Contacts of the helix formed by residues 214 - 220 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202C ALA* 3.7 11.7 - - + -
209C LEU* 3.9 20.0 - - + -
210C ASN 3.5 1.2 + - - -
211C ALA* 3.1 11.7 + - - +
213C ARG* 1.3 78.1 - - - +
215C ILE* 1.3 59.8 + - - +
216C SER* 3.5 21.1 - - - -
217C PHE* 3.0 6.2 + - - +
218C LEU* 2.9 27.6 + - - +
502C SF4 2.3 41.3 - - - -
503C B12 3.9 16.4 - - + -
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Residues in contact with ILE 215 (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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199C PRO* 3.7 27.1 - - + -
200C THR* 4.0 18.4 - - + -
213C ARG 3.6 1.0 + - - -
214C CYS* 1.3 71.0 - - - +
216C SER* 1.3 57.9 + - - +
218C LEU* 4.0 12.6 - - + -
219C THR* 2.8 41.3 + - + +
229C PHE* 6.3 0.9 - - + -
232C LYS* 3.6 24.9 - - + +
233C ILE* 4.7 11.2 - - + -
236C ARG* 3.6 37.2 - - - +
240C CYS* 3.8 5.4 - - + -
502C SF4 3.1 17.6 - - - -
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Residues in contact with SER 216 (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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214C CYS* 3.1 16.8 - - - -
215C ILE* 1.3 79.6 - - - +
217C PHE* 1.3 61.1 + - - +
219C THR* 2.9 18.0 + - - -
220C GLN* 2.9 23.8 + - - +
239C GLY* 3.7 12.7 - - - -
240C CYS* 3.8 6.5 - - - +
502C SF4 4.2 2.5 - - - -
503C B12 2.7 50.6 + - - +
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Residues in contact with PHE 217 (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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47C SER* 3.3 34.5 - - - -
49C PHE* 3.8 28.5 - + - -
211C ALA 3.2 28.3 - - - +
212C GLN* 3.6 28.3 - - - -
214C CYS 3.0 3.4 + - - +
216C SER* 1.3 79.1 - - - +
218C LEU* 1.3 73.6 + - + +
220C GLN* 2.9 21.9 + - - +
221C THR* 3.5 31.5 + - + +
503C B12 3.7 24.9 - - + +
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Residues in contact with LEU 218 (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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212C GLN 3.5 19.3 - - - +
213C ARG 3.9 13.0 - - - +
214C CYS 2.9 25.5 + - - +
215C ILE* 3.2 12.5 + - + +
217C PHE* 1.3 85.3 - - + +
219C THR* 1.3 58.0 + - + +
220C GLN 3.1 0.2 + - - -
221C THR* 2.9 17.9 + - + -
225C LEU* 3.8 19.3 - - + +
226C PRO* 4.9 5.8 - - + -
229C PHE* 3.4 50.7 - - + -
233C ILE* 6.3 0.4 - - - -
302C ARG* 2.9 20.4 + - - -
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Residues in contact with THR 219 (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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215C ILE* 2.8 37.7 + - + +
216C SER 2.9 17.7 + - - -
218C LEU* 1.3 73.0 - - + +
220C GLN* 1.3 61.8 + - - +
233C ILE* 4.3 16.2 - - + -
236C ARG* 4.6 2.9 - - + +
237C LEU 4.5 1.4 - - - +
238C TYR* 3.6 12.8 - - - +
239C GLY 2.9 29.6 + - - +
299C PRO* 3.5 13.7 - - - +
300C ILE* 5.6 0.2 - - - +
302C ARG* 3.6 3.7 + - - +
303C ASN* 3.1 32.9 + - - +
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Residues in contact with GLN 220 (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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49C PHE* 3.9 14.3 - - + -
216C SER* 2.9 32.8 + - - +
217C PHE 2.9 10.3 + - - +
219C THR* 1.3 78.8 - - - +
221C THR* 1.3 64.5 + - - +
238C TYR* 3.5 31.6 + - + -
239C GLY* 5.2 1.0 - - - +
294C TRP* 2.9 19.1 + - - +
295C ARG* 3.0 33.0 + - + +
299C PRO* 4.2 8.0 - - - +
503C B12 3.9 12.5 - - - +
504C GOL 2.8 31.1 + - - -
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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