Contacts of the helix formed by residues 235 - 245 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68F THR* 4.6 7.0 - - + +
69F ALA 3.9 8.3 - - - +
70F PRO* 3.9 26.5 - - + -
71F ALA 5.3 0.2 - - - +
85F GLY* 6.2 0.4 - - - -
121F ARG* 3.7 16.3 + - - +
125F ARG* 6.0 0.9 - - - +
231F ALA* 2.8 19.1 + - + +
234F ASP* 1.3 83.6 - - + +
236F THR* 1.3 74.5 + - - -
237F ALA 3.0 1.3 - - - -
238F ASP* 2.8 2.3 + - - +
239F GLU* 2.7 34.2 + - - +
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Residues in contact with THR 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F LYS* 4.6 1.5 + - + -
110F GLU* 4.4 12.8 - - - +
118F VAL* 5.8 1.8 - - + -
121F ARG* 2.7 31.4 + - - +
231F ALA 3.6 1.4 + - - -
232F HIS* 3.1 36.2 + - - +
235F THR* 1.3 83.9 + - - +
237F ALA* 1.3 61.4 + - - +
239F GLU* 3.4 3.8 + - - +
240F ILE* 2.8 46.6 + - + +
260F THR* 5.7 0.9 - - - -
264F ILE* 3.7 17.5 - - + -
373F ILE* 5.4 3.4 - - + -
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Residues in contact with ALA 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232F HIS 2.7 16.8 + - - +
233F TYR* 3.0 23.8 - - - +
235F THR 3.0 0.2 - - - -
236F THR* 1.3 74.2 - - - +
238F ASP* 1.3 63.4 + - - +
239F GLU 3.4 0.3 + - - -
240F ILE* 3.7 8.1 + - - +
241F LEU* 3.4 27.2 + - - +
264F ILE* 4.1 13.0 - - + +
267F LYS* 3.4 27.3 - - + +
268F LEU* 5.7 2.7 - - + +
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Residues in contact with ASP 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F THR 5.0 0.3 - - - +
69F ALA* 4.9 1.0 - - - -
70F PRO* 3.2 34.8 - - + +
233F TYR 4.0 0.9 + - - -
234F ASP* 2.7 23.8 - - - +
235F THR 2.8 4.9 + - - -
237F ALA* 1.3 73.4 - - - +
239F GLU* 1.3 66.3 + - - +
241F LEU* 3.8 7.3 + - - +
242F GLN* 3.2 21.7 + - - +
267F LYS* 3.6 29.2 + - - +
271F LYS* 5.9 0.2 - - - +
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Residues in contact with GLU 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F PRO* 4.9 11.0 - - + +
85F GLY* 3.4 0.9 - - - -
86F ASP* 2.3 43.2 + - - +
108F LYS* 2.7 43.2 + - - +
121F ARG* 2.9 23.0 + - - -
235F THR* 2.7 28.6 + - - +
236F THR* 3.5 3.1 - - - +
238F ASP* 1.3 75.3 - - - +
240F ILE* 1.3 72.1 + - - +
242F GLN* 2.6 19.8 + - - +
243F GLN* 3.0 16.1 + - - +
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Residues in contact with ILE 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F MET* 4.3 2.5 - - + -
108F LYS* 3.6 29.4 - - + +
236F THR* 2.8 42.8 + - + +
237F ALA* 4.1 6.1 - - - +
239F GLU* 1.3 79.9 - - - +
241F LEU* 1.3 63.3 + - + +
243F GLN* 3.1 7.4 + - - +
244F CYS* 3.0 26.5 + - - -
248F LEU* 4.1 22.0 - - + -
251F LEU* 4.5 12.8 - - + -
264F ILE* 4.0 15.5 - - + -
268F LEU* 5.5 1.6 - - + -
371F VAL* 4.2 26.0 - - + -
373F ILE* 5.6 2.5 - - + -
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Residues in contact with LEU 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237F ALA 3.4 17.3 + - - +
238F ASP* 4.3 6.3 - - - +
239F GLU 2.8 4.0 + - - -
240F ILE* 1.3 74.3 - - + +
242F GLN* 1.3 57.0 + - - +
244F CYS* 4.5 2.0 - - - +
245F ASP* 2.8 29.1 + - - -
246F GLY* 2.9 24.6 + - - +
248F LEU* 3.3 15.5 - - + -
267F LYS* 4.6 9.9 - - + -
268F LEU* 3.3 33.0 - - + -
271F LYS* 3.6 35.7 - - + -
272F CYS* 4.3 9.2 - - + -
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Residues in contact with GLN 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D SER* 2.8 52.6 - - - +
75E LYS* 3.8 22.2 + - + +
72F LYS* 6.0 2.3 - - - -
238F ASP 3.2 18.4 + - - +
239F GLU* 2.6 13.1 + - - +
241F LEU* 1.3 75.1 - - - +
243F GLN* 1.3 60.1 + - + +
245F ASP* 4.0 5.8 + - - +
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Residues in contact with GLN 243 (chain F).
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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75E LYS* 3.6 41.7 + - + +
76E ILE* 4.4 9.4 - - + +
77E LEU* 5.7 0.2 - - - +
86F ASP* 5.6 5.3 + - - +
87F THR 3.9 8.9 + - - -
88F PRO* 4.5 1.8 - - - +
89F MET* 3.2 51.6 - - + +
108F LYS* 3.5 20.1 + - - +
239F GLU* 3.0 11.6 + - - +
240F ILE* 3.8 5.5 - - - +
242F GLN* 1.3 79.3 - - + +
244F CYS* 1.3 59.9 + - - +
245F ASP* 2.9 22.9 + - - +
369F ARG* 4.6 0.7 + - - -
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Residues in contact with CYS 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E ILE* 5.3 0.9 - - - -
89F MET* 4.9 9.4 - - - -
106F LEU* 5.3 3.8 - - - -
240F ILE* 3.0 23.3 + - - +
241F LEU* 4.3 1.1 - - - +
243F GLN* 1.3 73.5 - - - +
245F ASP* 1.3 70.4 + - - +
246F GLY 4.5 0.2 - - - +
247F LYS* 3.1 32.3 + - - +
248F LEU* 4.2 9.0 - - + -
369F ARG* 3.2 36.8 + - - +
371F VAL* 3.7 29.8 - - - -
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Residues in contact with ASP 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E LYS* 2.8 34.3 + - - +
241F LEU 2.8 7.2 + - - -
242F GLN* 4.1 3.3 - - - +
243F GLN 2.9 17.0 - - - +
244F CYS* 1.3 80.3 - - - +
246F GLY* 1.3 56.5 + - - +
247F LYS* 2.8 24.3 - - + +
369F ARG* 4.5 10.1 + - - +
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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