Contacts of the helix formed by residues 214 - 220 (chain D) in PDB entry 5D0A
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202D ALA* 3.7 11.9 - - + -
209D LEU* 3.9 20.2 - - + -
210D ASN 3.5 1.2 + - - -
211D ALA 3.0 12.2 + - - +
213D ARG* 1.3 78.8 - - - +
215D ILE* 1.3 60.4 + - - +
216D SER* 3.4 21.8 - - - -
217D PHE* 3.0 6.6 + - - +
218D LEU* 2.8 27.5 + - - +
502D SF4 2.3 39.9 - - - -
503D B12 3.8 16.4 - - + -
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Residues in contact with ILE 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D PRO* 3.8 25.8 - - + -
200D THR* 3.8 18.8 - - + -
213D ARG 3.6 0.8 + - - +
214D CYS* 1.3 71.9 - - - +
216D SER* 1.3 63.1 + - - +
218D LEU* 4.0 11.7 - - + -
219D THR* 2.9 41.0 + - + +
229D PHE* 6.0 1.6 - - + -
232D LYS* 3.4 27.4 - - + +
233D ILE* 4.3 12.1 - - + -
236D ARG* 3.7 35.4 - - - +
240D CYS* 4.0 4.3 - - + -
502D SF4 3.1 17.3 - - - -
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Residues in contact with SER 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D CYS* 3.2 16.1 - - - -
215D ILE* 1.3 77.1 - - - +
217D PHE* 1.3 61.4 + - - +
219D THR* 2.8 19.4 + - - -
220D GLN* 3.0 24.4 + - - +
239D GLY* 3.9 12.7 - - - -
240D CYS* 3.8 7.2 - - - +
502D SF4 4.3 2.5 - - - -
503D B12 2.9 51.3 + - - +
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Residues in contact with PHE 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D SER* 3.3 31.4 - - - -
49D PHE* 3.8 26.0 - + - -
211D ALA 3.3 28.7 - - - +
212D GLN* 3.4 34.5 - - - -
214D CYS 3.0 4.0 + - - +
216D SER* 1.3 77.7 + - - +
218D LEU* 1.3 75.2 + - + +
220D GLN* 2.9 26.1 + - - +
221D THR* 3.6 29.7 + - + +
503D B12 3.7 24.2 - - + +
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Residues in contact with LEU 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D GLN 3.5 17.5 - - - +
213D ARG 3.8 13.9 - - - +
214D CYS 2.8 24.6 + - - +
215D ILE* 3.2 12.5 + - + +
217D PHE* 1.3 85.7 - - + +
219D THR* 1.3 59.3 + - + +
220D GLN 3.1 0.3 + - - -
221D THR* 2.9 26.8 + - + -
225D LEU* 3.8 22.7 - - + +
226D PRO* 4.7 6.5 - - + -
229D PHE* 3.5 48.9 - - + -
233D ILE* 6.0 1.3 - - + -
302D ARG* 2.9 11.6 + - - -
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Residues in contact with THR 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D ILE* 2.9 35.5 + - + +
216D SER 2.8 19.6 + - - -
218D LEU* 1.3 75.6 - - - +
220D GLN* 1.3 60.6 + - - +
233D ILE* 4.0 20.4 - - + -
236D ARG* 4.6 2.9 - - + +
237D LEU 4.4 0.9 - - - +
238D TYR* 3.7 11.4 - - - +
239D GLY 2.9 30.5 + - - +
299D PRO* 3.5 15.1 - - - +
300D ILE* 5.7 0.2 - - - +
302D ARG* 3.6 4.4 + - - +
303D ASN* 2.9 31.1 + - - +
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Residues in contact with GLN 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D PHE* 4.0 14.0 - - + -
216D SER* 3.0 33.5 + - - +
217D PHE 2.9 9.8 + - - +
219D THR* 1.3 80.9 + - - +
221D THR* 1.3 62.3 + - - +
238D TYR* 3.4 32.0 + - + -
239D GLY* 5.1 1.2 - - - +
294D TRP* 3.0 18.3 + - - +
295D ARG* 2.9 38.4 + - + +
299D PRO* 4.2 7.2 - - - +
503D B12 4.1 6.1 - - - +
504D GOL 2.6 37.4 + - - -
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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