Contacts of the helix formed by residues 214 - 220 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202B ALA* 3.8 10.5 - - + -
209B LEU* 3.9 18.8 - - + -
210B ASN 3.5 1.2 + - - -
211B ALA* 3.1 12.8 + - - +
213B ARG* 1.3 77.5 - - - +
215B ILE* 1.3 61.9 + - - +
216B SER* 3.6 20.4 - - - -
217B PHE* 3.0 6.1 + - - +
218B LEU* 2.8 27.6 + - - +
502B SF4 2.3 42.6 - - - -
503B B12 3.8 16.8 - - + -
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Residues in contact with ILE 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B PRO* 4.9 6.7 - - + -
200B THR* 3.7 26.2 - - + -
213B ARG 3.6 1.0 + - - -
214B CYS* 1.3 71.2 - - - +
216B SER* 1.3 57.1 + - - +
218B LEU* 4.1 16.2 - - + -
219B THR* 2.8 47.9 + - + +
229B PHE* 4.8 4.5 - - + -
232B LYS* 4.2 12.1 - - + +
233B ILE* 4.2 27.4 - - + +
236B ARG* 3.7 30.3 - - - +
240B CYS* 3.8 8.1 - - + -
502B SF4 3.2 22.1 - - - -
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Residues in contact with SER 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B CYS* 3.1 17.9 + - - -
215B ILE* 1.3 78.6 - - - +
217B PHE* 1.3 59.4 + - - +
219B THR* 2.8 19.2 + - - -
220B GLN* 3.0 24.2 + - - +
239B GLY* 3.8 13.1 + - - -
240B CYS* 3.8 5.6 - - - +
502B SF4 4.1 2.9 - - - -
503B B12 2.7 51.4 + - - +
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Residues in contact with PHE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B SER* 3.3 29.8 - - - -
49B PHE* 3.6 26.7 - + - -
211B ALA 3.3 29.2 - - - +
212B GLN* 3.7 32.5 - - - -
214B CYS 3.0 3.8 + - - +
216B SER* 1.3 79.8 + - - +
218B LEU* 1.3 74.8 + - + +
220B GLN* 2.8 26.8 + - - +
221B THR* 3.5 31.6 + - + +
503B B12 3.7 24.5 - - + +
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B GLN 3.5 19.7 - - - +
213B ARG 3.8 15.3 - - - +
214B CYS 2.8 25.8 + - - +
215B ILE* 3.2 13.0 + - + +
217B PHE* 1.3 83.0 - - + +
219B THR* 1.3 60.0 + - + +
220B GLN 3.0 0.2 + - - -
221B THR* 3.0 16.9 + - + -
225B LEU* 3.8 23.6 - - + +
226B PRO* 4.7 6.1 - - + -
229B PHE* 3.5 46.2 - - + -
233B ILE* 5.7 2.2 - - + -
302B ARG* 2.8 20.3 + - - -
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Residues in contact with THR 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B ILE* 2.8 34.3 + - + +
216B SER 2.8 20.4 + - - -
218B LEU* 1.3 72.3 - - + +
220B GLN* 1.3 59.4 + - - +
221B THR 3.4 0.2 - - - -
233B ILE* 3.8 24.7 - - + -
236B ARG* 4.3 6.5 - - + +
237B LEU 4.4 1.2 - - - +
238B TYR* 3.6 7.8 - - - -
239B GLY 2.9 29.2 + - - +
299B PRO* 3.4 14.9 - - - +
302B ARG* 3.6 3.8 + - - +
303B ASN* 3.0 31.6 + - - +
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Residues in contact with GLN 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B PHE* 4.0 13.6 - - + -
216B SER* 3.0 32.7 + - - +
217B PHE 2.8 9.6 + - - +
219B THR* 1.3 77.6 + - - +
221B THR* 1.3 63.1 + - - +
238B TYR* 3.4 37.4 + - + -
239B GLY 5.0 0.8 - - - +
294B TRP* 2.9 19.3 + - - +
295B ARG* 2.9 36.9 + - + +
299B PRO* 4.1 7.2 - - - +
503B B12 4.0 6.3 - - - +
504B GOL 2.8 36.3 + - - -
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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