Contacts of the helix formed by residues 148 - 155 (chain B) in PDB entry 2HCT
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 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B TYR* 3.5 4.5 - - - -
115B GLN* 3.6 13.2 - - + +
117B VAL* 4.0 20.4 - - + -
143B PHE* 4.9 0.9 - - + -
144B THR 4.2 3.1 - - - +
145B LEU* 2.6 27.1 + - + +
147B ASP* 1.3 77.8 - - - +
149B LEU* 1.3 65.4 + - - +
150B LEU* 3.8 4.5 + - - +
151B GLY 3.3 9.7 + - - -
152B TYR* 2.9 23.6 + - - +
196B PHE* 3.8 31.9 - - + -
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Residues in contact with LEU 149 (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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67B CYS* 4.3 11.2 - - - +
70B TYR* 3.3 47.4 - - + -
71B THR* 4.9 3.1 - - + -
77B MET* 4.0 20.0 - - + -
80B VAL* 4.0 26.5 - - + -
85B VAL* 4.7 8.1 - - + -
113B GLY* 4.6 14.4 - - - +
115B GLN* 2.9 21.6 - - - +
148B THR* 1.3 70.8 - - - +
150B LEU* 1.3 59.4 + - + +
152B TYR* 3.3 1.2 + - - +
153B LEU* 2.9 55.2 + - + +
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Residues in contact with LEU 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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85B VAL* 5.2 0.7 - - + -
89B PHE* 6.2 0.4 - - + -
109B LEU* 3.6 38.8 - - + +
110B MET* 3.8 37.2 - - + +
113B GLY* 3.9 37.0 + - - +
115B GLN* 4.8 0.6 - - - +
148B THR* 3.3 5.1 + - - +
149B LEU* 1.3 78.6 - - + +
151B GLY* 1.3 65.8 + - - +
153B LEU* 3.5 17.9 + - + +
154B ALA 3.4 14.6 + - - -
188B PHE* 3.4 17.2 - - + -
192B VAL* 4.3 13.7 - - + -
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Residues in contact with GLY 151 (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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145B LEU* 3.4 19.6 - - - +
146B GLU* 3.8 8.4 - - - -
148B THR* 3.3 9.3 + - - -
150B LEU* 1.3 77.3 - - - +
152B TYR* 1.3 52.4 + - - +
154B ALA 3.3 0.2 + - - -
155B ASP* 2.8 36.2 + - - +
188B PHE* 4.8 0.4 - - - -
189B TRP* 3.6 24.7 - - - -
192B VAL* 5.6 0.8 - - - +
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Residues in contact with TYR 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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66B ARG* 3.1 63.7 + - + +
69B LYS* 3.3 30.4 + - + +
70B TYR* 3.5 32.5 - + + -
73B ILE* 4.5 7.7 - - + +
74B HIS* 5.9 2.0 - + - -
146B GLU* 3.5 19.1 + - - +
147B ASP* 5.5 0.9 - - - -
148B THR 2.9 18.7 + - - +
149B LEU 3.4 4.3 - - - +
151B GLY* 1.3 74.5 - - - +
153B LEU* 1.3 66.3 + - + +
154B ALA 3.3 0.2 + - - -
155B ASP* 3.7 5.7 + - - +
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Residues in contact with LEU 153 (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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63B VAL* 3.6 27.4 - - + +
66B ARG* 3.1 25.3 + - + +
67B CYS* 3.5 36.3 - - + +
85B VAL* 3.5 31.0 - - + -
89B PHE* 4.5 15.5 - - + -
149B LEU* 2.9 32.6 + - + +
150B LEU* 3.6 24.7 - - + +
151B GLY 3.4 0.2 - - - -
152B TYR* 1.3 75.0 - - + +
154B ALA* 1.3 57.8 + - - +
157B LEU* 3.2 13.5 - - - +
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Residues in contact with ALA 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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66B ARG* 4.0 0.2 - - - -
89B PHE* 4.6 6.7 - - + -
150B LEU 3.4 6.3 + - - +
151B GLY 3.3 1.4 + - - -
152B TYR 3.2 0.4 - - - -
153B LEU* 1.3 78.8 - - + +
155B ASP* 1.3 68.1 + - - +
156B ASP 3.1 1.0 + - - -
157B LEU* 3.0 23.2 + - - +
159B TRP* 3.9 18.9 - - + -
188B PHE* 3.3 37.2 - - + -
189B TRP* 3.6 12.8 - - + -
302B NMN 4.5 0.2 - - - +
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Residues in contact with ASP 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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66B ARG* 2.9 32.6 + - - +
129B LYS* 2.3 34.4 + - - -
133B HIS* 4.2 9.7 + - - -
146B GLU* 3.9 16.4 - - + +
151B GLY 2.8 17.5 + - - +
152B TYR* 3.9 6.1 - - - +
153B LEU 3.6 1.6 - - - -
154B ALA* 1.3 73.4 - - - +
156B ASP* 1.3 71.9 + - - +
157B LEU 3.2 0.9 + - - -
189B TRP* 4.1 0.4 - - - -
302B NMN 2.9 16.5 + - - -
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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