Contacts of the helix formed by residues 202 - 211 (chain A) in PDB entry 4BJ3
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 THR 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ILE* 4.2 6.9 - - - +
177A PRO* 6.2 0.4 - - + -
201A LYS* 1.3 87.4 + - + +
203A LYS* 1.3 65.3 + - - +
204A GLU* 4.0 5.0 + - - +
205A GLU* 2.8 40.3 + - - +
206A MET* 3.8 20.6 + - - +
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Residues in contact with LYS 203 (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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170A VAL* 3.4 9.9 + - + +
171A GLN* 2.8 47.3 + - - +
173A LEU 3.1 20.8 + - - -
175A ILE* 3.7 30.6 + - + +
202A THR* 1.3 70.8 - - - +
204A GLU* 1.3 58.1 + - + +
205A GLU 3.0 4.7 - - - -
206A MET* 2.7 27.0 + - - +
207A ILE* 3.1 30.3 + - + +
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Residues in contact with GLU 204 (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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202A THR* 3.7 4.8 + - - +
203A LYS* 1.3 81.4 - - - +
205A GLU* 1.3 60.6 + - + +
207A ILE* 4.1 6.0 - - - +
208A VAL* 3.5 29.2 + - + +
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Residues in contact with GLU 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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199A THR 4.7 1.4 - - - +
200A TYR* 3.4 27.9 - - + -
201A LYS* 3.5 22.2 + - - +
202A THR* 2.8 40.6 + - - +
203A LYS 3.0 0.4 - - - -
204A GLU* 1.3 80.2 - - + +
206A MET* 1.3 58.6 - - - +
208A VAL* 4.4 1.9 - - - +
209A ALA* 3.3 25.1 + - - +
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Residues in contact with MET 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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170A VAL* 4.1 21.8 - - + -
175A ILE* 3.7 18.4 - - + -
181A GLN* 5.3 0.4 - - - -
182A VAL* 3.3 60.3 - - + +
195A PHE* 4.4 14.2 - - + -
197A LEU 5.0 0.9 - - - +
200A TYR* 3.3 45.5 - - + +
202A THR 3.8 6.1 - - - +
203A LYS 2.7 15.0 + - - +
205A GLU* 1.3 70.9 - - - +
207A ILE* 1.3 59.8 + - - +
209A ALA* 3.2 4.5 + - - +
210A THR* 2.9 34.2 + - - -
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Residues in contact with ILE 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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167A GLU* 3.8 37.2 - - + +
170A VAL* 3.7 26.2 - - + -
171A GLN* 3.7 24.9 - - + +
203A LYS* 3.1 26.4 + - + +
204A GLU* 4.3 6.5 - - - +
206A MET* 1.3 75.6 - - - +
208A VAL* 1.3 65.8 + - + +
210A THR* 3.5 8.8 + - + +
211A SER* 3.2 23.0 + - - +
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Residues in contact with VAL 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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204A GLU* 3.5 18.9 + - + +
205A GLU* 4.4 2.5 - - - +
206A MET 3.3 0.4 - - - -
207A ILE* 1.3 77.2 - - + +
209A ALA* 1.3 61.9 + - - +
210A THR 3.1 4.5 - - - -
211A SER* 2.8 24.4 + - - +
212A GLN* 3.5 20.2 + - - +
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Residues in contact with ALA 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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194A VAL* 5.3 5.0 - - - +
195A PHE* 5.0 10.5 - - + -
200A TYR* 3.5 34.1 - - + +
205A GLU 3.3 18.6 + - - +
206A MET* 3.2 4.8 + - - +
208A VAL* 1.3 79.0 - - - +
210A THR* 1.3 57.7 + - - +
212A GLN* 3.4 31.3 + - - +
213A THR* 4.0 7.6 + - - -
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Residues in contact with THR 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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163A LYS* 4.1 8.1 - - - +
166A LEU* 3.8 26.6 - - + +
167A GLU* 3.9 34.8 - - + +
170A VAL* 5.3 6.4 - - + +
184A LEU* 4.4 9.8 - - - +
195A PHE* 4.7 10.1 - - - -
206A MET* 2.9 14.8 + - - +
207A ILE* 3.5 12.3 - - - +
209A ALA* 1.3 75.2 - - - +
211A SER* 1.3 62.1 + - - +
212A GLN 3.1 5.2 - - - -
213A THR* 3.3 26.9 - - - +
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Residues in contact with SER 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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163A LYS* 3.7 25.3 + - - +
167A GLU* 5.0 14.1 - - - -
207A ILE* 3.2 11.7 + - - -
208A VAL* 2.8 23.6 + - - +
210A THR* 1.3 80.4 - - - +
212A GLN* 1.3 56.9 + - - +
213A THR 3.6 0.7 - - - -
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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