Contacts of the helix formed by residues 196 - 205 (chain A) in PDB entry 1BHL
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 ALA 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A SER* 3.6 9.2 - - - +
82A GLY* 3.6 8.3 - - - +
83A TYR* 3.6 31.3 - - - +
183A HIS* 4.2 11.9 + - + +
184A ASN* 3.4 9.7 + - - +
186A LYS 4.1 3.2 + - - -
195A SER* 1.3 74.0 - - - +
197A GLY* 1.3 56.8 + - - +
199A ARG* 3.3 19.3 + - - +
200A ILE* 2.9 31.5 + - - +
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Residues in contact with GLY 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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83A TYR* 4.3 9.9 - - - -
184A ASN* 2.9 22.3 + - - +
185A HIS* 5.7 2.5 - - - -
195A SER* 4.1 0.7 - - - -
196A ALA* 1.3 78.9 - - - +
198A GLU* 1.3 60.3 + - - +
200A ILE* 3.2 21.0 - - - +
201A VAL* 3.6 11.6 + - - +
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Residues in contact with GLU 198 (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 ARG* 3.7 24.4 + - - +
193A GLY 3.8 4.9 - - - +
194A TYR* 3.2 25.4 - - + +
195A SER* 3.0 36.0 + - - +
197A GLY* 1.3 73.7 - - - +
199A ARG* 1.3 66.4 + - - +
201A VAL* 3.4 6.4 + - - +
202A ASP* 3.1 24.1 + - - +
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Residues in contact with ARG 199 (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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80A ALA 4.5 4.3 + - - -
81A SER* 2.7 38.3 + - - +
82A GLY* 4.8 1.4 - - - -
188A LYS* 4.5 22.5 - - - +
194A TYR* 3.4 34.6 + - + +
195A SER 2.9 12.7 + - - +
196A ALA* 3.5 21.3 - - - +
198A GLU* 1.3 77.9 - - - +
200A ILE* 1.3 57.2 + - - +
202A ASP* 3.4 5.1 + - - +
203A ILE* 2.9 43.3 + - + +
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Residues in contact with ILE 200 (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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61A TRP* 3.7 11.2 - - + -
78A HIS* 3.7 28.5 - - + +
81A SER* 3.5 15.1 - - - +
83A TYR* 3.4 44.4 - - + -
108A TRP* 3.9 32.3 - - + -
196A ALA 2.9 14.3 + - - +
197A GLY* 3.2 15.0 - - - +
199A ARG* 1.3 75.9 - - - +
201A VAL* 1.3 67.2 + - + +
203A ILE* 3.4 2.4 + - - +
204A ILE* 2.9 34.6 + - + +
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Residues in contact with VAL 201 (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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108A TRP* 4.6 20.9 - - + -
197A GLY 4.0 10.3 - - - +
198A GLU* 3.4 9.0 + - - +
199A ARG 3.4 0.4 - - - -
200A ILE* 1.3 81.6 - - + +
202A ASP* 1.3 59.8 + - - +
204A ILE* 4.0 3.7 - - - +
205A ALA* 2.8 38.0 + - + +
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Residues in contact with ASP 202 (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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198A GLU 3.1 17.2 + - - +
199A ARG* 3.8 5.8 - - - +
201A VAL* 1.3 77.7 - - - +
203A ILE* 1.3 63.3 + - + +
205A ALA* 4.3 5.1 - - - +
206A THR* 2.7 47.6 + - - -
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Residues in contact with ILE 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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58A PRO* 3.6 30.7 - - + -
78A HIS* 4.3 8.3 - - + -
80A ALA* 4.1 22.0 - - + +
81A SER* 4.0 18.2 - - - -
199A ARG* 2.9 36.5 + - + +
200A ILE* 3.9 4.0 - - - +
202A ASP* 1.3 80.8 - - + +
204A ILE* 1.3 62.2 + - + +
206A THR* 4.0 4.0 - - - -
207A ASP* 3.2 22.5 + - - +
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Residues in contact with ILE 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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58A PRO* 3.7 31.0 - - + +
61A TRP* 6.2 0.2 - - - +
78A HIS* 4.1 12.1 - - + +
108A TRP* 4.1 17.5 - - + -
109A PRO* 3.9 36.6 - - + -
200A ILE* 2.9 32.6 + - + +
201A VAL* 4.1 3.8 - - - +
203A ILE* 1.3 74.3 - - - +
205A ALA* 1.3 67.1 + - - +
207A ASP* 3.1 22.5 + - + +
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Residues in contact with ALA 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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201A VAL* 2.8 29.5 + - + +
202A ASP* 3.7 5.8 - - - +
204A ILE* 1.3 70.0 - - - +
206A THR* 1.3 68.1 + - - +
207A ASP* 2.8 11.6 - - - +
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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