Contacts of the helix formed by residues 247 - 255 (chain L) in PDB entry 5DST
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 MET 247 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90K LEU* 4.4 2.7 - - + -
122K THR* 4.3 23.3 - - + +
124K ILE* 4.1 18.6 - - + -
127K MET* 4.2 15.7 - - + -
152K ILE* 4.1 29.6 - - + -
239L TRP* 2.9 47.9 + - + +
242L VAL* 3.7 41.1 - - + +
245L PHE* 3.5 1.8 + - + +
246L ASP* 1.3 77.4 - - - +
248L THR* 1.3 63.1 + - - +
249L CYS* 3.2 4.0 - - - +
250L ILE* 3.1 14.2 + - + +
251L ARG 3.3 8.1 + - - -
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Residues in contact with THR 248 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239L TRP 4.4 0.4 - - - -
240L GLU* 3.8 20.0 - - + -
246L ASP* 3.1 31.3 + - - +
247L MET* 1.3 76.7 - - - +
249L CYS* 1.3 59.4 + - - +
251L ARG* 3.1 41.2 + - - +
252L ASP* 2.9 34.9 + - - -
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Residues in contact with CYS 249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148K TYR* 3.9 23.9 - - + -
151K LYS* 4.0 29.6 - - + +
152K ILE* 3.6 33.2 - - - -
155K ALA* 6.4 1.3 - - + -
246L ASP* 4.7 0.8 + - - -
247L MET 3.2 1.2 - - - -
248L THR* 1.3 80.8 + - - +
250L ILE* 1.3 62.1 + - - +
252L ASP* 4.1 9.4 + - - +
253L VAL* 3.7 20.4 + - - +
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Residues in contact with ILE 250 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83K PHE* 3.8 20.0 - - + -
122K THR* 4.0 14.6 - - + -
145K ILE* 4.9 7.9 - - + -
148K TYR* 4.2 24.0 - - + -
152K ILE* 3.7 28.9 - - + -
239L TRP* 3.5 48.2 - - + +
247L MET* 3.1 9.9 + - - +
248L THR 3.1 0.4 - - - -
249L CYS* 1.3 76.3 - - - +
251L ARG* 1.3 59.0 + - - +
252L ASP 3.1 1.6 - - - -
253L VAL* 2.7 28.8 + - + +
254L ALA* 2.8 11.3 + - + -
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Residues in contact with ARG 251 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236L ILE* 3.1 38.1 - - + +
237L HIS* 5.0 2.4 + - - -
239L TRP* 3.6 26.4 - - + +
240L GLU* 3.1 32.7 + - + +
247L MET 3.3 3.0 + - - -
248L THR* 3.2 35.9 - - - +
250L ILE* 1.3 77.6 - - - +
252L ASP* 1.3 93.8 + - - +
254L ALA* 3.1 4.1 + - - +
255L MET* 3.0 38.1 + - - +
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Residues in contact with ASP 252 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248L THR* 2.9 23.9 + - - +
249L CYS* 4.1 9.3 - - - +
251L ARG* 1.3 106.4 + - - +
253L VAL* 1.3 61.5 + - + +
255L MET* 4.0 9.9 - - - +
256L LYS* 3.5 23.0 + - - +
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Residues in contact with VAL 253 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83K PHE* 4.3 18.4 - - + -
148K TYR* 3.4 32.8 - - + +
249L CYS 3.7 14.8 - - - +
250L ILE* 2.7 17.7 + - + +
252L ASP* 1.3 72.8 - - + +
254L ALA* 1.3 64.6 + - - +
255L MET 3.4 0.2 - - - -
256L LYS* 3.1 22.2 + - + +
257L GLU* 3.6 7.1 + - - +
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Residues in contact with ALA 254 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83K PHE* 3.9 33.7 - - + -
235L LYS 4.9 2.5 - - - +
236L ILE* 4.9 9.2 - - + -
239L TRP* 4.3 14.6 - - + +
250L ILE 2.8 15.1 + - - +
251L ARG* 3.5 12.3 - - - +
253L VAL* 1.3 70.4 - - - +
255L MET* 1.3 56.9 + - - +
257L GLU* 2.8 34.0 + - - +
259L LEU* 5.3 2.8 - - - +
341L TYR* 6.0 0.9 - - - -
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Residues in contact with MET 255 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232L LYS* 3.8 5.4 - - - -
236L ILE* 3.7 36.0 - - + +
237L HIS* 5.5 2.0 - - + -
251L ARG* 3.0 27.7 + - - +
252L ASP* 4.0 9.6 - - - +
254L ALA* 1.3 74.9 - - - +
256L LYS* 1.3 69.2 + - - +
257L GLU 3.2 6.2 + - - +
258L PRO* 5.6 0.2 - - - +
341L TYR* 3.8 34.5 + - - +
342L LEU 3.4 23.6 - - - +
343L GLU* 3.7 23.6 - - + +
391L TYR* 3.5 20.4 - - - -
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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