Contacts of the helix formed by residues 242 - 254 (chain J) in PDB entry 5EF6
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 242 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C T 3.8 37.0 - - - +
17C C 3.3 5.4 - - - -
238J ASN* 4.8 10.5 - - - +
240J PHE 4.2 8.5 - - - +
241J ILE* 1.3 82.3 - - - +
243J LYS* 1.3 65.7 + - - +
244J ASP* 3.7 8.0 + - - +
245J LYS* 3.1 29.9 + - + +
246J ARG* 3.1 18.6 + - - +
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Residues in contact with LYS 243 (chain J).
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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17C C 2.8 36.7 + - + +
18C C 3.0 29.9 + - - -
241J ILE 4.1 0.2 + - - -
242J THR* 1.3 72.1 - - - +
244J ASP* 1.3 65.0 + - - +
246J ARG* 3.3 32.2 + - - +
247J ARG* 3.3 30.2 + - - +
3L A 3.4 13.1 + - - -
4L C 2.7 29.8 + - - +
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Residues in contact with ASP 244 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C T 5.5 7.0 - - - +
17C C 4.5 3.0 + - - +
242J THR* 3.2 8.6 + - - +
243J LYS* 1.3 78.6 - - - +
245J LYS* 1.3 73.9 + - + +
247J ARG* 3.2 23.8 + - - +
248J LYS* 2.6 44.5 + - - +
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Residues in contact with LYS 245 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H A 5.4 7.0 + - - -
234J GLU* 3.9 35.4 - - + +
241J ILE* 3.5 20.6 - - + -
242J THR* 3.1 21.6 + - + +
244J ASP* 1.3 92.8 + - + +
246J ARG* 1.3 57.3 + - - +
248J LYS* 3.2 9.0 + - + +
249J ILE* 2.8 36.4 + - + +
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Residues in contact with ARG 246 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241J ILE* 3.8 17.5 + - + +
242J THR 3.1 12.7 + - - +
243J LYS* 3.5 33.8 - - - +
244J ASP 3.2 0.6 - - - -
245J LYS* 1.3 72.9 - - - +
247J ARG* 1.3 89.6 + - - +
249J ILE* 4.4 3.4 - - - -
250J SER* 3.0 25.5 + - - -
257J GLU* 3.4 43.3 + - - +
260J ILE* 3.6 27.6 - - + +
261J THR* 3.4 18.9 + - - -
4L C 2.7 38.6 + - - -
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Residues in contact with ARG 247 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243J LYS* 3.3 29.4 + - - +
244J ASP* 3.2 11.2 + - - +
246J ARG* 1.3 107.5 - - - +
248J LYS* 1.3 64.3 + - + +
250J SER* 3.1 17.7 + - - -
251J ALA* 3.1 13.7 + - - +
257J GLU* 2.7 42.6 + - - +
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Residues in contact with LYS 248 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244J ASP* 2.6 43.6 + - - +
245J LYS* 3.2 10.8 + - + +
247J ARG* 1.3 81.9 - - + +
249J ILE* 1.3 64.8 + - - +
251J ALA* 3.5 7.2 + - - +
252J ALA* 3.1 24.6 + - - +
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Residues in contact with ILE 249 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230J GLU* 3.6 36.6 - - + +
231J LEU* 4.5 11.2 - - + +
234J GLU* 3.9 24.9 - - + -
241J ILE* 4.8 9.4 - - + -
245J LYS* 2.8 25.2 + - + +
246J ARG* 3.8 5.8 - - - +
248J LYS* 1.3 77.3 - - - +
250J SER* 1.3 51.7 + - - +
251J ALA 3.0 0.5 + - - -
252J ALA* 3.1 2.8 + - - -
253J THR* 2.6 55.0 + - + +
260J ILE* 3.4 31.4 - - + -
264J PHE* 5.5 1.8 - - + -
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Residues in contact with SER 250 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246J ARG 3.0 11.7 + - - -
247J ARG 3.4 3.6 - - - -
249J ILE* 1.3 77.1 - - - +
251J ALA* 1.3 57.7 + - - +
253J THR* 3.8 1.3 - - - -
254J SER* 3.0 25.0 + - - -
255J LEU 2.5 26.4 + - - +
256J SER* 4.2 0.9 - - - -
257J GLU* 3.0 32.5 + - - +
260J ILE* 3.7 8.7 - - - -
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Residues in contact with ALA 251 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247J ARG 3.1 12.0 + - - +
248J LYS* 3.8 9.4 - - - +
249J ILE 3.1 0.6 - - - -
250J SER* 1.3 79.0 - - - +
252J ALA* 1.3 65.3 + - - +
253J THR 3.2 1.2 + - - -
254J SER* 3.8 8.8 + - - -
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Residues in contact with ALA 252 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230J GLU* 4.5 19.7 - - + +
248J LYS 3.1 15.3 + - - +
249J ILE* 3.1 4.6 + - - +
251J ALA* 1.3 80.1 - - - +
253J THR* 1.3 66.1 + - + +
254J SER* 4.6 1.9 + - - -
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Residues in contact with THR 253 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227J GLN* 2.9 45.4 + - - +
230J GLU* 3.6 32.8 - - + -
231J LEU* 5.3 0.4 - - + -
249J ILE* 2.6 45.0 + - + +
250J SER* 3.8 0.9 - - - -
252J ALA* 1.3 76.7 - - + +
254J SER* 1.3 68.4 + - - +
255J LEU* 3.4 27.7 + - + +
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Residues in contact with SER 254 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227J GLN* 4.7 4.2 + - - -
250J SER 3.0 17.2 + - - -
251J ALA 3.8 7.5 + - - -
252J ALA 3.7 2.3 + - - -
253J THR* 1.3 80.2 + - - +
255J LEU* 1.3 60.4 + - - +
259J GLN* 5.0 0.2 - - - +
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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