Contacts of the helix formed by residues 204 - 217 (chain A) in PDB entry 3FR0
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 ASN 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A THR* 5.9 1.5 - - + +
150A PHE 3.6 7.4 - - - -
152A PHE 3.8 13.5 + - - +
156A HIS* 5.4 4.2 + - - +
203A VAL* 1.3 77.5 - - - +
205A ASP* 1.3 82.4 + - - +
206A THR* 2.8 27.7 + - - +
207A VAL* 3.1 22.2 + - + +
208A ALA 3.1 10.2 + - - -
231A ASN* 3.5 0.6 + - - -
254A ASN* 3.2 29.1 - - + +
256A GLU* 3.5 0.8 + - - -
500A GLC 2.7 35.0 + - - -
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Residues in contact with ASP 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ASP* 5.5 0.2 - - - +
149A THR* 4.0 17.7 - - + +
151A SER* 3.4 23.3 + - - +
203A VAL 3.8 0.8 + - - -
204A ASN* 1.3 73.0 - - - +
206A THR* 1.3 64.6 + - - -
208A ALA* 3.9 3.6 - - - +
209A THR* 3.1 28.3 + - - +
225A ILE* 3.6 19.3 - - + +
445A SER* 4.7 5.5 - - - +
500A GLC 2.6 51.7 + - - -
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Residues in contact with THR 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ASN* 2.8 24.7 + - - +
205A ASP* 1.3 77.8 + - - +
207A VAL* 1.3 67.5 + - - +
209A THR* 3.5 1.4 + - - -
210A MET 3.1 22.3 + - - -
223A GLY* 3.5 14.8 - - - +
225A ILE* 3.5 20.4 - - + -
231A ASN* 3.5 44.4 + - - +
232A ALA 3.7 0.4 - - - +
233A CYS* 3.3 30.8 - - - +
254A ASN* 4.4 1.4 + - - -
500A GLC 3.8 2.7 - - - +
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Residues in contact with VAL 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A THR* 4.0 19.1 - - + -
62A VAL* 4.2 20.0 - - + -
203A VAL* 4.2 16.8 - - + -
204A ASN* 3.4 19.3 - - + +
206A THR* 1.3 88.8 + - - +
208A ALA* 1.3 67.5 + - - +
210A MET* 3.0 4.8 + - + +
211A ILE* 2.9 38.6 + - + +
233A CYS* 3.5 10.1 - - + -
252A CYS* 3.9 26.7 - - - -
254A ASN* 5.2 0.7 - - + -
452A VAL* 5.2 0.2 - - + -
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Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A THR* 3.8 12.1 - - - +
203A VAL* 4.0 6.7 - - + +
204A ASN 3.1 8.7 + - - +
205A ASP* 3.9 6.5 - - - +
207A VAL* 1.3 78.3 - - - +
209A THR* 1.3 56.6 + - - +
211A ILE* 3.2 4.2 + - - +
212A SER* 2.9 25.8 + - - -
444A GLY 3.1 22.2 - - - +
445A SER* 3.6 20.4 - - - +
448A GLY* 3.3 14.0 - - - -
449A ALA 3.9 3.1 - - - +
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Residues in contact with THR 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ASP 3.1 18.2 + - - -
206A THR* 3.6 4.5 - - - +
208A ALA* 1.3 74.4 - - - +
210A MET* 1.3 66.7 + - - +
212A SER* 3.3 2.3 + - - -
213A CYS* 3.1 23.7 + - - -
224A MET 4.7 2.5 - - - +
225A ILE* 3.8 12.7 - - - +
407A GLY* 3.8 29.4 - - - +
408A VAL* 3.8 9.2 - - - +
409A ASP* 3.8 6.1 + - + +
441A SER* 3.5 25.5 + - - +
444A GLY* 3.8 14.3 + - - -
445A SER* 4.6 1.0 + - - -
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Residues in contact with MET 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A THR 3.1 14.2 + - - +
207A VAL* 3.0 7.9 + - + +
209A THR* 1.3 76.8 - - - +
211A ILE* 1.3 83.0 + - + +
213A CYS* 3.3 3.1 + - - +
214A TYR* 2.9 26.6 + - - +
220A CYS* 3.8 16.1 - - - +
221A GLU* 3.5 27.4 - - - +
222A VAL 3.7 17.3 - - - +
