Contacts of the helix formed by residues 191 - 199 (chain B) in PDB entry 3RC0
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 ILE 191 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B ALA 3.6 22.7 - - - +
116B LEU* 4.2 20.2 - - + +
117B GLN 3.3 27.4 - - - +
118B SER* 4.4 11.2 - - - -
123B VAL* 4.3 10.8 - - + -
187B GLU* 2.7 24.9 + - + +
189B GLN 3.7 0.4 - - - -
190B SER* 1.3 91.7 - - - +
192B VAL* 1.3 64.3 + - + +
193B LEU 3.6 1.1 - - - -
194B PRO* 3.7 4.6 - - - +
195B PHE* 3.1 26.0 + - - +
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B VAL* 4.1 24.7 - - + +
126B LEU* 5.8 0.2 - - + -
127B LEU* 4.1 17.9 - - + +
130B LEU* 4.2 4.0 - - + -
187B GLU 2.7 19.2 + - - +
188B TYR* 3.8 23.1 - - + -
191B ILE* 1.3 73.2 - - - +
193B LEU* 1.3 66.6 + - - +
195B PHE* 3.2 6.2 + - - +
196B MET* 3.0 35.5 + - + +
213B TYR* 3.5 37.7 - - + +
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Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B TYR* 2.9 61.0 + - + +
189B GLN* 4.8 9.2 - - - +
192B VAL* 1.3 72.5 - - - +
194B PRO* 1.3 67.1 - - + +
196B MET* 3.1 16.5 + - + -
197B GLU* 2.9 51.6 + - + +
208B ARG* 4.2 12.6 - - + +
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Residues in contact with PRO 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B TYR 3.5 2.0 - - - +
189B GLN 3.5 23.1 - - - +
190B SER* 4.0 13.7 - - - +
191B ILE* 3.7 9.4 - - - +
192B VAL 3.7 2.0 - - - -
193B LEU* 1.3 95.7 - - + +
195B PHE* 1.3 56.5 + - - +
197B GLU* 3.3 10.4 + - + +
198B ALA* 2.9 31.6 + - - +
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Residues in contact with PHE 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ILE* 5.2 0.2 - - + -
108B LEU* 3.9 29.6 - - + -
109B LEU* 4.1 15.0 - - + -
112B GLU* 4.1 22.0 - - + -
115B ALA* 6.3 1.3 - - + -
116B LEU* 3.8 22.9 - - + -
127B LEU* 3.8 22.7 - - + -
191B ILE 3.1 21.6 + - - +
192B VAL 3.2 5.4 + - - +
194B PRO* 1.3 76.6 - - - +
196B MET* 1.3 61.6 + - - +
198B ALA* 3.3 5.1 + - + -
199B HIS* 3.2 47.9 + + - +
203B PHE* 3.6 29.6 - + - -
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Residues in contact with MET 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B LEU* 4.2 9.2 - - + -
130B LEU* 4.3 14.4 - - + -
188B TYR* 3.9 23.1 - - + -
192B VAL* 3.0 22.4 + - + +
193B LEU* 3.1 10.9 + - + +
195B PHE* 1.3 77.9 - - - +
197B GLU* 1.3 60.9 + - - +
199B HIS 3.3 19.8 + - - +
200B PRO* 3.4 6.4 - - - +
203B PHE* 3.7 47.2 - - + +
207B VAL* 3.8 15.3 - - - +
208B ARG* 3.7 42.8 - - + -
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Residues in contact with GLU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B LEU* 2.9 47.6 + - + +
194B PRO* 4.0 8.3 - - + +
196B MET* 1.3 76.3 - - - +
198B ALA* 1.3 59.4 + - - +
199B HIS 3.3 0.2 - - - -
200B PRO* 3.5 12.7 - - - +
208B ARG* 3.9 24.5 + - - +
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Residues in contact with ALA 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B PRO 2.9 17.9 + - - +
195B PHE* 3.6 7.9 - - - +
196B MET 3.2 0.2 - - - -
197B GLU* 1.3 76.8 - - - +
199B HIS* 1.3 77.5 + - + +
200B PRO* 3.4 7.7 - - - +
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Residues in contact with HIS 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LEU* 3.9 28.1 - - + +
112B GLU* 5.4 6.6 + - + -
195B PHE* 3.2 50.2 + + - +
196B MET 3.4 3.8 - - - -
198B ALA* 1.3 96.7 + - + +
200B PRO* 1.3 59.0 - - - +
201B ASP* 3.1 4.9 - - - -
202B LEU* 2.9 36.6 + - + -
203B PHE* 3.5 16.6 + - + -
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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