Contacts of the helix formed by residues 247 - 255 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239K TRP* 3.1 47.2 + - + +
242K VAL* 3.8 38.4 - - + -
245K PHE* 3.6 2.7 + - + +
246K ASP* 1.3 79.0 - - - +
248K THR* 1.3 62.8 + - - +
249K CYS 3.1 3.8 - - - +
250K ILE* 3.0 15.3 + - + +
251K ARG 3.3 7.6 + - - -
90L LEU* 4.5 2.2 - - + -
122L THR* 4.2 24.5 - - + -
124L ILE* 4.2 19.5 - - + -
127L MET* 4.3 14.6 - - + -
152L ILE* 4.1 29.4 - - + -
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Residues in contact with THR 248 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239K TRP 4.5 0.2 - - - -
240K GLU* 3.7 30.1 - - + -
246K ASP* 3.1 31.5 + - - +
247K MET* 1.3 73.5 - - - +
249K CYS* 1.3 66.1 + - - +
250K ILE 3.1 0.2 - - - -
251K ARG* 3.4 31.1 - - - +
252K ASP* 3.0 29.3 + - - +
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Residues in contact with CYS 249 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246K ASP* 4.7 0.6 + - - -
247K MET* 3.1 1.2 - - - -
248K THR* 1.3 82.0 + - - +
250K ILE* 1.3 65.4 + - - +
252K ASP* 3.9 10.5 - - - +
253K VAL* 3.8 19.2 + - - +
148L TYR* 4.1 22.0 - - + -
151L LYS* 4.2 29.2 - - + -
152L ILE* 3.5 32.8 - - - -
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Residues in contact with ILE 250 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239K TRP* 3.5 48.7 - - + -
247K MET* 3.0 10.3 + - - +
249K CYS* 1.3 80.2 - - - +
251K ARG* 1.3 57.9 + - - +
252K ASP 3.0 1.8 - - - -
253K VAL* 2.7 29.9 + - + +
254K ALA* 2.9 10.6 + - + +
83L PHE* 3.8 20.0 - - + -
86L HIS* 6.2 0.2 - - + -
122L THR* 4.0 14.6 - - + -
145L ILE* 4.7 9.0 - - + -
148L TYR* 4.3 17.9 - - + -
152L ILE* 3.7 29.6 - - + -
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Residues in contact with ARG 251 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236K ILE* 3.0 39.4 - - + +
237K HIS* 4.9 3.5 + - - -
239K TRP* 3.5 27.0 - - + -
240K GLU* 3.1 31.0 + - + +
247K MET 3.3 3.4 + - - -
248K THR* 3.4 35.5 - - - +
250K ILE* 1.3 76.9 - - - +
252K ASP* 1.3 87.4 + - - +
254K ALA* 3.1 3.8 + - - +
255K MET* 3.0 38.5 + - - +
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Residues in contact with ASP 252 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248K THR* 3.0 17.7 + - - +
249K CYS* 3.9 11.4 - - - +
251K ARG* 1.3 109.8 + - - +
253K VAL* 1.3 61.8 + - + +
255K MET* 3.8 9.7 - - - +
256K LYS* 3.5 23.7 + - - +
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Residues in contact with VAL 253 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249K CYS 3.8 6.7 - - - +
250K ILE* 2.7 15.9 + - + +
252K ASP* 1.3 74.4 - - + +
254K ALA* 1.3 63.3 + - - +
256K LYS* 3.1 22.4 + - + +
257K GLU* 3.6 7.4 + - - +
83L PHE* 4.3 19.3 - - + -
148L TYR* 3.2 42.4 - - + +
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Residues in contact with ALA 254 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235K LYS 5.0 2.0 - - - +
236K ILE* 5.0 8.7 - - + -
239K TRP* 4.2 17.9 - - + +
250K ILE 2.9 10.8 + - - +
251K ARG* 3.1 10.1 + - - +
253K VAL* 1.3 74.4 - - - +
255K MET* 1.3 60.1 + - - +
257K GLU* 3.0 28.9 + - - +
259K LEU* 5.3 3.1 - - - +
341K TYR* 5.9 1.4 - - - -
83L PHE* 3.9 34.1 - - + -
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Residues in contact with MET 255 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232K LYS* 3.8 4.5 - - - +
236K ILE* 3.7 36.0 - - + +
237K HIS* 5.5 1.8 - - + -
251K ARG* 3.0 28.3 + - - +
252K ASP* 3.8 10.3 - - - +
254K ALA* 1.3 76.7 - - - +
256K LYS* 1.3 68.7 + - - +
257K GLU 3.2 3.7 + - - +
341K TYR* 3.8 33.5 + - - +
342K LEU 3.7 24.5 - - - +
343K GLU* 3.7 23.8 - - + +
391K TYR* 3.4 21.7 - - - -
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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