Contacts of the helix formed by residues 247 - 256 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239C TRP* 3.0 47.9 + - + +
242C VAL* 3.7 39.0 - - + -
245C PHE* 4.4 2.2 - - + +
246C ASP* 1.3 78.3 - - - +
248C THR* 1.3 64.6 + - - +
249C CYS* 3.2 3.4 - - - -
250C ILE* 3.1 14.1 + - + +
251C ARG 3.3 8.3 + - - -
90D LEU* 4.4 2.9 - - + -
122D THR* 4.1 25.1 - - + +
124D ILE* 4.3 11.2 - - + -
127D MET* 4.2 22.7 - - + -
152D ILE* 3.9 29.8 - - + -
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Residues in contact with THR 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C GLU* 3.8 21.3 - - + -
246C ASP* 2.9 33.1 + - - +
247C MET* 1.3 78.1 - - - +
249C CYS* 1.3 64.0 + - - +
251C ARG* 3.2 39.5 + - - +
252C ASP* 2.9 29.2 + - - -
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Residues in contact with CYS 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C ASP* 4.7 0.4 + - - -
247C MET 3.2 1.2 - - - -
248C THR* 1.3 81.0 + - - +
250C ILE* 1.3 63.3 + - - +
252C ASP* 3.8 10.7 + - - +
253C VAL* 3.7 20.8 + - - +
148D TYR* 3.9 24.0 - - + -
151D LYS* 3.9 33.2 - - + -
152D ILE* 3.7 31.0 - - - -
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Residues in contact with ILE 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C TRP* 3.5 41.7 - - + +
247C MET* 3.1 9.2 + - - +
248C THR 3.1 0.2 - - - -
249C CYS* 1.3 75.5 - - - +
251C ARG* 1.3 67.3 + - - +
252C ASP 3.0 1.1 - - - -
253C VAL* 2.8 18.6 + - + +
254C ALA 2.9 10.2 + - - -
83D PHE* 3.6 26.2 - - + -
86D HIS* 6.2 0.2 - - + -
122D THR* 4.1 13.5 - - + -
145D ILE* 4.6 9.6 - - + -
148D TYR* 4.1 28.0 - - + -
152D ILE* 3.9 25.6 - - + -
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Residues in contact with ARG 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C ILE* 3.0 38.3 - - + +
237C HIS* 5.0 2.0 + - - -
239C TRP* 3.6 27.9 - - + +
240C GLU* 3.4 29.5 + - + +
247C MET 3.3 3.2 + - - -
248C THR* 3.2 36.7 + - - +
250C ILE* 1.3 77.1 - - - +
252C ASP* 1.3 92.8 + - - +
254C ALA* 3.1 2.2 + - - +
255C MET* 3.0 34.7 + - - +
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Residues in contact with ASP 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C THR* 2.9 19.7 + - - +
249C CYS* 3.8 10.7 - - - +
250C ILE 3.0 0.4 - - - -
251C ARG* 1.3 110.7 + - - +
253C VAL* 1.3 62.3 + - + +
255C MET* 3.7 11.2 - - - +
256C LYS* 3.5 22.2 + - - +
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Residues in contact with VAL 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C CYS 3.8 13.2 - - - +
250C ILE* 2.8 15.8 + - + +
252C ASP* 1.3 73.4 - - + +
254C ALA* 1.3 64.3 + - - +
256C LYS* 3.1 22.0 + - + +
257C GLU* 3.7 8.9 + - - +
83D PHE* 4.4 16.8 - - + -
148D TYR* 3.2 32.1 - - + +
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Residues in contact with ALA 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C LYS 4.9 2.0 - - - +
236C ILE* 4.9 9.6 - - + -
239C TRP* 4.3 13.2 - - + +
250C ILE 2.9 10.8 + - - +
251C ARG* 3.1 12.5 + - - +
253C VAL* 1.3 77.0 - - - +
255C MET* 1.3 57.2 + - - +
257C GLU* 2.9 30.7 + - - +
259C LEU* 5.3 2.9 - - - +
341C TYR* 6.1 0.7 - - - -
83D PHE* 3.8 35.8 - - + -
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Residues in contact with MET 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C LYS* 3.8 5.6 - - - -
236C ILE* 3.6 37.3 - - + +
237C HIS* 5.4 1.8 - - + -
251C ARG* 3.0 26.4 + - - +
252C ASP* 3.7 13.5 - - - +
254C ALA* 1.3 75.5 - - - +
256C LYS* 1.3 67.1 + - - +
257C GLU 3.2 7.1 + - - +
258C PRO* 5.5 0.2 - - - +
341C TYR* 3.8 32.9 + - - +
342C LEU 3.6 21.8 - - - +
343C GLU* 3.8 23.3 - - + +
391C TYR* 3.4 21.2 - - - -
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Residues in contact with LYS 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C ASP 3.5 18.1 + - - +
253C VAL* 3.1 14.7 + - + +
255C MET* 1.3 85.3 - - - +
257C GLU* 1.3 57.7 + - - +
343C GLU* 5.7 11.8 + - - -
389C ASN* 5.4 9.1 - - + +
390C ASP* 2.9 38.3 + - + +
391C TYR* 3.2 10.5 - - + +
392C LYS* 2.8 34.5 + - + +
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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