Contacts of the helix formed by residues 182 - 186 (chain D) in PDB entry 3RIK
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 PRO 182 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D THR* 3.6 16.5 - - + +
136D ALA* 3.4 19.3 - - + +
137D ASP* 4.7 1.3 - - - +
144D LEU* 5.6 0.2 - - + -
181D SER* 1.4 103.7 + - - +
183D THR* 1.3 63.0 + - - +
184D TRP* 3.3 35.4 - - + +
185D LEU* 3.2 14.8 + - + -
186D LYS* 3.7 0.9 - - - +
209D TRP* 3.6 6.1 - - + -
212D TYR* 3.5 36.3 - - + -
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Residues in contact with THR 183 (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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407A THR* 3.4 41.6 + - + -
134D THR* 5.8 0.7 - - + -
137D ASP* 5.3 3.9 + - - +
181D SER 4.2 2.0 - - - +
182D PRO* 1.3 69.5 - - - +
184D TRP* 1.3 63.2 + - - +
185D LEU 3.0 5.6 - - - -
186D LYS* 3.0 31.3 + - - +
189D GLY* 3.5 28.6 + - - -
190D ALA* 3.7 3.4 - - - -
191D VAL* 3.7 42.6 - - + +
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Residues in contact with TRP 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A THR* 5.5 2.2 - - - +
136D ALA* 2.9 29.0 + - + -
137D ASP* 4.3 5.8 - - - -
138D THR 3.0 12.4 + - - -
139D PRO* 3.5 19.3 - - + -
140D ASP* 3.3 34.4 - - - +
141D ASP* 3.3 36.6 - - + -
142D PHE* 3.8 21.1 - + - -
144D LEU* 4.1 7.9 - - + -
182D PRO* 3.3 17.7 - - + +
183D THR* 1.3 87.0 + - - +
185D LEU* 1.3 88.1 + - + +
186D LYS 3.3 0.9 - - - -
198D LYS* 4.1 15.7 - - - +
205D TYR* 4.1 8.0 - - - -
208D THR* 4.1 10.3 - - + -
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Residues in contact with LEU 185 (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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142D PHE* 4.2 1.6 - - + -
144D LEU* 6.0 0.2 - - + -
181D SER* 3.9 6.5 - - - +
182D PRO* 3.2 25.7 + - + +
183D THR 3.0 1.4 - - - -
184D TRP* 1.3 107.9 - - + +
186D LYS* 1.3 59.5 + - - +
197D LEU* 3.4 12.7 - - + +
198D LYS* 2.9 27.1 + - - +
205D TYR* 3.9 35.5 - - + +
208D THR* 4.2 12.8 - - + -
209D TRP* 4.0 42.6 - - + +
212D TYR* 5.6 1.3 - - + -
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Residues in contact with LYS 186 (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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180D THR* 3.1 14.6 + - - +
181D SER* 3.1 22.2 - - - +
182D PRO 3.7 7.2 - - - +
183D THR* 3.0 13.2 + - - +
184D TRP 3.3 0.4 - - - -
185D LEU* 1.3 80.6 - - - +
187D THR* 1.3 65.4 + - - +
188D ASN* 3.2 17.6 + - - +
189D GLY* 3.2 9.6 + - - +
190D ALA 2.7 28.4 + - - +
191D VAL 3.0 12.7 + - - -
192D ASN* 4.0 4.8 + - - +
193D GLY 5.0 0.6 + - - -
195D GLY* 4.2 8.5 + - - -
196D SER 3.2 5.8 - - - +
198D LYS* 3.7 15.0 + - - -
248D CYS* 2.7 30.5 + - - -
249D LEU* 3.8 17.0 - - + -
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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