223A GLY* 3.8 15.9 - - - -
233A CYS* 4.1 2.9 - - - +
234A TYR* 4.6 0.4 - - - -
235A MET* 3.5 28.7 - - - +
252A CYS* 3.8 23.3 - - + -
407A GLY* 5.2 0.4 - - - -
501A AJB 4.1 8.5 - - - -
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Residues in contact with ILE 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A VAL* 4.1 7.0 - - + -
207A VAL* 2.9 24.8 + - + +
208A ALA* 3.6 6.1 - - - +
210A MET* 1.3 87.2 - - + +
212A SER* 1.3 66.1 + - - +
214A TYR* 3.0 18.4 + - + +
215A TYR* 3.6 12.0 - - + -
448A GLY 3.9 3.6 - - - +
451A LEU* 3.8 29.2 - - + -
452A VAL* 3.6 25.6 - - + -
501A AJB 3.7 48.2 - - + +
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Residues in contact with SER 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A ALA 2.9 6.3 + - - -
209A THR 3.3 8.9 + - - -
211A ILE* 1.3 77.0 - - - +
213A CYS* 1.3 64.1 + - - +
215A TYR* 3.4 10.9 + - - +
216A GLU* 3.9 7.1 + - - +
441A SER* 4.5 6.3 - - - -
443A GLU 4.0 0.9 + - - -
444A GLY* 2.9 41.8 + - - -
447A ARG* 3.9 27.0 + - - +
448A GLY* 3.2 10.2 + - - -
451A LEU* 4.0 11.4 - - - +
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Residues in contact with CYS 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A THR 3.1 16.6 + - - +
210A MET 3.7 4.0 - - - +
212A SER* 1.3 79.1 - - - +
214A TYR* 1.3 60.7 + - - +
216A GLU* 3.0 11.2 + - - +
217A ASP* 2.8 29.6 + - - +
220A CYS* 3.7 17.9 - - + -
407A GLY* 3.8 17.9 - - - -
439A ILE* 3.8 30.5 - - + -
441A SER* 3.9 22.4 - - - -
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Residues in contact with TYR 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A PRO* 4.9 11.2 - - + +
96A GLU 5.6 0.2 - - - -
210A MET 2.9 13.7 + - - +
211A ILE* 3.0 13.6 + - - +
213A CYS* 1.3 78.1 - - - +
215A TYR* 1.3 85.9 + + - +
217A ASP 3.2 13.4 - - - -
218A HIS* 2.8 75.6 + + + -
220A CYS* 4.1 7.9 - - - +
501A AJB 3.4 71.1 + + + -
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Residues in contact with TYR 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A PRO* 4.3 6.8 - - + +
96A GLU 4.8 0.2 - - - -
97A GLY* 3.5 15.5 - - - -
98A GLN* 3.4 60.1 + - + +
211A ILE* 3.6 10.3 - - + -
212A SER 3.4 7.0 + - - +
213A CYS 3.2 0.2 - - - -
214A TYR* 1.3 102.8 - + - +
216A GLU* 1.3 62.5 + - - +
218A HIS* 4.3 12.0 - + - -
447A ARG* 5.8 2.0 - - - +
451A LEU* 3.4 42.1 + - + -
455A VAL* 4.4 0.9 - - - +
501A AJB 2.9 34.2 + + - -
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Residues in contact with GLU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A SER 3.9 3.5 + - - +
213A CYS* 3.0 17.1 + - - +
215A TYR* 1.3 83.3 - - - +
217A ASP* 1.3 59.5 + - - +
218A HIS* 5.4 0.2 - - - -
439A ILE* 4.6 18.6 - - + +
447A ARG* 6.4 0.2 - - - +
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Residues in contact with ASP 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A CYS 2.8 4.8 + - - +
214A TYR* 3.2 9.0 + - - +
215A TYR 3.4 0.2 - - - -
216A GLU* 1.3 82.1 - - - +
218A HIS* 1.3 58.7 + - - +
219A GLN* 3.1 22.1 + - - +
220A CYS* 3.0 24.4 + - - +
405A THR* 2.6 32.5 + - + +
437A THR* 4.5 6.4 - - - +
439A ILE* 3.7 21.9 - - + +
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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