Contacts of the helix formed by residues 153 - 161 (chain C) in PDB entry 2BHT
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 153 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C GLY* 5.6 1.1 - - - -
43C ARG* 2.5 34.5 + - - +
149C ALA* 2.7 23.6 + - + +
151C TYR 3.5 0.8 - - - -
152C THR* 1.3 92.7 - - - +
154C THR* 1.3 66.4 + - - +
155C GLY 3.3 1.1 - - - -
156C PRO* 3.3 2.8 - - - +
157C GLU* 3.1 36.6 + - - +
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Residues in contact with THR 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LYS* 5.3 2.2 - - - -
32C GLU* 5.1 5.2 - - + +
43C ARG* 2.8 35.5 + - - +
149C ALA 3.9 0.4 + - - -
150C HIS* 2.6 36.9 + - - +
153C THR* 1.3 81.5 + - - +
155C GLY* 1.3 61.1 + - - +
157C GLU* 3.7 1.7 - - - +
158C ILE* 2.8 44.8 + - + +
178C THR* 4.6 7.6 - - + -
182C VAL* 3.8 15.9 - - + -
278C ILE* 4.8 7.4 - - + -
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Residues in contact with GLY 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C HIS 2.5 20.3 + - - -
154C THR* 1.3 75.5 - - - +
156C PRO* 1.3 70.7 - - - +
158C ILE* 3.3 0.3 + - - -
159C TRP 3.1 14.2 + - - -
182C VAL* 3.9 18.1 - - - +
185C PHE* 3.2 24.5 - - - -
186C MET* 3.4 4.0 - - - +
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Residues in contact with PRO 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C TYR 3.2 27.1 - - - +
152C THR* 3.6 17.5 - - - +
153C THR* 3.3 10.3 - - - +
155C GLY* 1.3 86.9 - - - +
157C GLU* 1.3 56.8 + - + +
159C TRP* 2.8 6.8 + - - +
160C GLN* 2.7 35.4 + - - +
185C PHE* 3.6 23.1 - - + -
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Residues in contact with GLU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C GLY* 3.7 2.3 - - - -
10C ASN* 2.8 41.6 + - - +
30C LYS* 2.7 28.9 + - - +
43C ARG* 2.7 36.2 + - - -
153C THR* 3.1 21.6 + - - +
154C THR 3.7 3.1 - - - +
156C PRO* 1.3 77.4 - - + +
158C ILE* 1.3 51.4 + - - +
160C GLN* 3.2 9.0 - - - +
161C GLN* 2.5 45.2 + - + +
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Residues in contact with ILE 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 4.0 17.9 - - + -
30C LYS* 4.3 14.6 - - + -
154C THR* 2.8 30.3 - - + +
155C GLY* 3.9 3.8 - - - +
156C PRO 3.3 0.2 - - - -
157C GLU* 1.3 72.1 - - - +
159C TRP* 1.3 56.1 + - - +
161C GLN* 2.9 14.5 + - + +
162C THR* 2.6 30.3 + - + -
166C ILE* 5.3 2.5 - - + -
169C PHE* 4.1 8.5 - - + -
182C VAL* 5.1 3.1 - - + -
186C MET* 4.7 7.0 - - + -
276C VAL* 3.3 37.0 - - + -
278C ILE* 3.6 30.3 - - + -
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Residues in contact with TRP 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C GLY 3.1 4.6 + - - -
156C PRO* 2.8 9.7 + - + +
158C ILE* 1.3 74.0 - - - +
160C GLN* 1.3 64.2 + - - +
162C THR* 2.7 18.2 + - - -
164C GLY* 3.0 46.6 + - - -
166C ILE* 3.3 38.6 - - + -
185C PHE* 3.3 34.5 - + + -
186C MET* 3.8 15.1 - - + +
189C GLN* 3.4 29.7 + - + -
190C SER 4.2 17.5 - - - -
191C LYS* 5.3 4.5 - - + -
193C VAL* 5.4 4.3 - - + -
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Residues in contact with GLN 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C PRO 2.7 13.5 + - - +
157C GLU* 3.2 12.5 + - - +
159C TRP* 1.3 77.8 - - - +
161C GLN* 1.3 73.4 + - - +
162C THR 3.2 4.5 + - - -
163C GLY* 3.4 10.8 + - - -
164C GLY 5.3 0.4 - - - +
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Residues in contact with GLN 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ASN* 4.9 2.0 - - - +
11C THR 2.9 24.0 + - - +
13C LEU* 3.1 31.7 - - + +
28C TRP* 5.1 4.0 - - - -
30C LYS* 2.5 36.5 + - - +
157C GLU* 2.5 27.6 + - - +
158C ILE* 2.9 12.5 + - - +
160C GLN* 1.3 86.2 - - - +
162C THR* 1.3 56.1 + - - +
163C GLY 3.6 0.2 - - - -
1D MET* 3.7 27.6 - - + +
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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