Contacts of the helix formed by residues 242 - 250 (chain H) in PDB entry 5TWV
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 LYS 242 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238H LYS 3.0 12.9 + - - +
239H THR* 3.0 14.6 + - - +
240H ALA 3.2 0.7 - - - +
241H HIS* 1.3 77.2 - - - +
243H LYS* 1.3 64.3 + - - +
244H PRO* 4.6 3.1 - - + -
245H ILE* 3.4 28.7 - - + +
246H ASP* 3.2 12.5 + - - +
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Residues in contact with LYS 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241H HIS 3.4 4.4 + - - +
242H LYS* 1.3 71.3 - - - +
244H PRO* 1.3 80.8 - - + +
246H ASP* 3.5 11.8 + - - +
247H LEU* 3.6 11.3 + - - +
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Residues in contact with PRO 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242H LYS* 3.8 3.8 - - + -
243H LYS* 1.3 99.5 - - + +
245H ILE* 1.3 62.2 + - - +
247H LEU* 3.6 11.1 + - + +
248H ARG* 3.7 10.7 + - - +
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Residues in contact with ILE 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239H THR* 3.8 15.9 - - - +
242H LYS* 3.4 23.7 + - + +
243H LYS 3.3 0.4 - - - -
244H PRO* 1.3 79.9 - - - +
246H ASP* 1.3 59.2 + - - +
248H ARG* 3.3 7.0 + - - +
249H ALA* 2.8 31.6 + - + +
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Residues in contact with ASP 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239H THR 3.5 10.3 + - - +
240H ALA* 3.8 14.1 - - - +
242H LYS 3.2 19.6 + - - +
243H LYS* 3.8 6.1 - - - +
244H PRO 3.3 0.6 - - - -
245H ILE* 1.3 76.5 - - - +
247H LEU* 1.3 60.7 + - - +
249H ALA* 3.8 5.1 - - - +
250H ILE* 2.8 34.6 + - + +
1184H VAL* 6.0 3.8 - - + -
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Residues in contact with LEU 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243H LYS 3.6 9.3 + - - +
244H PRO* 4.0 8.3 - - + +
245H ILE 3.3 0.4 - - - -
246H ASP* 1.3 80.7 - - - +
248H ARG* 1.3 63.5 + - - +
250H ILE* 3.6 8.5 + - - +
251H ALA* 3.6 16.1 + - - +
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Residues in contact with ARG 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A ASP* 6.0 1.6 - - - +
244H PRO 3.7 8.9 + - - +
245H ILE* 3.3 9.6 + - - +
246H ASP 3.3 0.4 - - - -
247H LEU* 1.3 80.0 - - - +
249H ALA* 1.3 59.7 + - - +
251H ALA* 3.3 4.3 + - - +
252H LYS* 3.2 28.1 + - - +
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Residues in contact with ALA 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239H THR* 4.4 17.7 - - - -
240H ALA* 6.4 0.2 - - - -
245H ILE* 2.8 23.3 + - + +
246H ASP* 3.8 6.1 - - - +
248H ARG* 1.3 74.9 - - - +
250H ILE* 1.3 56.0 + - - +
251H ALA 3.1 5.1 + - - -
252H LYS 5.3 0.7 - - - -
253H LEU* 3.3 29.3 + - - +
256H ALA* 4.9 8.4 - - + +
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Residues in contact with ILE 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246H ASP* 2.8 22.4 + - + +
247H LEU* 4.0 5.2 - - - +
248H ARG 3.4 0.2 - - - -
249H ALA* 1.3 72.3 - - - +
251H ALA* 1.3 58.0 + - - +
253H LEU* 4.8 5.2 - - - -
1188H ASP* 3.5 37.2 - - + +
1191H GLN* 5.6 3.6 - - - +
1192H LEU* 5.5 4.6 - - - +
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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