Contacts of the helix formed by residues 247 - 256 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A LEU* 4.4 2.2 - - + -
122A THR* 4.1 31.9 - - + +
124A ILE* 4.1 18.6 - - + -
127A MET* 4.2 15.0 - - + -
152A ILE* 3.9 29.4 - - + -
239B TRP* 2.8 44.3 + - + +
242B VAL* 3.7 40.2 - - + -
245B PHE* 4.4 2.7 - - + +
246B ASP* 1.3 79.3 - - - +
248B THR* 1.3 62.5 + - - +
249B CYS* 3.2 3.4 - - - -
250B ILE* 3.1 14.1 + - + +
251B ARG 3.1 8.8 + - - -
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Residues in contact with THR 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B TRP 4.6 0.2 - - - -
240B GLU* 3.9 20.0 - - + -
246B ASP* 3.1 31.5 + - - +
247B MET* 1.3 72.8 - - - +
249B CYS* 1.3 62.6 + - - +
250B ILE 3.0 2.5 - - - -
251B ARG* 3.0 37.3 + - - +
252B ASP* 2.8 35.9 + - - -
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Residues in contact with CYS 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A TYR* 3.8 32.0 - - + -
151A LYS* 4.0 28.0 - - + +
152A ILE* 3.6 31.9 - - - -
246B ASP* 4.8 0.2 + - - -
247B MET 3.2 0.6 - - - -
248B THR* 1.3 82.3 + - - +
250B ILE* 1.3 64.5 + - - +
252B ASP* 3.9 9.6 + - - +
253B VAL* 3.7 20.8 + - - +
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Residues in contact with ILE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PHE* 3.5 25.1 - - + -
86A HIS* 5.9 0.2 - - + -
122A THR* 4.0 15.0 - - + -
145A ILE* 4.4 15.9 - - + -
148A TYR* 4.1 22.7 - - + -
152A ILE* 3.9 24.7 - - + -
239B TRP* 3.4 43.1 - - + -
247B MET* 3.1 9.9 + - - +
248B THR 3.0 0.6 - - - -
249B CYS* 1.3 76.4 - - - +
251B ARG* 1.3 66.3 + - - +
253B VAL* 2.8 19.0 + - + +
254B ALA* 2.9 10.4 + - - +
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Residues in contact with ARG 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B ILE* 3.0 38.8 - - + +
237B HIS* 4.9 3.7 + - - -
239B TRP* 3.5 26.4 - - + +
240B GLU* 3.3 31.0 + - + +
247B MET 3.1 5.3 + - - -
248B THR* 3.0 35.4 + - + +
250B ILE* 1.3 75.8 - - - +
252B ASP* 1.3 85.7 + - - +
254B ALA* 3.1 3.1 + - - +
255B MET* 3.0 38.0 + - - +
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Residues in contact with ASP 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B THR* 2.8 21.8 + - - +
249B CYS* 4.0 9.4 - - - +
250B ILE 3.1 0.2 - - - -
251B ARG* 1.3 107.6 + - - +
253B VAL* 1.3 61.4 + - + +
255B MET* 3.6 11.4 - - - +
256B LYS* 3.4 24.1 + - - +
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Residues in contact with VAL 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PHE* 4.2 19.3 - - + -
148A TYR* 3.1 43.7 - - + +
249B CYS 3.7 5.4 - - - +
250B ILE* 2.8 10.4 + - + +
252B ASP* 1.3 77.0 - - + +
254B ALA* 1.3 65.5 + - - +
256B LYS* 3.0 22.5 + - + +
257B GLU* 3.7 7.7 + - - +
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Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PHE* 3.7 37.0 - - + -
235B LYS 4.9 4.9 - - - +
236B ILE* 4.9 6.1 - - + -
239B TRP* 4.1 19.5 - - + +
250B ILE 2.9 11.0 + - - +
251B ARG* 3.6 8.1 - - - +
253B VAL* 1.3 73.9 - - - +
255B MET* 1.3 66.1 + - - +
257B GLU* 3.0 23.2 + - - +
259B LEU* 5.3 3.3 - - - +
341B TYR* 5.9 1.4 - - - -
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Residues in contact with MET 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B LYS* 3.9 2.0 - - - -
236B ILE* 3.7 37.8 - - + +
237B HIS* 5.5 2.2 - - + -
251B ARG* 3.0 26.8 + - - +
252B ASP* 3.6 14.1 - - - +
254B ALA* 1.3 76.0 - - - +
256B LYS* 1.3 68.2 + - - +
257B GLU 3.1 7.7 + - - +
341B TYR* 3.9 32.4 + - - +
342B LEU 3.6 22.4 - - - +
343B GLU* 3.8 27.1 - - + +
391B TYR* 3.5 19.6 - - - -
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Residues in contact with LYS 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B ASP 3.4 20.1 + - - +
253B VAL* 3.0 14.5 + - + +
255B MET* 1.3 86.6 - - - +
257B GLU* 1.3 57.6 + - - +
343B GLU* 5.6 12.5 - - - -
389B ASN* 5.4 8.0 - - - +
390B ASP* 3.0 39.2 + - + +
391B TYR* 3.1 11.8 - - + +
392B LYS* 2.9 32.5 + - + +
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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