Contacts of the helix formed by residues 206 - 218 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204D ASP* 4.9 0.7 - - - +
205D GLU* 1.3 89.4 + - + +
207D SER* 1.3 59.4 + - - +
208D GLU* 2.8 34.0 + - - +
209D ASP* 3.0 14.1 + - - +
210D ARG* 3.0 28.1 + - - +
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Residues in contact with SER 207 (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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206D ASP* 1.3 79.4 + - - +
208D GLU* 1.3 61.4 + - - +
210D ARG* 3.4 14.3 + - - +
211D LEU* 3.1 35.6 + - - +
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Residues in contact with GLU 208 (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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206D ASP* 2.8 10.5 + - - +
207D SER* 1.3 80.1 + - - +
209D ASP* 1.3 64.5 + - - +
211D LEU* 3.6 15.5 + - + +
212D VAL* 3.5 20.1 + - - +
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Residues in contact with ASP 209 (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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203D PHE 3.9 4.9 - - - +
204D ASP* 3.5 7.3 - - - -
205D GLU* 2.8 31.1 + - + +
206D ASP* 3.0 25.2 + - - +
207D SER 3.3 0.2 - - - -
208D GLU* 1.3 78.9 - - - +
210D ARG* 1.3 61.1 + - - +
212D VAL* 3.2 19.1 - - - +
213D ASN* 3.3 24.0 + - - +
272D ASN* 4.7 9.6 + - - -
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Residues in contact with ARG 210 (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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204D ASP* 3.8 27.1 - - + +
206D ASP 3.0 17.5 + - - +
207D SER* 3.7 12.1 + - - +
208D GLU 3.3 0.4 - - - -
209D ASP* 1.3 76.2 - - - +
211D LEU* 1.3 81.7 + - - +
213D ASN* 3.3 6.0 + - - +
214D GLU* 3.0 68.2 + - - +
217D ARG* 5.0 0.2 - - - +
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Residues in contact with LEU 211 (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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207D SER* 3.1 23.6 + - - +
208D GLU* 3.9 10.3 - - - +
209D ASP 3.4 0.4 - - - -
210D ARG* 1.3 97.4 - - - +
212D VAL* 1.3 62.4 + - + +
214D GLU* 3.3 17.0 + - + +
215D LYS* 3.4 17.8 + - - +
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Residues in contact with VAL 212 (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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208D GLU 3.5 13.7 + - - +
209D ASP* 3.2 24.5 - - - +
211D LEU* 1.3 75.6 - - + +
213D ASN* 1.3 66.9 + - - +
215D LYS* 3.5 25.2 + - + +
216D PHE* 3.5 10.7 + - - +
268D THR* 5.7 8.1 - - + -
269D HIS* 4.1 13.1 + - + +
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Residues in contact with ASN 213 (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* 3.6 25.2 - - + +
203D PHE 5.3 1.6 + - - -
204D ASP* 2.5 26.4 + - - +
209D ASP* 3.3 29.5 + - - +
210D ARG 3.3 5.8 + - - +
211D LEU 3.2 0.6 - - - -
212D VAL* 1.3 79.6 - - - +
214D GLU* 1.3 59.1 + - - +
216D PHE* 3.1 6.2 + - - +
217D ARG* 3.0 45.1 + - - +
269D HIS* 3.4 19.6 + - - -
272D ASN* 4.5 8.4 + - - +
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Residues in contact with GLU 214 (chain D).
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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210D ARG* 3.0 48.2 + - - +
211D LEU* 3.3 13.4 + - + +
213D ASN* 1.3 78.0 - - - +
215D LYS* 1.3 57.9 + - + +
217D ARG* 2.6 29.3 + - - +
218D GLU* 3.0 51.9 + - - +
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Residues in contact with LYS 215 (chain D).
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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211D LEU 3.4 14.3 + - - +
212D VAL* 3.6 18.8 - - + +
213D ASN 3.3 0.4 - - - -
214D GLU* 1.3 77.1 - - + +
216D PHE* 1.3 59.3 + - - +
218D GLU* 4.0 14.4 + - - +
219D MET* 3.3 23.6 + - - +
260D TYR* 3.7 27.2 + - - +
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Residues in contact with PHE 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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165D VAL* 4.2 12.6 - - + -
198D TYR* 3.5 23.6 - + - -
199D PRO* 3.4 21.3 - - + -
212D VAL 3.5 3.7 + - - +
213D ASN 3.1 9.4 + - - +
214D GLU 3.1 0.6 - - - -
215D LYS* 1.3 78.8 - - - +
217D ARG* 1.3 64.6 + - - +
219D MET* 3.1 19.7 + - - +
220D ILE* 3.5 11.0 + - + +
222D PHE* 3.5 21.9 - + - -
261D LEU* 4.3 0.2 - - + -
264D LEU* 3.4 46.0 - - + -
265D LEU* 3.6 23.8 - - + -
269D HIS* 3.6 33.2 - + - +
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Residues in contact with ARG 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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187D THR* 5.8 3.3 - - - +
197D VAL* 5.8 3.6 - - + -
199D PRO* 2.7 37.3 + - + +
201D LYS* 3.5 17.6 - - - +
204D ASP* 2.6 41.4 + - - -
210D ARG* 4.4 1.2 + - - +
213D ASN* 3.0 24.6 + - - +
214D GLU* 2.6 52.1 + - - +
216D PHE* 1.3 77.3 - - - +
218D GLU* 1.3 62.7 + - + +
220D ILE* 3.2 31.5 + - + +
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Residues in contact with GLU 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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183D LYS* 4.8 8.5 - - - +
214D GLU* 3.0 39.2 + - - +
215D LYS* 4.2 13.6 - - - +
216D PHE 3.2 0.2 - - - -
217D ARG* 1.3 78.0 - - + +
219D MET* 1.3 64.2 + - + +
220D ILE 3.4 3.6 - - - +
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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