Contacts of the helix formed by residues 153 - 162 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A GLY* 6.1 0.2 - - - -
43A ARG* 3.4 22.1 + - - +
149A ALA* 2.5 34.0 + - + +
150A HIS 3.0 0.2 + - - -
152A THR* 1.3 86.6 - - - +
154A THR* 1.3 66.0 + - - +
155A GLY 3.2 1.3 + - - -
156A PRO* 3.4 3.5 - - - +
157A GLU* 2.8 39.5 + - - +
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Residues in contact with THR 154 (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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30A LYS* 4.8 2.9 - - + -
32A GLU* 4.6 3.4 - - - +
43A ARG* 2.9 41.9 + - - +
150A HIS* 3.0 35.6 + - + -
153A THR* 1.3 80.5 + - - +
155A GLY* 1.3 57.4 + - - +
157A GLU* 3.2 5.4 + - - +
158A ILE* 3.0 41.4 + - + +
182A VAL* 3.9 15.7 - - + -
278A ILE* 4.5 15.3 - - + -
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Residues in contact with GLY 155 (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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150A HIS 2.7 18.4 + - - -
154A THR* 1.3 70.5 - - - +
156A PRO* 1.3 69.6 - - - +
157A GLU 3.1 0.9 + - - -
158A ILE* 3.2 14.9 + - - +
159A TRP* 3.3 9.7 + - - +
182A VAL* 4.1 17.7 - - - +
185A PHE* 3.7 23.9 - - - -
186A MET* 4.8 2.6 - - - +
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Residues in contact with PRO 156 (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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150A HIS 3.7 0.7 - - - +
151A TYR 3.6 13.7 - - - +
152A THR 3.1 24.7 - - - +
153A THR 3.4 8.5 - - - +
155A GLY* 1.3 91.3 - - - +
157A GLU* 1.3 59.3 + - + +
159A TRP* 4.0 2.5 - - - +
160A GLN* 3.4 22.9 + - - +
185A PHE* 3.6 37.0 - - + -
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Residues in contact with GLU 157 (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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9A GLY* 4.2 0.3 - - - -
10A ASN* 2.9 38.2 + - - +
11A THR 3.4 6.6 + - - -
30A LYS* 2.9 27.9 + - - +
43A ARG* 2.6 32.2 + - - -
153A THR* 2.8 27.6 + - - +
154A THR* 3.3 6.7 - - - +
155A GLY 3.0 0.2 - - - -
156A PRO* 1.3 74.1 - - + +
158A ILE* 1.3 67.8 + - - +
159A TRP 3.1 2.0 + - - -
160A GLN* 3.1 4.0 + - - +
161A GLN* 3.0 34.2 + - - +
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Residues in contact with ILE 158 (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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13A LEU* 5.0 1.6 - - + -
30A LYS* 4.1 22.9 - - + +
154A THR* 3.0 29.8 + - + +
155A GLY* 3.2 7.1 + - - +
157A GLU* 1.3 75.0 - - - +
159A TRP* 1.3 63.0 + - - +
161A GLN* 3.4 3.3 + - - +
162A THR* 3.1 24.9 + - - +
166A ILE* 3.7 34.5 - - + -
169A PHE* 3.7 30.7 - - + -
182A VAL* 3.9 18.6 - - + -
186A MET* 4.6 5.2 - - + -
276A VAL* 3.8 22.7 - - + -
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Residues in contact with TRP 159 (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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155A GLY 3.3 12.2 + - - +
156A PRO 4.0 4.0 - - - +
157A GLU 3.1 0.6 - - - -
158A ILE* 1.3 81.1 - - - +
160A GLN* 1.3 56.4 + - + +
162A THR* 3.3 4.2 + - - -
163A GLY 2.5 56.3 + - - +
164A GLY* 3.3 36.7 - - - -
165A ARG 4.0 0.7 - - - -
166A ILE* 3.6 26.2 - - + -
185A PHE* 3.8 18.8 - + + -
186A MET* 4.0 12.8 - - - +
189A GLN* 3.7 37.5 + - + -
191A LYS* 4.3 21.1 - - + -
193A VAL* 3.5 27.1 - - + -
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Residues in contact with GLN 160 (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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156A PRO 3.4 13.4 + - - +
157A GLU* 3.1 5.3 + - - +
159A TRP* 1.3 82.3 - - + +
161A GLN* 1.3 63.6 + - + +
162A THR 3.3 0.2 - - - -
163A GLY* 2.8 37.3 + - - -
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Residues in contact with GLN 161 (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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10A ASN* 5.2 2.8 - - - +
11A THR 3.0 21.8 + - - +
12A PRO* 4.4 1.6 - - - +
13A LEU* 3.2 39.1 - - + +
28A TRP* 5.8 2.9 - - - -
30A LYS* 3.1 29.4 - - - +
157A GLU* 3.0 20.0 + - - +
158A ILE 4.1 0.7 - - - +
160A GLN* 1.3 79.6 - - + +
162A THR* 1.3 60.0 + - - +
163A GLY 3.4 0.4 - - - -
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Residues in contact with THR 162 (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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13A LEU* 3.6 22.7 - - + -
28A TRP* 5.0 4.3 - - + -
158A ILE 3.1 18.3 + - - +
159A TRP 3.3 4.4 + - - -
161A GLN* 1.3 75.0 - - - +
163A GLY* 1.3 55.8 + - - +
165A ARG* 2.9 43.7 + - - +
166A ILE* 3.2 34.5 + - + +
274A VAL* 4.7 6.5 - - + -
276A VAL* 3.8 19.5 - - + -
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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