Contacts of the helix formed by residues 183 - 193 (chain A) in PDB entry 3BNF
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 VAL 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A THR* 4.4 14.8 - - + +
138A VAL* 4.9 3.8 - - + -
139A PRO* 5.6 3.6 - - + -
142A ILE* 4.8 9.6 - - + -
181A SER* 3.4 12.2 + - - +
182A LYS* 1.3 85.2 - - + +
184A PRO* 1.3 67.6 - - + +
185A TYR* 3.3 49.9 + - + +
186A LEU* 3.5 8.1 + - + +
187A ASP* 4.4 2.8 + - - +
213A GLN* 3.8 33.2 - - + +
214A CYS* 6.4 0.9 - - - -
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Residues in contact with PRO 184 (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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142A ILE* 4.9 21.5 - - + -
147A GLU* 3.6 19.1 - - + +
151A PHE* 6.3 0.2 - - + -
182A LYS 4.1 5.8 - - - +
183A VAL* 1.3 82.7 - - + +
185A TYR* 1.3 66.9 + - + +
186A LEU 3.2 1.0 + - - -
187A ASP* 3.5 7.5 + - + +
188A ARG* 3.2 45.5 + - - +
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Residues in contact with TYR 185 (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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132A THR* 3.5 23.0 + - + +
133A CYS* 3.3 19.6 - - - -
142A ILE* 6.3 0.4 - - + -
147A GLU* 5.0 1.3 - - - -
151A PHE* 4.4 10.5 - + - -
183A VAL* 3.4 29.2 - - + +
184A PRO* 1.3 81.1 - - + +
186A LEU* 1.3 63.8 + - + +
188A ARG* 3.3 19.3 - - + +
189A GLY* 2.9 25.1 + - - -
213A GLN 2.6 31.4 + - - -
214A CYS* 4.8 0.7 - - - -
216A VAL* 5.1 0.4 - - + -
238A VAL* 3.4 51.6 - - + +
239A THR* 5.0 2.0 - - - -
240A LEU* 3.9 25.9 + - + +
508A HEM 4.3 2.5 - - + -
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Residues in contact with LEU 186 (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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181A SER* 3.6 23.6 - - - +
183A VAL* 3.5 17.8 + - + +
184A PRO 3.2 1.0 - - - -
185A TYR* 1.3 84.5 - - + +
187A ASP* 1.3 58.7 + - - +
189A GLY* 3.3 1.7 + - - -
190A LEU* 2.8 53.8 + - + +
198A PHE* 4.8 1.1 - - + -
209A LEU* 3.5 34.5 - - + +
212A ALA* 3.9 21.5 - - + +
213A GLN* 3.8 10.8 - - + +
240A LEU* 3.9 17.9 - - + -
242A TRP* 4.1 9.4 - - + -
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Residues in contact with ASP 187 (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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181A SER* 5.2 5.1 - - - -
183A VAL 4.4 2.3 + - - -
184A PRO* 3.5 10.6 + - + +
185A TYR 3.4 0.4 - - - -
186A LEU* 1.3 78.2 - - - +
188A ARG* 1.3 54.0 + - - +
190A LEU* 3.2 8.6 + - - +
191A SER* 2.8 40.3 + - - -
197A THR* 3.6 25.0 - - + +
198A PHE* 2.8 37.5 + - - +
199A ALA* 4.9 2.6 + - - +
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Residues in contact with ARG 188 (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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147A GLU* 2.8 43.4 + - - -
184A PRO* 3.2 29.9 + - - +
185A TYR* 3.3 25.0 - - - +
187A ASP* 1.3 76.4 - - - +
189A GLY* 1.3 61.3 + - - +
191A SER* 3.7 5.2 + - - -
192A ALA* 3.2 23.8 + - - +
237A VAL* 4.4 11.7 - - - +
238A VAL 4.8 0.8 + - - -
239A THR* 6.5 2.2 - - - +
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Residues in contact with GLY 189 (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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185A TYR 2.9 15.4 + - - -
186A LEU 3.7 2.2 - - - -
188A ARG* 1.3 71.8 - - - +
190A LEU* 1.3 67.0 + - - +
192A ALA* 3.1 7.5 + - - +
193A ALA* 3.0 19.8 + - - +
240A LEU* 4.1 17.2 - - - +
242A TRP* 3.4 26.3 - - - +
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Residues in contact with LEU 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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186A LEU* 2.8 36.9 + - + +
187A ASP* 3.4 23.8 - - - +
189A GLY* 1.3 73.8 - - - +
191A SER* 1.3 61.3 + - - +
193A ALA* 3.3 1.6 + - - -
194A GLY 3.2 3.8 + - - -
195A PHE* 2.9 59.4 + - + +
196A LYS 3.5 22.2 - - - +
197A THR* 4.5 0.9 - - - -
198A PHE 3.9 6.3 - - - +
209A LEU* 4.0 24.9 - - + -
242A TRP* 3.7 15.1 - - + -
280A TRP* 4.0 10.3 - - + -
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Residues in contact with SER 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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187A ASP 2.8 21.5 + - - -
188A ARG* 4.0 5.4 - - - -
190A LEU* 1.3 71.3 - - - +
192A ALA* 1.3 56.2 + - - +
194A GLY* 2.7 24.9 + - - -
195A PHE 3.9 7.8 + - - -
197A THR* 3.6 20.8 - - - +
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Residues in contact with ALA 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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188A ARG 3.2 15.7 + - - +
189A GLY* 3.1 9.5 + - - +
191A SER* 1.3 79.4 - - - +
193A ALA* 1.3 59.0 + - - +
194A GLY 3.2 1.0 + - - -
240A LEU 5.8 1.1 - - - +
242A TRP 3.9 2.0 - - - +
243A SER* 3.5 43.2 - - - +
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Residues in contact with ALA 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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189A GLY 3.0 14.4 + - - +
190A LEU 3.3 0.2 + - - -
191A SER 3.1 0.2 - - - -
192A ALA* 1.3 76.6 - - - +
194A GLY* 1.3 59.4 + - - +
195A PHE* 3.4 30.3 + - + -
242A TRP* 3.1 27.1 - - + +
245A GLY* 4.3 10.6 - - - +
246A ILE* 4.1 7.4 - - + -
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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