Contacts of the helix formed by residues 200 - 210 (chain F) in PDB entry 3RBQ
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 200 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198F PRO 4.1 1.6 + - - -
199F LEU* 1.3 76.6 - - - +
201F GLU* 1.3 65.0 + - - +
202F GLU* 3.7 13.2 + - - +
203F LEU* 3.2 22.7 + - - +
204F ILE* 3.1 20.4 + - - +
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Residues in contact with GLU 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F ARG* 2.8 45.7 + - - -
199F LEU 5.4 0.8 - - - +
200F SER* 1.3 72.9 - - - +
202F GLU* 1.3 66.3 + - - +
204F ILE* 3.5 7.8 + - - +
205F SER* 3.1 29.8 + - - -
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Residues in contact with GLU 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200F SER* 3.7 11.6 + - - +
201F GLU* 1.3 89.2 + - - +
203F LEU* 1.3 56.3 + - - +
205F SER* 3.7 5.8 - - - -
206F GLU* 2.9 35.8 + - + +
209F ARG* 4.4 1.1 + - - +
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Residues in contact with LEU 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F PHE* 3.3 38.6 - - + -
170F GLN* 4.3 20.0 - - - +
172F LEU* 3.8 17.5 - - + -
198F PRO 5.4 1.1 - - - +
199F LEU* 3.7 29.4 - - + -
200F SER* 3.2 21.0 + - - +
202F GLU* 1.3 77.1 - - - +
204F ILE* 1.3 55.7 + - - +
206F GLU* 3.0 4.5 + - + +
207F MET* 2.7 48.2 + - + +
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Residues in contact with ILE 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F PRO 5.5 0.4 - - - +
138F LEU* 4.1 30.5 - - + +
139F ARG* 4.0 40.8 - - - +
199F LEU* 3.4 48.2 - - + +
200F SER 3.1 13.2 + - - +
201F GLU* 4.0 7.9 - - - +
203F LEU* 1.3 74.1 - - - +
205F SER* 1.3 64.9 + - - +
207F MET* 3.2 4.7 + - - +
208F ILE* 3.0 46.4 + - + +
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Residues in contact with SER 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201F GLU 3.1 18.0 + - - -
202F GLU* 3.7 4.9 - - - -
204F ILE* 1.3 81.9 - - - +
206F GLU* 1.3 62.2 + - - +
208F ILE* 3.4 9.0 + - - +
209F ARG* 2.8 57.7 + - - +
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Residues in contact with GLU 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F PHE* 3.8 18.8 - - + -
168F ARG* 4.0 13.5 + - - +
202F GLU* 2.9 30.3 + - + +
203F LEU* 3.0 8.0 + - + +
205F SER* 1.3 72.9 + - - +
207F MET* 1.3 57.4 + - - +
209F ARG* 2.7 32.8 + - - +
210F HIS* 3.0 58.2 + - - +
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Residues in contact with MET 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F LEU* 3.9 22.7 - - + -
167F PHE* 3.8 27.3 - - + -
172F LEU* 3.9 15.7 - - + -
199F LEU* 4.4 16.8 - - - -
203F LEU* 2.7 42.4 + - + +
204F ILE* 3.5 5.4 - - - +
206F GLU* 1.3 72.3 - - - +
208F ILE* 1.3 62.3 + - - +
210F HIS 3.4 18.2 + - - +
211F PRO* 4.2 1.0 - - - +
214F THR* 3.3 36.0 + - + +
236F TYR* 3.9 28.6 + - + +
500L DAO 4.9 5.4 - - + -
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Residues in contact with ILE 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F PRO* 3.8 39.0 - - + -
138F LEU* 3.7 14.6 - - + -
139F ARG* 6.0 0.4 - - - +
204F ILE* 3.0 39.7 + - + +
205F SER* 3.6 8.3 - - - +
207F MET* 1.3 76.6 - - - +
209F ARG* 1.3 66.8 + - + +
210F HIS 3.4 0.5 + - - -
211F PRO* 3.7 9.7 - - - +
236F TYR* 4.3 12.5 + - - +
237F SER* 4.1 15.7 + - - -
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Residues in contact with ARG 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C ASP 5.5 2.6 - - - +
202F GLU* 4.4 1.4 + - - +
205F SER* 2.8 41.3 + - - +
206F GLU* 2.7 45.6 + - - +
208F ILE* 1.3 83.7 - - + +
210F HIS* 1.3 68.7 + - + +
211F PRO* 3.2 9.6 - - - +
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Residues in contact with HIS 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C ASP* 6.1 2.7 - - - -
178C HIS* 4.6 6.6 + + - -
167F PHE* 3.8 18.0 - + + -
168F ARG* 3.1 25.1 + - - -
206F GLU* 3.0 51.0 + - - +
207F MET 3.4 8.3 + - - +
208F ILE 3.3 1.0 - - - -
209F ARG* 1.3 92.9 + - + +
211F PRO* 1.4 68.8 - - - +
212F TYR 3.5 0.2 + - - -
213F GLU* 2.8 40.1 + - - +
214F THR* 4.4 2.1 + - - -
234F TYR 4.9 0.3 - - - +
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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