Contacts of the helix formed by residues 237 - 253 (chain A) in PDB entry 1W45
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 HIS 237 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ARG* 4.8 9.2 + - - +
198A GLU* 5.5 5.0 + - - -
236A THR* 1.3 77.8 - - - +
238A GLY* 1.3 74.6 + - - +
239A SER 3.5 1.4 + - - -
240A LEU* 3.5 7.8 + - - +
241A GLU* 3.2 20.7 + - - -
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Residues in contact with GLY 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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237A HIS* 1.3 83.9 - - - +
239A SER* 1.3 60.0 + - - -
241A GLU* 3.3 10.3 + - - +
242A GLU* 3.1 25.1 + - - +
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Residues in contact with SER 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLU* 3.5 28.2 + - - -
117A ILE* 3.7 10.3 - - - +
155A LEU* 3.6 27.5 - - - +
237A HIS 3.5 0.6 + - - -
238A GLY* 1.3 70.1 - - - -
240A LEU* 1.3 61.8 + - - +
242A GLU* 3.3 12.8 + - - +
243A ALA* 2.9 28.2 + - - +
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Residues in contact with LEU 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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154A TYR* 3.6 48.0 - - + +
155A LEU* 4.0 8.9 - - + +
158A ILE* 4.1 18.6 - - + -
198A GLU* 3.9 12.6 - - + +
202A ILE* 4.5 2.0 - - + -
236A THR* 3.6 24.7 - - + -
237A HIS 3.5 7.6 + - - +
238A GLY 3.3 0.4 - - - -
239A SER* 1.3 79.3 + - - +
241A GLU* 1.3 65.0 + - - +
243A ALA* 3.2 3.9 + - - +
244A MET* 3.0 46.9 + - + +
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Residues in contact with GLU 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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232A ILE* 4.3 11.8 - - + +
233A LYS* 3.1 38.0 - - - +
236A THR* 3.8 20.5 + - - +
237A HIS* 3.2 20.9 + - - -
238A GLY* 3.4 12.9 + - - +
240A LEU* 1.3 77.6 - - - +
242A GLU* 1.3 58.5 + - - +
244A MET* 3.1 2.4 + - - +
245A LEU* 2.9 48.3 + - + +
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Residues in contact with GLU 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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113A GLU* 6.5 0.2 - - - -
114A GLY* 3.7 25.3 + - - +
117A ILE* 4.4 13.6 - - + +
238A GLY 3.1 10.9 + - - +
239A SER* 3.3 14.5 + - - +
241A GLU* 1.3 80.7 + - - +
243A ALA* 1.3 53.4 + - - +
245A LEU* 4.0 7.1 - - - +
246A THR* 2.7 42.5 + - - +
261A ARG* 4.5 11.8 + - - -
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Residues in contact with ALA 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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117A ILE* 3.9 27.1 - - + +
121A ALA* 5.2 0.5 - - - +
155A LEU* 4.2 3.1 - - + -
158A ILE* 4.0 28.7 - - + -
159A LEU* 5.4 1.1 - - + -
162A LEU* 6.0 2.0 - - + -
239A SER 2.9 17.0 + - - +
240A LEU 3.6 6.1 - - - +
241A GLU 3.1 0.4 - - - -
242A GLU* 1.3 76.8 - - - +
244A MET* 1.3 60.6 + - - +
246A THR* 3.4 2.8 + - - -
247A VAL* 3.2 29.0 + - + +
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Residues in contact with MET 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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158A ILE* 4.1 10.5 - - + -
198A GLU 4.1 3.1 - - - +
201A PHE* 3.7 29.4 - - + -
202A ILE* 3.9 21.8 - - + +
205A LEU* 3.7 19.0 - - + +
232A ILE* 3.8 29.8 - - + -
236A THR* 4.0 20.0 - - + -
240A LEU* 3.0 42.0 + - + +
241A GLU 3.1 2.9 + - - +
243A ALA* 1.3 75.0 - - - +
245A LEU* 1.3 64.9 + - - +
247A VAL* 3.3 6.4 + - - +
248A VAL* 3.1 28.5 + - - +
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Residues in contact with LEU 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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229A GLU* 4.0 31.1 - - + +
232A ILE* 3.7 26.9 - - + -
233A LYS* 4.3 15.9 - - + -
241A GLU* 2.9 43.5 + - + +
