Contacts of the helix formed by residues 214 - 221 (chain C) in PDB entry 5AO4
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 SER 214 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ILE* 4.0 2.1 - - - +
148C LYS 3.3 7.1 + - - -
149C GLN 3.2 18.3 + - - -
150C LEU 5.5 0.2 - - - -
164C ARG* 2.9 33.5 + - - +
210C HIS* 3.3 27.3 + - - -
211C GLY 3.1 12.0 + - - +
213C PHE* 1.3 78.9 - - - +
215C HIS* 1.3 63.8 + - - -
216C MET 3.1 0.2 - - - -
217C PHE* 2.8 30.8 + - - +
218C ASP* 4.0 1.4 - - - +
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Residues in contact with HIS 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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149C GLN 5.2 0.6 + - - -
164C ARG* 3.6 27.3 + - - -
210C HIS* 3.6 18.6 + + - -
213C PHE 3.3 1.2 + - - -
214C SER* 1.3 79.8 - - - +
216C MET* 1.3 62.2 + - - +
217C PHE 3.1 0.9 + - - -
218C ASP* 3.3 12.1 - - - +
219C GLY* 3.3 23.9 + - - -
220C ARG* 4.7 0.2 - - - +
233C HIS* 4.3 13.3 - + - -
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Residues in contact with MET 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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212C PRO 3.5 20.9 - - - +
213C PHE* 3.5 31.2 + - + +
214C SER 2.9 0.6 + - - -
215C HIS* 1.3 78.4 - - - +
217C PHE* 1.3 64.6 + - + +
220C ARG* 3.2 12.9 + - + +
221C PHE* 3.2 22.8 + - + +
383C ASP* 3.4 49.0 + - + +
386C ILE* 3.6 18.2 - - + -
387C THR* 3.3 19.1 - - - +
390C PHE* 3.8 24.0 - - + -
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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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211C GLY* 3.9 18.4 - - - +
212C PRO* 3.6 33.7 + - + +
214C SER 2.8 14.1 + - - +
216C MET* 1.3 82.1 - - + +
218C ASP* 1.3 61.3 + - + +
219C GLY 3.4 0.2 + - - -
221C PHE* 3.5 20.7 - + - +
222C ILE* 3.2 42.7 + - + +
231C TRP* 4.4 9.0 - - - -
390C PHE* 5.0 7.4 - + - -
409C ILE* 3.9 23.3 - - + -
413C ILE* 3.7 26.5 - - + -
419C TYR* 4.0 10.3 - + - -
422C LEU* 3.7 23.8 - - + -
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Residues in contact with ASP 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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210C HIS* 4.6 1.4 - - - -
214C SER 4.0 2.6 - - - +
215C HIS* 3.3 27.9 - - - +
217C PHE* 1.3 76.2 - - + +
219C GLY* 1.3 57.3 + - - +
220C ARG 3.8 0.4 - - - -
222C ILE* 4.6 1.4 - - - +
223C PRO* 3.9 10.6 - - - +
231C TRP* 3.8 38.0 - - + +
232C THR* 4.1 5.2 - - - +
233C HIS* 3.2 42.5 + - + +
470C ARG* 3.3 27.0 + - - -
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Residues in contact with GLY 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 HIS 3.3 13.4 + - - -
218C ASP* 1.3 80.4 + - - +
220C ARG* 1.3 64.1 + - - +
223C PRO* 4.4 7.7 - - - +
470C ARG* 3.8 21.9 + - - -
473C TYR* 5.0 9.5 + - - -
501C ASP* 5.6 0.3 - - - +
502C VAL 4.9 8.1 - - - +
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Residues in contact with ARG 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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215C HIS 4.7 0.4 - - - +
216C MET* 3.2 22.5 + - + +
219C GLY* 1.3 80.6 - - - +
221C PHE* 1.3 63.5 + - - +
223C PRO* 4.1 5.7 - - - +
224C LEU* 4.7 6.3 - - - +
383C ASP* 5.8 4.3 - - + -
384C THR* 5.8 4.9 - - + +
387C THR* 3.1 24.3 - - - +
473C TYR* 6.5 1.6 - - - -
501C ASP* 4.9 13.2 - - - +
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Residues in contact with PHE 221 (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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216C MET* 3.2 10.1 + - + +
217C PHE* 3.5 25.5 + + + +
220C ARG* 1.3 81.1 - - - +
222C ILE* 1.3 91.2 + - + +
223C PRO* 3.2 1.5 - - - +
224C LEU* 2.7 27.1 + - - +
225C ALA* 2.8 25.4 + - + -
387C THR* 3.7 26.7 - - + +
390C PHE* 3.6 28.7 - + + -
391C LEU* 3.4 25.1 - - + -
394C ASP* 4.8 2.2 - - - -
409C ILE* 4.0 30.5 - - + -
410C SER* 4.3 8.1 - - - -
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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