Contacts of the helix formed by residues 239 - 254 (chain A) in PDB entry 5Z7R
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 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A VAL* 3.6 41.7 - - + +
235A GLU 4.3 2.5 - - - +
236A CYS* 2.9 18.2 + - - +
237A PHE 4.4 0.7 - - - +
238A SER* 1.3 88.6 - - - +
240A GLU* 1.3 65.7 + - - +
241A ASP* 3.7 10.6 - - - +
242A GLN* 3.1 24.9 + - - +
243A LYS* 3.7 13.3 + - - +
138C GLY 4.3 2.6 + - - -
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Residues in contact with GLU 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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238A SER 4.0 4.0 + - - +
239A THR* 1.3 74.8 - - - +
241A ASP* 1.3 69.0 + - - +
243A LYS* 3.0 15.4 + - - +
244A ASP* 2.9 41.7 + - - +
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Residues in contact with ASP 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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203A ALA* 4.2 17.3 - - + -
204A PRO* 3.1 33.2 - - - +
205A VAL* 5.1 5.8 + - + +
239A THR* 3.3 10.8 + - + +
240A GLU* 1.3 78.5 - - - +
242A GLN* 1.3 57.0 + - - +
244A ASP* 3.0 7.9 + - - +
245A ALA* 2.7 38.0 + - + +
138C GLY* 4.5 1.6 - - - +
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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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236A CYS 3.3 22.2 - - - +
237A PHE* 3.4 48.8 - - + +
239A THR* 3.1 11.4 + - - +
241A ASP* 1.3 76.9 - - - +
243A LYS* 1.3 67.1 + - - +
246A MET* 3.3 38.2 + - + +
72C LYS 3.1 25.7 + - - +
74C MET 4.1 3.0 + - - +
137C LEU 3.8 10.3 - - - -
138C GLY* 3.7 9.9 - - - +
139C ILE* 3.8 22.0 - - + -
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Residues in contact with LYS 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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239A THR 4.2 7.2 - - - +
240A GLU* 3.0 22.3 + - - +
242A GLN* 1.3 88.6 + - - +
244A ASP* 1.3 64.3 + - - +
246A MET 4.0 0.2 - - - -
247A THR* 2.7 45.9 + - - +
72C LYS* 3.6 21.5 - - + +
73C GLU* 2.6 35.9 + - - +
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Residues in contact with ASP 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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240A GLU* 2.9 34.8 + - - +
241A ASP* 3.9 5.6 - - - +
243A LYS* 1.3 88.7 - - - +
245A ALA* 1.3 58.6 + - - +
246A MET 3.3 0.7 - - - -
247A THR* 4.0 4.6 + - - +
248A ALA* 2.8 31.4 + - - +
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Residues in contact with ALA 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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203A ALA* 5.8 1.8 - - + -
241A ASP* 2.7 21.4 + - + +
244A ASP* 1.3 74.0 - - - +
246A MET* 1.3 58.4 + - - +
248A ALA* 3.7 4.6 - - - +
249A PHE* 2.9 30.3 + - - +
136C GLY 3.5 25.2 - - - +
137C LEU* 3.6 17.5 - - - +
138C GLY* 4.1 1.3 - - - +
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Residues in contact with MET 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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237A PHE* 4.5 2.0 - - + -
242A GLN* 3.3 35.5 + - + +
245A ALA* 1.3 78.5 - - - +
247A THR* 1.3 61.0 + - - +
249A PHE* 3.9 3.1 - - - -
250A ILE* 2.9 34.9 + - - +
68C ILE* 3.5 30.0 - - + +
71C MET* 4.0 15.3 - - + -
72C LYS* 4.0 24.0 - - + -
137C LEU* 3.7 18.6 - - + +
139C ILE* 3.5 51.6 - - + -
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Residues in contact with THR 247 (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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243A LYS* 2.7 31.1 + - - +
244A ASP* 4.0 5.8 - - - -
246A MET* 1.3 72.8 - - - +
248A ALA* 1.3 68.0 + - - +
250A ILE* 3.4 5.1 + - - +
251A GLU* 3.4 35.5 + - - +
72C LYS* 3.2 28.0 + - + +
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Residues in contact with ALA 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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244A ASP 2.8 19.2 + - - +
245A ALA* 3.7 6.5 - - - +
247A THR* 1.3 78.8 - - - +
249A PHE* 1.3 55.0 + - - +
250A ILE 3.2 0.3 + - - -
251A GLU* 3.8 2.6 - - - -
252A LYS* 2.6 41.3 + - + +
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Residues in contact with PHE 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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245A ALA 2.9 19.2 + - - +
246A MET* 4.1 5.8 - - - +
247A THR 3.3 0.2 - - - -
248A ALA* 1.3 76.3 - - - +
250A ILE* 1.3 72.6 + - + +
252A LYS* 4.3 16.8 - - - +
253A ARG* 3.0 58.5 + - + +
68C ILE* 3.8 36.6 - - + -
137C LEU* 4.3 27.8 - - + -
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Residues in contact with ILE 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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246A MET 2.9 21.3 + - - +
247A THR* 3.8 4.5 - - - +
248A ALA 3.2 0.6 - - - -
249A PHE* 1.3 83.4 - - + +
251A GLU* 1.3 75.4 + - - +
253A ARG* 4.1 0.7 - - - +
254A LYS* 2.8 26.4 + - - -
68C ILE* 4.3 19.5 - - + -
69C SER* 4.5 21.8 - - - +
72C LYS* 3.6 27.8 - - + -
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Residues in contact with GLU 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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247A THR* 3.4 26.8 + - - +
248A ALA* 3.4 6.4 + - - +
250A ILE* 1.3 86.5 - - - +
252A LYS* 1.3 67.9 + - - +
254A LYS* 2.8 18.5 + - - +
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Residues in contact with LYS 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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248A ALA* 2.6 29.2 + - + +
249A PHE* 4.0 16.3 - - + +
251A GLU* 1.3 73.3 - - - +
253A ARG* 1.3 88.1 + - + +
254A LYS* 2.8 11.1 + - - +
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Residues in contact with ARG 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 PHE* 3.0 52.7 + - + +
250A ILE* 4.1 1.1 - - - +
252A LYS* 1.3 89.6 - - + +
254A LYS* 1.3 91.6 + - - +
25C LEU* 5.5 8.8 - - - +
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Residues in contact with LYS 254 (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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250A ILE* 2.8 14.5 + - - -
251A GLU* 2.8 14.2 + - - +
252A LYS 2.8 13.0 + - - +
253A ARG* 1.3 117.9 + - - +
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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