Contacts of the helix formed by residues 214 - 219 (chain A) in PDB entry 5T8Y
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 CYS 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A ALA* 3.6 15.7 - - + +
209A LEU* 4.2 8.5 - - + -
210A ASN 3.1 3.6 + - - -
211A ALA* 3.2 20.9 + - - +
213A ARG* 1.3 76.4 - - - +
215A ILE* 1.3 65.5 + - - +
216A SER* 3.5 24.0 - - - -
217A PHE* 3.1 4.9 + - - +
218A LEU* 3.1 22.3 + - - +
502A SF4 2.3 37.5 - - - -
503A B12 3.9 14.6 - - + -
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Residues in contact with ILE 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A PRO* 3.7 30.5 - - + -
200A THR* 3.8 16.8 - - + -
213A ARG 3.4 0.2 + - - -
214A CYS* 1.3 70.4 - - - +
216A SER* 1.3 62.6 + - - +
218A LEU* 3.6 11.6 - - + +
219A THR* 3.0 37.9 + - + +
229A PHE* 6.4 0.2 - - + -
232A LYS 3.5 25.1 - - - +
233A ILE* 4.4 13.0 - - + -
236A ARG* 3.8 30.5 - - - +
239A GLY 4.8 0.4 - - - +
240A CYS* 4.1 6.1 - - + -
502A SF4 3.0 17.6 - - - -
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Residues in contact with SER 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A CYS* 3.2 17.9 - - - -
215A ILE* 1.3 78.7 - - - +
217A PHE* 1.3 58.0 + - - +
219A THR* 3.0 12.8 + - - -
220A GLN* 2.8 30.4 + - - +
239A GLY* 3.8 14.4 + - - -
240A CYS* 3.9 6.0 - - - +
502A SF4 4.2 4.5 - - - -
503A B12 2.8 49.3 + - - +
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Residues in contact with PHE 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A SER* 3.1 37.5 - - - -
49A PHE* 3.5 36.6 - + - -
211A ALA 3.2 29.2 - - - +
212A GLN* 3.6 27.4 - - - -
214A CYS 3.1 3.3 + - - +
216A SER* 1.3 78.1 - - - +
218A LEU* 1.3 73.4 + - + +
219A THR 3.2 0.2 - - - -
220A GLN* 3.0 15.6 + - - +
221A THR* 3.4 30.1 + - + +
503A B12 3.7 20.1 - - + +
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Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A GLN 3.3 20.0 - - - +
213A ARG 3.6 15.5 - - - +
214A CYS 3.1 15.8 + - - +
215A ILE* 3.1 17.9 + - + +
217A PHE* 1.3 85.5 - - + +
219A THR* 1.3 59.8 + - + +
220A GLN 3.1 0.2 - - - -
221A THR* 2.5 30.4 + - + -
225A LEU* 3.6 21.0 - - + +
226A PRO* 4.9 5.6 - - + -
229A PHE* 3.5 44.9 - - + -
233A ILE* 6.2 0.2 - - - -
302A ARG* 2.8 10.4 + - - -
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Residues in contact with THR 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ILE* 3.0 24.4 + - + +
216A SER 3.0 17.3 + - - -
218A LEU* 1.3 76.9 - - + +
220A GLN* 1.3 60.9 + - - +
221A THR 3.5 0.4 - - - -
233A ILE* 3.9 27.4 - - + -
236A ARG* 4.2 9.6 - - + +
237A LEU 4.0 9.5 - - - +
238A TYR* 3.8 4.8 - - - +
239A GLY 3.2 20.0 + - - +
299A PRO* 3.7 11.3 - - - +
300A ILE* 5.8 0.7 - - - +
302A ARG* 4.1 2.6 + - - +
303A ASN* 3.0 31.7 + - - +
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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