242A GLU* 4.0 6.7 - - - +
244A MET* 1.3 76.8 - - - +
246A THR* 1.3 60.3 + - - +
248A VAL* 3.4 5.8 + - + +
249A LYS* 3.1 44.8 + - + +
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Residues in contact with THR 246 (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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117A ILE* 3.7 16.2 - - + +
118A GLU* 4.9 0.4 - - - -
121A ALA* 3.6 23.8 - - + -
242A GLU* 2.7 27.7 + - - +
243A ALA 3.5 5.8 - - - -
244A MET 3.1 0.2 - - - -
245A LEU* 1.3 74.3 - - - +
247A VAL* 1.3 60.6 + - - +
249A LYS* 3.1 8.0 + - - +
250A CYS* 2.9 32.3 + - - +
257A TYR* 3.6 37.5 + - + +
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Residues in contact with VAL 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ALA* 4.1 12.8 - - + +
158A ILE* 4.8 7.6 - - + -
162A LEU* 4.0 32.8 - - + -
167A ARG* 6.0 7.4 - - + -
205A LEU* 3.5 39.3 - - + +
213A LEU* 4.7 3.4 - - + -
243A ALA 3.2 15.3 + - - +
244A MET* 3.3 8.9 + - - +
246A THR* 1.3 75.4 - - - +
248A VAL* 1.3 57.0 + - - +
250A CYS* 3.6 6.6 + - - +
251A THR* 2.7 39.5 + - - +
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Residues in contact with VAL 248 (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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205A LEU* 4.3 10.8 - - + -
217A PHE* 4.0 17.0 - - + -
228A ILE* 3.7 31.9 - - + -
229A GLU* 4.3 13.0 - - + +
232A ILE* 4.9 8.1 - - + -
244A MET 3.1 18.4 + - - +
245A LEU* 3.6 11.4 - - + +
247A VAL* 1.3 77.4 - - - +
249A LYS* 1.3 58.4 + - + +
251A THR* 3.1 9.1 + - - -
252A GLN* 3.1 50.9 + - - +
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Residues in contact with LYS 249 (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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229A GLU* 5.7 7.9 - - + +
245A LEU* 3.1 37.0 + - - +
246A THR* 3.1 5.4 + - - +
248A VAL* 1.3 74.3 - - + +
250A CYS* 1.3 61.8 + - - +
252A GLN* 4.1 13.5 - - - +
253A ASN 2.9 35.7 + - - +
257A TYR* 4.1 26.2 - - + +
260A GLU* 2.7 38.4 + - - +
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Residues in contact with CYS 250 (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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121A ALA 3.9 16.4 - - - +
122A SER* 3.9 15.9 - - - -
167A ARG* 4.3 14.1 + - - +
246A THR* 2.9 22.5 + - - +
247A VAL* 3.9 5.2 - - - +
249A LYS* 1.3 76.2 - - - +
251A THR* 1.3 60.9 + - - +
254A LEU* 3.7 42.3 + - + +
257A TYR* 3.7 32.1 - - - -
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Residues in contact with THR 251 (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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167A ARG* 5.8 6.5 + - - +
210A ALA* 3.5 43.9 - - + +
213A LEU* 4.0 25.4 - - + +
214A LEU* 3.6 20.8 - - + +
217A PHE* 4.2 8.3 - - + -
247A VAL* 2.7 21.4 + - - +
248A VAL* 3.1 10.1 + - - -
250A CYS* 1.3 77.5 - - - +
252A GLN* 1.3 64.9 + - - +
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Residues in contact with GLN 252 (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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214A LEU* 4.0 18.1 - - + +
217A PHE* 4.6 13.6 - - + +
228A ILE* 5.2 1.4 - - - +
229A GLU* 3.5 25.3 + - - +
248A VAL* 3.1 31.7 + - + +
249A LYS* 4.1 12.2 - - - +
251A THR* 1.3 79.0 - - - +
253A ASN* 1.3 66.2 + - + +
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Residues in contact with ASN 253 (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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249A LYS 2.9 15.8 + - - +
251A THR 3.5 0.2 - - - -
252A GLN* 1.3 84.0 + - + +
254A LEU* 1.3 63.3 + - - +
255A HIS* 3.2 25.6 + - - +
256A SER* 3.1 22.3 + - - -
257A TYR 3.1 17.2 + - - -
294A HIS* 3.4 23.5 + - - -
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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