Contacts of the helix formed by residues 235 - 244 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68E THR* 4.7 5.2 - - - +
69E ALA 4.4 5.4 - - - +
70E PRO* 3.9 26.4 - - + +
71E ALA 5.2 0.9 - - - +
121E ARG* 3.7 15.1 + - - +
125E ARG* 6.3 2.0 - - - -
231E ALA* 2.7 25.9 + - + +
234E ASP* 1.3 80.7 - - + +
236E THR* 1.3 69.1 + - - -
237E ALA 2.8 14.1 + - - -
238E ASP* 3.0 13.5 + - - +
239E GLU* 3.1 22.5 + - - +
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Residues in contact with THR 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E LYS* 5.3 3.8 - - + -
110E GLU* 4.8 6.1 - - - +
118E VAL* 6.0 0.4 - - + -
121E ARG* 2.6 53.4 + - - +
232E HIS* 2.9 28.1 + - + +
235E THR* 1.3 80.1 + - - +
237E ALA* 1.3 62.8 + - - +
239E GLU* 4.1 5.5 - - - +
240E ILE* 3.4 24.4 + - + +
260E THR* 6.3 0.7 - - + -
264E ILE* 4.2 19.5 - - + -
373E ILE* 6.1 2.2 - - + -
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Residues in contact with ALA 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E HIS 2.6 20.3 + - - +
233E TYR* 3.2 19.7 - - - +
235E THR 2.8 1.6 + - - -
236E THR* 1.3 79.4 - - - +
238E ASP* 1.3 63.2 - - - +
239E GLU 3.2 5.3 + - - -
240E ILE* 3.5 4.4 + - - +
241E LEU* 3.3 22.8 + - - +
263E GLY 4.5 2.7 - - - +
264E ILE* 4.8 12.6 - - + -
267E LYS* 3.6 22.2 - - + -
268E LEU* 5.0 6.4 - - + +
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Residues in contact with ASP 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E PRO* 4.0 19.0 - - + +
233E TYR 3.4 1.6 - - - +
234E ASP 3.7 9.5 - - - +
235E THR 3.0 6.5 + - - +
237E ALA* 1.3 81.0 - - - +
239E GLU* 1.3 52.5 + - - +
241E LEU* 4.2 15.2 - - + +
242E GLN* 2.6 40.4 + - + +
267E LYS* 3.0 38.3 + - - +
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Residues in contact with GLU 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E PRO* 5.2 8.1 - - + +
71E ALA 5.4 2.4 - - - +
85E GLY* 3.7 1.6 - - - -
86E ASP* 3.0 29.1 + - - -
87E THR 3.4 0.5 + - - -
108E LYS* 2.6 38.6 + - - +
121E ARG* 2.9 36.2 + - - -
235E THR* 3.1 21.2 + - - +
236E THR* 4.2 2.9 - - - +
237E ALA 3.2 0.4 - - - -
238E ASP* 1.3 76.2 - - - +
240E ILE* 1.3 58.7 + - - +
242E GLN* 2.8 4.4 + - - -
243E GLN* 2.5 46.0 + - + +
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Residues in contact with ILE 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E MET* 3.3 20.4 - - + +
108E LYS* 3.7 27.6 - - + +
236E THR* 3.4 14.8 - - + +
237E ALA 3.7 4.9 - - - +
239E GLU* 1.3 78.6 - - - +
241E LEU* 1.3 55.5 + - - +
243E GLN* 3.6 0.5 - - - +
244E CYS* 2.7 36.6 + - - +
248E LEU* 3.7 22.0 - - + -
251E LEU* 3.6 15.0 - - + -
264E ILE* 3.5 34.5 - - + -
268E LEU* 5.4 2.9 - - + -
371E VAL* 3.7 17.5 - - + -
373E ILE* 4.8 2.9 - - + -
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Residues in contact with LEU 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E ALA 3.3 13.2 + - - +
238E ASP* 4.2 17.7 - - + +
240E ILE* 1.3 79.7 - - - +
242E GLN* 1.3 56.8 + - - +
244E CYS* 4.3 4.3 - - - -
246E GLY* 3.1 43.4 + - - +
248E LEU* 5.8 5.2 - - + -
267E LYS* 5.2 6.5 - - + +
268E LEU* 4.7 12.8 - - + -
271E LYS* 3.7 32.1 - - + +
272E CYS* 3.7 29.8 - - + -
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Residues in contact with GLN 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E LYS* 4.0 19.7 + - - +
238E ASP* 2.6 24.6 + - + +
239E GLU* 2.8 7.0 + - - +
241E LEU* 1.3 76.1 - - - +
243E GLN* 1.3 67.1 + - + +
245E ASP* 3.1 16.9 + - - +
75F LYS* 3.4 14.8 - - - +
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Residues in contact with GLN 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E ASP* 5.1 6.7 + - - +
87E THR 3.2 12.5 + - - -
88E PRO* 3.6 2.4 - - - +
89E MET* 3.0 52.6 - - + +
108E LYS* 2.9 32.9 - - - -
239E GLU* 2.5 29.2 + - + +
240E ILE 3.6 1.8 - - - +
242E GLN* 1.3 72.9 - - + +
244E CYS* 1.3 55.5 + - - +
245E ASP* 2.3 23.6 - - - +
74F PRO 5.6 0.6 + - - -
75F LYS* 3.1 40.7 + - + +
76F ILE* 4.1 8.0 - - + +
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Residues in contact with CYS 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E MET* 4.2 5.2 - - - -
106E LEU* 4.1 13.0 - - - -
240E ILE 2.7 20.8 + - - +
241E LEU* 4.9 2.9 - - - -
243E GLN* 1.3 71.5 - - - +
245E ASP* 1.3 71.5 + - - +
246E GLY 5.0 0.2 - - - +
247E LYS 3.3 21.3 + - - +
248E LEU* 4.4 4.5 - - + -
369E ARG* 3.1 43.9 + - - +
371E VAL* 3.4 32.5 - - - -
76F ILE* 4.4 1.1 - - - -
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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