Contacts of the helix formed by residues 247 - 256 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239E TRP* 2.9 47.7 + - + +
242E VAL* 3.7 39.0 - - + +
245E PHE* 4.3 1.3 - - + +
246E ASP* 1.3 79.1 - - - +
248E THR* 1.3 60.3 + - - +
249E CYS* 3.1 3.4 - - - +
250E ILE* 2.9 20.1 + - + +
251E ARG 3.2 7.6 + - - -
90F LEU* 4.4 2.5 - - + -
122F THR* 4.0 31.2 - - + -
124F ILE* 4.1 19.1 - - + -
127F MET* 4.3 13.9 - - + -
152F ILE* 3.9 24.9 - - + +
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Residues in contact with THR 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E TRP 4.5 0.2 - - - -
240E GLU* 3.9 29.8 - - + -
246E ASP* 3.1 31.3 + - - +
247E MET* 1.3 76.9 - - - +
249E CYS* 1.3 64.8 + - - +
251E ARG* 3.2 30.4 - - - +
252E ASP* 2.9 30.0 + - - -
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Residues in contact with CYS 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E ASP* 4.6 0.8 + - - -
247E MET 3.1 1.6 - - - -
248E THR* 1.3 83.2 + - - +
250E ILE* 1.3 62.2 - - - +
252E ASP* 4.0 9.2 + - - +
253E VAL* 3.8 12.1 + - - +
148F TYR* 3.8 35.9 - - + -
151F LYS* 4.1 26.2 - - + -
152F ILE* 3.5 34.3 - - - -
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Residues in contact with ILE 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E TRP* 3.6 33.2 - - + -
247E MET* 2.9 9.1 + - - +
249E CYS* 1.3 76.4 - - - +
251E ARG* 1.3 56.4 + - - +
252E ASP 3.2 1.6 - - - -
253E VAL* 2.8 9.5 + - + +
254E ALA* 2.8 31.4 + - + -
83F PHE* 3.5 28.7 - - + -
86F HIS* 6.1 0.2 - - + -
122F THR* 3.9 20.6 - - + -
145F ILE* 4.4 11.0 - - + -
148F TYR* 4.0 27.4 - - + -
152F ILE* 3.9 24.2 - - + -
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Residues in contact with ARG 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E ILE* 3.2 38.7 - - + +
237E HIS* 4.9 4.5 + - - -
239E TRP* 3.6 25.9 - - + +
240E GLU* 3.3 34.6 + - + +
247E MET 3.2 2.6 + - - -
248E THR* 3.2 31.3 - - + +
250E ILE* 1.3 78.3 - - - +
252E ASP* 1.3 92.8 + - - +
254E ALA* 3.1 3.8 + - - +
255E MET* 3.0 42.6 + - - +
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Residues in contact with ASP 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E THR* 2.9 22.2 + - - +
249E CYS* 4.0 9.1 - - - +
250E ILE 3.2 0.2 - - - -
251E ARG* 1.3 105.6 + - - +
253E VAL* 1.3 61.5 + - + +
255E MET* 3.7 11.5 - - - +
256E LYS* 3.5 22.9 + - - +
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Residues in contact with VAL 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249E CYS 3.8 4.7 + - - +
250E ILE* 2.8 11.9 + - + +
252E ASP* 1.3 76.4 - - + +
254E ALA* 1.3 62.4 + - - +
256E LYS* 3.1 23.4 + - + +
257E GLU* 3.7 7.7 + - - +
83F PHE* 4.3 17.0 - - + -
148F TYR* 3.1 43.5 - - + +
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Residues in contact with ALA 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E LYS 5.0 4.7 - - - +
236E ILE* 5.0 5.8 - - + -
239E TRP* 4.2 18.4 - - + +
250E ILE 2.8 15.8 + - - +
251E ARG* 3.1 8.0 + - - +
253E VAL* 1.3 69.7 - - - +
255E MET* 1.3 66.7 + - - +
257E GLU* 3.0 23.7 + - - +
259E LEU* 5.3 3.6 - - - +
341E TYR* 5.9 0.7 - - - -
83F PHE* 3.7 35.9 - - + -
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Residues in contact with MET 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E LYS* 3.9 2.0 - - - -
236E ILE* 3.6 37.0 - - + +
237E HIS* 5.5 2.0 - - + -
251E ARG* 3.0 30.6 + - - +
252E ASP* 3.7 11.4 - - - +
254E ALA* 1.3 74.8 - - - +
256E LYS* 1.3 66.5 + - - +
257E GLU 3.1 7.2 + - - +
341E TYR* 3.9 32.4 + - - +
342E LEU 3.7 22.0 - - - +
343E GLU* 3.8 27.8 - - + +
391E TYR* 3.5 20.4 - - - -
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Residues in contact with LYS 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252E ASP 3.5 19.0 + - - +
253E VAL* 3.1 13.9 + - + +
255E MET* 1.3 82.6 - - - +
257E GLU* 1.3 57.9 + - - +
343E GLU* 5.6 13.3 + - - -
389E ASN* 5.4 7.8 - - - +
390E ASP* 2.9 38.0 + - + +
391E TYR* 3.0 11.6 - - + +
392E LYS* 2.8 33.8 + - + +
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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