Contacts of the helix formed by residues 189 - 197 (chain A) in PDB entry 3BFR
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 LYS 189 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A GLN 4.6 2.2 + - - -
186A TYR* 2.8 51.0 + - - +
187A GLN* 3.2 11.2 + - - -
188A ASN* 1.3 90.7 - - - +
190A LYS* 1.3 63.7 + - - +
191A ALA* 3.3 3.1 - - - -
192A ASP* 3.3 39.1 + - + +
193A TYR 3.6 3.6 + - - -
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Residues in contact with LYS 190 (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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133A LEU 5.2 0.8 + - - +
134A ALA* 3.4 36.2 + - + +
136A VAL 4.2 11.3 + - - -
137A GLN* 6.0 0.4 - - - +
182A TYR* 3.5 41.3 - - + +
188A ASN 2.8 14.4 + - - +
189A LYS* 1.3 70.0 - - - +
191A ALA* 1.3 64.4 + - + +
193A TYR* 3.1 5.7 + - - +
194A PHE* 2.9 50.4 + - + -
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Residues in contact with ALA 191 (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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134A ALA* 5.8 4.7 - - + -
189A LYS 3.3 1.3 - - - -
190A LYS* 1.3 82.9 - - + +
192A ASP* 1.3 61.2 + - - +
194A PHE* 3.4 13.2 + - + +
195A LYS* 2.9 29.1 + - - +
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Residues in contact with ASP 192 (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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186A TYR* 3.7 18.1 - - + -
189A LYS* 3.3 37.7 + - - +
190A LYS 3.2 0.4 - - - -
191A ALA* 1.3 77.6 - - - +
193A TYR* 1.3 60.5 + - - +
195A LYS* 3.6 8.3 + - - +
196A ALA* 3.0 30.0 + - - +
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Residues in contact with TYR 193 (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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25A TYR 4.9 0.9 - - - -
26A ILE* 4.2 15.5 - - + -
92A PHE* 3.7 8.5 - - - -
175A ILE* 4.5 2.0 - - + +
176A ASP 2.9 29.0 + - - -
181A ALA* 3.6 25.3 + - + +
182A TYR* 3.4 36.1 - + + -
186A TYR* 3.7 36.0 - + + -
189A LYS 3.6 2.2 + - - +
190A LYS 3.1 7.5 + - - +
192A ASP* 1.3 76.9 - - - +
194A PHE* 1.3 93.6 + + - +
196A ALA* 3.1 1.4 + - - +
197A ILE* 3.0 55.9 + - + +
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Residues in contact with PHE 194 (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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130A ASN* 3.5 24.2 - - + +
133A LEU* 3.6 47.3 - - + -
134A ALA* 3.6 25.1 - - + -
175A ILE* 4.8 1.1 - - + -
177A ALA* 4.2 15.7 - - + -
182A TYR* 4.8 2.9 - + - -
190A LYS* 2.9 52.3 + - + +
191A ALA* 3.8 9.6 - - - +
193A TYR* 1.3 103.8 - + - +
195A LYS* 1.3 58.0 + - - +
197A ILE* 3.4 8.7 - - - +
198A TRP* 2.9 30.7 + - - -
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Residues in contact with LYS 195 (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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130A ASN* 4.2 12.0 - - - +
191A ALA 2.9 17.9 + - - +
192A ASP* 3.7 9.2 - - - +
194A PHE* 1.3 79.0 - - - +
196A ALA* 1.3 62.3 + - - +
198A TRP* 3.7 14.6 + - - +
199A ASN* 4.2 4.7 - - - +
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Residues in contact with ALA 196 (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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25A TYR* 3.6 23.1 - - + +
186A TYR* 3.3 24.7 - - + +
192A ASP 3.0 18.6 + - - +
193A TYR 3.1 2.6 + - - +
195A LYS* 1.3 78.0 - - - +
197A ILE* 1.3 65.5 + - - +
198A TRP 3.2 0.2 - - - -
199A ASN* 2.9 30.1 + - - +
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Residues in contact with ILE 197 (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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25A TYR* 5.0 2.9 - - - -
26A ILE* 3.9 21.3 - - + -
92A PHE* 3.8 26.7 - - + -
96A LEU* 4.0 13.9 - - + -
175A ILE* 4.2 26.2 - - + -
193A TYR* 3.0 43.3 + - + +
194A PHE* 3.4 20.4 - - - +
196A ALA* 1.3 76.3 - - - +
198A TRP* 1.3 68.0 + - + +
199A ASN 3.1 0.2 - - - -
200A VAL* 3.0 25.6 + - + +
201A VAL* 3.3 8.4 + - + +
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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