4 3.4 - - + -
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Residues in contact with ALA 237 (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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232D HIS 2.8 20.5 + - - +
233D TYR 3.7 11.4 + - - +
235D THR 3.3 0.2 - - - -
236D THR* 1.3 74.4 - - - +
238D ASP* 1.3 60.8 + - - +
240D ILE* 4.2 5.5 - - - +
241D LEU* 3.4 26.2 + - - +
264D ILE* 3.3 37.5 - - + +
267D LYS* 4.0 14.8 - - + +
268D LEU* 4.8 2.2 - - + +
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Residues in contact with ASP 238 (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 4.9 1.4 - - - +
69D ALA* 5.3 0.2 - - - -
70D PRO* 3.7 24.8 - - + +
233D TYR 4.4 0.2 + - - -
234D ASP* 2.7 27.5 + - - +
235D THR 3.1 5.1 + - - +
237D ALA* 1.3 80.3 - - - +
239D GLU* 1.3 60.3 + - - +
241D LEU* 3.2 19.0 + - - +
242D GLN* 3.0 27.2 + - - +
267D LYS* 3.1 22.3 + - - +
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Residues in contact with GLU 239 (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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70D PRO* 5.1 12.1 - - + +
85D GLY* 3.7 0.3 - - - -
86D ASP* 2.5 43.3 + - - +
87D THR 5.4 0.2 - - - +
108D LYS* 2.9 21.2 + - - +
121D ARG* 2.7 36.3 + - - -
235D THR* 2.8 23.1 + - - +
236D THR* 3.8 2.2 - - - +
238D ASP* 1.3 76.3 - - - +
240D ILE* 1.3 55.1 + - - +
242D GLN* 2.8 11.5 + - - +
243D GLN* 2.8 43.4 + - + +
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Residues in contact with ILE 240 (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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89D MET* 4.1 4.3 - - + -
108D LYS* 3.7 29.4 - - + -
236D THR* 2.9 25.8 + - + +
237D ALA* 4.4 5.6 - - - +
239D GLU* 1.3 77.9 - - - +
241D LEU* 1.3 59.2 + - - +
243D GLN* 4.4 6.1 - - - -
244D CYS* 3.3 24.8 + - - +
248D LEU* 4.1 13.6 - - + +
251D LEU* 4.0 15.7 - - + -
264D ILE* 3.8 32.1 - - + -
268D LEU* 5.1 4.3 - - + -
371D VAL* 3.8 28.5 - - + -
373D ILE* 4.9 2.2 - - + -
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Residues in contact with LEU 241 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237D ALA 3.4 18.6 - - - +
238D ASP* 3.2 20.3 + - - +
239D GLU 3.2 0.6 - - - -
240D ILE* 1.3 79.2 - - - +
242D GLN* 1.3 58.6 + - - +
244D CYS* 4.6 0.4 - - - -
245D ASP 3.1 1.0 - - - -
246D GLY* 2.5 49.4 + - - +
248D LEU* 5.5 3.4 - - + -
267D LYS* 4.2 7.2 - - + -
268D LEU* 3.6 26.5 - - + -
271D LYS* 4.0 30.7 - - + +
272D CYS* 4.3 17.9 - - + -
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Residues in contact with GLN 242 (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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75C LYS* 3.9 29.0 + - - +
72D LYS* 6.3 0.4 - - - +
238D ASP 3.0 13.2 + - - +
239D GLU* 2.8 15.1 + - - +
241D LEU* 1.3 75.2 - - - +
243D GLN* 1.3 69.7 + - + +
245D ASP* 3.0 17.3 + - - +
61F SER* 3.6 35.9 + - - +
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Residues in contact with GLN 243 (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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75C LYS* 3.4 36.9 + - + +
76C ILE* 4.3 12.1 - - + +
87D THR 3.5 13.5 + - - -
88D PRO* 4.0 2.0 - - - +
89D MET* 3.3 40.2 - - + +
108D LYS* 3.3 31.4 + - - +
239D GLU* 2.8 26.2 + - + +
240D ILE 4.8 0.7 - - - +
242D GLN* 1.3 71.5 - - + +
244D CYS* 1.3 52.4 - - - +
245D ASP* 2.2 34.1 + - - +
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Residues in contact with CYS 244 (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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76C ILE* 4.8 0.2 - - - -
89D MET* 3.4 24.2 - - - -
106D LEU* 3.2 31.9 - - - -
240D ILE 3.3 14.4 + - - +
241D LEU 3.5 1.3 - - - -
243D GLN* 1.3 73.5 - - - +
245D ASP* 1.3 50.0 - - - +
246D GLY* 1.4 41.7 + - - -
247D LYS 3.3 13.2 + - - +
248D LEU* 4.5 10.8 - - + -
369D ARG* 3.7 18.6 - - - +
371D VAL* 4.0 13.0 - - - -
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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