Contacts of the helix formed by residues 148 - 158 (chain B) in PDB entry 1TAD
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 148 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B SER* 3.4 31.6 + - - +
80B ILE* 5.1 0.2 - - + -
136B PHE* 4.4 3.8 - - + -
144B LEU* 3.7 22.9 - - + -
145B ASN 3.1 20.3 + - - +
146B ASP 3.2 1.6 - - - +
147B SER* 1.3 76.7 - - - +
149B GLY* 1.3 58.8 + - - +
151B TYR* 3.9 2.2 - - - +
152B LEU* 2.8 41.3 + - + +
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Residues in contact with GLY 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B TRP* 4.0 12.3 - - - -
136B PHE* 3.8 25.7 - - - -
146B ASP 4.6 3.4 + - - -
147B SER 3.4 0.4 - - - -
148B ALA* 1.3 78.6 - - - +
150B TYR* 1.3 51.7 + - - +
153B SER* 2.8 42.1 + - - -
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Residues in contact with TYR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ASP 5.4 0.2 + - - -
147B SER* 3.1 12.6 + - - +
149B GLY* 1.3 77.7 - - - +
151B TYR* 1.3 88.8 + + - +
153B SER* 3.6 5.9 + - - -
154B ASP* 3.3 25.6 + - - +
157B ARG* 3.9 11.5 + - - -
166B THR* 4.2 0.9 + - - -
168B GLN* 3.2 37.1 - - + +
169B ASP* 2.7 30.2 + - - -
172B ARG* 3.7 48.5 - - + +
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Residues in contact with TYR 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ILE* 3.6 20.5 - - + +
72B ASN* 3.8 29.8 - - + -
73B THR* 3.4 28.0 - - - +
76B SER* 5.6 0.4 - - - -
147B SER* 3.0 37.6 + - - +
148B ALA* 4.0 2.9 - - - +
150B TYR* 1.3 97.9 - + - +
152B LEU* 1.3 67.4 + - - +
154B ASP* 2.9 13.8 + - - -
155B LEU* 2.9 15.0 + - - -
158B LEU* 3.7 21.9 - - + +
169B ASP* 2.7 30.6 + - + -
172B ARG* 3.9 6.7 - - + -
173B SER* 2.9 21.3 + - - -
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B THR* 3.6 38.6 - - + +
76B SER* 3.9 20.2 - - - -
77B ILE* 4.1 12.8 - - + +
80B ILE* 4.1 10.1 - - + -
123B ILE* 4.1 21.5 - - + +
124B GLN* 5.8 0.9 - - - +
127B TRP* 3.8 50.0 - - + +
148B ALA 2.8 26.4 + - - +
151B TYR* 1.3 73.3 - - - +
153B SER* 1.3 60.7 + - - +
154B ASP 3.2 1.0 + - - -
155B LEU* 3.3 17.5 + - + +
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Residues in contact with SER 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B TRP* 3.4 25.0 - - - +
149B GLY 2.8 28.0 + - - -
150B TYR* 3.6 7.1 + - - -
152B LEU* 1.3 73.5 - - - +
154B ASP* 1.3 60.9 + - - +
155B LEU 3.6 0.2 - - - -
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Residues in contact with ASP 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B TYR* 3.3 23.3 - - - +
151B TYR* 2.9 7.6 + - - +
153B SER* 1.3 83.1 + - - +
155B LEU* 1.3 63.1 + - - +
156B GLU* 3.3 3.1 - - - -
157B ARG* 3.0 56.3 + - - +
158B LEU* 3.2 13.1 + - + +
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B TYR* 5.9 1.3 - - + -
73B THR* 3.9 24.7 - - + -
115B MET* 4.8 5.2 - - + -
120B SER* 3.6 18.6 - - - +
123B ILE* 3.7 26.9 - - + -
124B GLN* 3.5 31.2 - - + +
151B TYR 2.9 6.4 + - - +
152B LEU* 3.3 15.9 + - + +
153B SER 3.6 0.8 - - - -
154B ASP* 1.3 77.4 - - - +
156B GLU* 1.3 64.5 + - - +
158B LEU* 2.9 13.9 + - + -
159B VAL* 2.9 46.2 + - + +
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Residues in contact with GLU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B GLN* 4.0 23.1 + - - +
154B ASP 3.3 1.2 - - - -
155B LEU* 1.3 77.9 - - - +
157B ARG* 1.3 52.7 + - - +
159B VAL* 3.7 10.7 - - + +
160B THR* 2.7 34.9 + - - +
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Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B TYR* 3.9 8.7 + - - -
154B ASP* 3.0 45.1 + - - +
156B GLU* 1.3 78.4 - - - +
158B LEU* 1.3 72.1 + - - +
160B THR* 3.3 21.9 + - - +
163B TYR* 3.7 22.6 - - + -
166B THR* 3.8 16.4 + - - +
169B ASP* 2.9 42.2 + - - -
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ILE* 4.0 8.5 - - + -
70B TYR* 2.7 36.5 + - + -
73B THR* 3.9 11.0 - - - +
151B TYR* 3.7 46.7 - - + +
154B ASP* 3.4 10.8 - - + +
155B LEU* 2.9 17.8 + - + +
157B ARG* 1.3 99.7 - - - +
159B VAL* 1.3 52.6 + - - +
163B TYR* 3.2 46.3 - - + +
169B ASP* 4.1 4.0 - - - +
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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