Contacts of the helix formed by residues 206 - 218 (chain C) in PDB entry 5CYP
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 ASP 206 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204C ASP 4.9 0.2 - - - -
205C GLU* 1.3 89.6 + - - +
207C SER* 1.3 58.6 + - - +
208C GLU* 2.9 32.9 + - - +
209C ASP* 3.0 14.0 + - - +
210C ARG* 2.9 29.3 + - - +
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Residues in contact with SER 207 (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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206C ASP* 1.3 76.8 - - - +
208C GLU* 1.3 62.0 + - - +
210C ARG* 3.5 14.6 + - - +
211C LEU* 3.2 31.7 + - - +
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Residues in contact with GLU 208 (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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206C ASP* 2.9 10.5 + - - +
207C SER* 1.3 77.2 - - - +
209C ASP* 1.3 63.8 + - - +
210C ARG 3.6 0.2 + - - -
211C LEU* 3.7 9.0 + - - +
212C VAL* 3.4 25.3 + - - +
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Residues in contact with ASP 209 (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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203C PHE 3.8 4.7 - - - +
204C ASP* 3.4 6.9 - - - -
205C GLU* 2.7 32.1 + - + +
206C ASP* 3.0 27.4 + - - +
208C GLU* 1.3 76.1 - - - +
210C ARG* 1.3 63.1 + - - +
212C VAL* 3.2 13.8 - - - +
213C ASN* 3.2 31.2 + - - +
272C ASN* 5.0 6.7 + - - -
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Residues in contact with ARG 210 (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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204C ASP* 4.0 25.5 - - + +
206C ASP 2.9 18.7 + - - +
207C SER* 3.7 11.7 + - - +
208C GLU 3.3 0.2 - - - -
209C ASP* 1.3 77.1 - - - +
211C LEU* 1.3 83.7 + - - +
213C ASN* 3.3 5.7 + - - +
214C GLU* 2.8 66.9 + - - +
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Residues in contact with LEU 211 (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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207C SER* 3.2 20.7 + - - +
208C GLU* 4.1 9.0 - - - +
209C ASP 3.4 0.2 - - - -
210C ARG* 1.3 104.4 - - - +
212C VAL* 1.3 63.5 + - + +
214C GLU* 3.3 8.9 + - + +
215C LYS* 3.2 20.6 + - - +
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Residues in contact with VAL 212 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208C GLU 3.4 14.6 + - - +
209C ASP* 3.2 24.2 - - - +
211C LEU* 1.3 75.9 - - + +
213C ASN* 1.3 65.6 + - - +
215C LYS* 3.5 9.5 + - - +
216C PHE 3.4 13.5 + - - -
268C THR* 5.7 9.2 - - + -
269C HIS* 4.1 15.8 + - + +
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Residues in contact with ASN 213 (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 21.6 - - + +
200C GLN 5.0 0.2 + - - -
203C PHE* 5.0 1.8 + - - +
204C ASP* 2.4 31.4 + - - +
209C ASP* 3.2 30.3 + - - +
210C ARG 3.3 4.7 + - - +
211C LEU 3.2 0.4 - - - -
212C VAL* 1.3 81.3 - - - +
214C GLU* 1.3 63.2 + - - +
216C PHE* 3.1 6.1 + - - +
217C ARG* 3.0 37.0 + - - +
269C HIS* 3.6 18.1 + - - -
272C ASN* 4.6 11.1 + - - +
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Residues in contact with GLU 214 (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 ARG* 2.8 52.3 + - - +
211C LEU* 3.3 11.4 + - + +
213C ASN* 1.3 78.0 - - - +
215C LYS* 1.3 56.1 + - - +
217C ARG* 2.8 33.8 + - - +
218C GLU* 2.9 51.2 + - - +
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Residues in contact with LYS 215 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211C LEU 3.2 9.5 + - - +
212C VAL* 3.6 12.8 - - - +
213C ASN 3.2 0.4 - - - -
214C GLU* 1.3 78.4 - - - +
216C PHE* 1.3 60.8 + - - +
218C GLU* 4.0 14.6 + - - +
219C MET* 3.3 23.9 + - - +
264C LEU* 5.4 2.2 - - - +
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Residues in contact with PHE 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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165C VAL* 4.0 21.8 - - + -
198C TYR* 3.6 21.1 - + - -
199C PRO* 3.4 19.1 - - + -
212C VAL 3.4 2.8 + - - +
213C ASN 3.1 9.5 + - - +
214C GLU 3.1 0.2 - - - -
215C LYS* 1.3 78.3 - - - +
217C ARG* 1.3 65.2 + - - +
218C GLU 3.2 0.2 - - - -
219C MET* 3.1 16.6 + - - +
220C ILE* 3.4 12.6 + - + +
222C PHE* 3.4 24.2 - + - -
261C LEU* 4.3 0.9 - - + -
264C LEU* 3.5 38.1 - - + -
265C LEU* 4.2 15.0 - - + -
269C HIS* 3.3 43.7 - + + +
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Residues in contact with ARG 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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187C THR* 5.5 3.8 + - - +
197C VAL* 5.6 4.3 - - + -
199C PRO* 2.6 61.2 + - + +
201C LYS* 3.8 17.0 - - - +
204C ASP* 2.8 33.8 + - - -
210C ARG* 4.1 2.2 + - - +
213C ASN* 3.0 24.6 + - - +
214C GLU* 2.8 41.8 + - - +
216C PHE* 1.3 75.8 - - - +
218C GLU* 1.3 62.6 + - + +
219C MET 3.3 0.7 + - - -
220C ILE* 3.3 30.9 + - + +
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Residues in contact with GLU 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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183C LYS* 4.8 7.3 + - - +
214C GLU* 2.9 42.7 + - - +
215C LYS* 4.1 12.6 + - - +
216C PHE 3.2 0.4 - - - -
217C ARG* 1.3 77.5 - - - +
219C MET* 1.3 62.2 + - + +
220C ILE 4.3 3.2 - - - +
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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