Contacts of the helix formed by residues 235 - 245 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A THR* 4.2 18.2 - - - +
70A PRO* 3.6 21.2 - - + +
85A GLY* 6.0 2.2 - - - -
121A ARG* 3.6 17.9 + - - +
231A ALA* 2.5 35.3 + - - +
234A ASP* 1.3 75.1 - - + +
236A THR* 1.3 65.9 + - - -
237A ALA 3.4 0.7 - - - -
238A ASP* 3.2 4.9 + - - +
239A GLU* 3.2 30.0 + - - +
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Residues in contact with THR 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LYS* 5.3 2.7 - - + -
110A GLU* 5.0 6.5 - - - +
118A VAL* 6.3 0.2 - - + -
121A ARG* 2.7 38.9 + - - +
231A ALA 3.3 1.2 + - - -
232A HIS* 2.8 39.1 + - - +
235A THR* 1.3 72.6 + - - +
237A ALA* 1.3 55.8 + - - +
238A ASP 2.8 15.4 + - - -
239A GLU* 3.0 12.5 + - - +
240A ILE* 3.2 22.0 + - + +
260A THR* 6.1 0.7 - - + -
264A ILE* 3.9 24.2 - - + -
373A ILE* 5.4 1.6 - - + -
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Residues in contact with ALA 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A HIS 2.4 33.7 + - - +
233A TYR* 3.1 20.9 - - - +
235A THR 3.4 0.4 - - - -
236A THR* 1.3 69.0 - - - +
238A ASP* 1.3 57.9 + - - +
240A ILE* 4.6 3.4 - - - -
241A LEU* 3.4 25.6 + - - +
264A ILE* 4.0 22.2 - - + -
267A LYS* 3.6 21.9 - - + +
268A LEU* 4.0 5.2 - - + +
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Residues in contact with ASP 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A PRO* 4.0 17.8 - - + +
234A ASP 3.2 14.5 - - - +
235A THR 3.2 8.6 + - - +
236A THR 2.8 2.6 + - - -
237A ALA* 1.3 77.6 - - - +
239A GLU* 1.3 53.5 + - - +
240A ILE 3.3 1.1 - - - -
241A LEU* 3.1 16.1 + - - +
242A GLN* 2.7 36.8 + - - +
267A LYS* 3.0 29.1 + - - +
271A LYS* 3.4 19.4 + - - -
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Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PRO* 5.6 6.5 - - + +
71A ALA 5.7 0.3 - - - +
85A GLY* 3.8 2.4 - - - -
86A ASP* 3.0 30.3 + - - -
87A THR 3.7 3.5 + - - +
108A LYS* 2.8 21.0 + - - +
121A ARG* 2.7 43.0 + - - -
235A THR* 3.2 14.6 + - - +
236A THR* 3.0 3.1 + - - +
238A ASP* 1.3 73.7 - - + +
240A ILE* 1.3 57.4 + - - +
241A LEU 2.9 0.3 + - - -
242A GLN* 3.0 6.4 + - - +
243A GLN* 2.6 47.0 + - - +
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Residues in contact with ILE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A MET* 4.1 9.4 - - + -
108A LYS* 3.8 32.0 - - + +
236A THR* 3.4 17.5 - - + +
237A ALA 4.6 4.9 - - - +
239A GLU* 1.3 78.8 - - - +
241A LEU* 1.3 57.4 + - + +
243A GLN* 3.5 0.3 - - - +
244A CYS* 3.0 31.0 + - - +
248A LEU* 4.1 25.4 - - + -
251A LEU* 4.2 9.6 - - + -
264A ILE* 3.6 37.2 - - + -
268A LEU* 4.7 12.8 - - + -
371A VAL* 4.3 12.6 - - + -
373A ILE* 4.4 1.6 - - + -
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Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A ALA 3.4 21.5 - - - +
238A ASP* 3.1 22.7 + - - +
239A GLU 2.9 1.0 + - - -
240A ILE* 1.3 77.1 - - + +
242A GLN* 1.3 63.9 + - - +
243A GLN 2.9 5.9 + - - -
244A CYS* 3.3 1.8 + - - -
245A ASP 3.1 19.1 + - - -
246A GLY* 3.1 26.5 + - - +
248A LEU* 6.4 1.6 - - + -
267A LYS* 4.3 5.8 - - + +
268A LEU* 4.1 14.4 - - + -
271A LYS* 3.8 30.5 - - + -
272A CYS* 4.1 26.0 - - + +
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Residues in contact with GLN 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LYS* 4.9 18.3 + - - +
238A ASP 2.7 19.7 + - - +
239A GLU* 3.9 6.1 - - - +
241A LEU* 1.3 71.4 - - - +
243A GLN* 1.3 64.3 + - - +
245A ASP* 3.9 6.9 + - - +
75B LYS* 3.9 26.0 - - - +
61C SER* 3.1 51.1 + - - +
62C GLU* 5.1 0.6 - - - +
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Residues in contact with GLN 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ASP* 6.2 1.6 - - - -
87A THR 3.8 8.2 + - - +
89A MET* 3.7 32.2 - - + +
108A LYS* 3.2 29.1 + - - -
239A GLU* 2.6 25.4 + - - +
240A ILE 3.5 5.8 - - - +
241A LEU 2.9 0.6 - - - -
242A GLN* 1.3 74.3 - - - +
244A CYS* 1.3 59.8 + - - +
245A ASP* 2.8 19.6 + - - +
75B LYS* 3.3 40.7 + - - +
76B ILE* 4.0 16.8 - - + +
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Residues in contact with CYS 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A MET* 4.0 3.6 - - - -
106A LEU* 3.8 9.9 - - - -
240A ILE 3.0 18.6 + - - +
241A LEU* 3.3 1.1 + - - +
243A GLN* 1.3 79.6 - - - +
245A ASP* 1.3 63.8 + - - +
246A GLY 3.1 6.2 + - - +
247A LYS* 3.2 21.9 + - - +
248A LEU* 3.8 11.9 - - + -
369A ARG* 2.3 46.9 + - - +
371A VAL* 3.6 30.5 - - - -
76B ILE* 4.4 1.8 - - - -
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Residues in contact with ASP 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A LEU 3.1 5.1 + - - -
242A GLN* 4.4 5.0 + - - +
243A GLN 2.8 17.7 + - - +
244A CYS* 1.3 80.2 - - - +
246A GLY* 1.3 56.9 + - - +
247A LYS* 3.2 22.5 + - + +
369A ARG* 4.3 6.1 + - - +
75B LYS* 4.2 23.0 - - - +
76B ILE* 5.7 1.6 - - - +
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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