Contacts of the helix formed by residues 204 - 211 (chain D) in PDB entry 1R5I
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 204 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61D GLY 6.0 0.4 - - - -
64D ASN* 4.6 12.8 + - - -
65D ASP* 3.3 22.8 + - - -
185D LYS* 5.2 5.9 - - - +
201D LYS 3.8 1.5 - - - +
202D THR 3.4 3.2 - - - -
203D THR* 1.3 91.8 - - - +
205D ASP* 1.3 56.2 + - - +
206D PHE* 3.9 3.3 - - - +
207D ALA* 3.0 16.3 + - - +
208D LYS* 2.7 36.4 + - - +
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Residues in contact with ASP 205 (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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4D ARG* 2.7 43.0 + - - +
65D ASP* 2.8 16.0 + - - +
66D TYR* 2.6 29.3 + - + +
132D TRP* 3.8 7.9 - - + -
204D SER* 1.3 71.2 - - - +
206D PHE* 1.3 57.7 + - - +
208D LYS* 3.4 13.6 + - - +
209D ALA* 2.9 29.5 + - - +
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Residues in contact with PHE 206 (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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65D ASP* 3.3 18.5 + - - +
132D TRP* 3.7 24.0 - + + +
135D ALA* 4.2 7.6 - - + -
136D VAL* 3.8 22.0 - - + -
139D THR* 3.6 20.4 - - - -
182D LEU* 3.4 60.1 - - + -
185D LYS* 4.2 17.7 - - + -
186D GLY* 4.4 10.8 - - - -
189D LEU* 4.3 7.4 - - + -
204D SER* 3.0 2.7 - - - +
205D ASP* 1.3 75.3 - - - +
207D ALA* 1.3 67.3 + - - +
209D ALA* 3.0 4.0 + - - +
210D VAL* 3.0 38.6 + - + +
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Residues in contact with ALA 207 (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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189D LEU* 3.9 22.7 - - + -
200D LEU 3.3 24.2 - - - +
201D LYS* 4.4 2.1 - - - +
203D THR* 3.5 12.3 - - + -
204D SER* 3.0 20.0 + - - +
206D PHE* 1.3 79.2 - - - +
208D LYS* 1.3 62.3 + - - +
210D VAL* 3.3 1.5 + - - -
211D PHE* 3.0 34.4 + - + +
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Residues in contact with LYS 208 (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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201D LYS* 3.4 35.3 + - + +
204D SER 2.7 12.5 + - - +
205D ASP* 3.4 17.9 - - - +
207D ALA* 1.3 73.3 - - - +
209D ALA* 1.3 60.6 + - - +
211D PHE 3.7 0.7 - - - -
212D GLU* 2.9 59.9 + - - +
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Residues in contact with ALA 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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2D LYS* 6.3 3.1 - - + -
132D TRP* 3.9 24.5 - - + -
136D VAL* 3.8 13.5 - - + +
140D LYS* 3.4 18.4 + - - -
205D ASP 2.9 16.9 + - - +
206D PHE 3.0 4.2 + - - +
208D LYS* 1.3 77.4 - - - +
210D VAL* 1.3 61.3 + - - +
212D GLU* 3.9 8.9 + - - +
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Residues in contact with VAL 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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136D VAL* 4.0 15.5 - - + -
139D THR* 3.6 35.2 - - + -
140D LYS* 3.2 37.0 + - + +
143D LYS* 3.9 14.2 + - + -
189D LEU* 5.8 0.9 - - + -
190D ILE* 5.2 0.4 - - + -
206D PHE* 3.0 38.2 + - + +
207D ALA* 3.7 4.7 - - - +
208D LYS 3.2 0.2 - - - -
209D ALA* 1.3 77.0 - - - +
211D PHE* 1.3 84.9 + - + +
212D GLU 3.2 1.2 + - - -
213D ASP* 4.2 0.7 - - - +
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Residues in contact with PHE 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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143D LYS* 3.7 35.6 + - + +
189D LEU* 3.8 49.6 - - + -
190D ILE* 4.0 6.5 - - + -
193D TYR* 3.6 40.2 - + + -
200D LEU* 3.8 23.6 - - + -
201D LYS* 3.8 21.9 - - + +
207D ALA* 3.0 27.2 + - - +
208D LYS 3.7 1.3 - - - -
210D VAL* 1.3 86.5 - - + +
212D GLU* 1.3 57.7 + - - +
213D ASP* 3.5 5.9 + - - -
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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