Contacts of the helix formed by residues 146 - 152 (chain A) in PDB entry 2P6U
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 GLU 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A LYS* 6.2 0.9 - - - +
76A PRO* 3.6 15.4 - - + +
80A LEU* 3.1 20.4 - - - +
145A ASP* 1.3 85.0 + - - +
147A ILE* 1.3 59.3 + - - +
148A HIS* 3.1 30.2 + - + -
149A LEU* 3.0 47.5 + - + +
159A LEU* 4.4 2.1 - - - +
178A LEU 3.0 8.2 + - - -
365A GLN* 5.8 1.2 - - - +
708A PO4 2.8 31.6 + - - +
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Residues in contact with ILE 147 (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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44A LEU* 3.9 15.7 - - + -
144A VAL* 3.5 40.6 - - + +
145A ASP 3.0 3.2 + - - -
146A GLU* 1.3 68.3 - - - +
148A HIS* 1.3 60.5 + - - +
149A LEU 2.9 5.8 - - - -
150A LEU* 3.0 33.5 + - + +
159A LEU* 4.3 6.9 - - + +
163A VAL* 5.1 3.4 - - + -
175A VAL* 5.8 0.2 - - + -
177A GLY* 4.1 3.8 - - - -
178A LEU 2.8 17.1 + - - +
179A SER* 3.2 25.1 - - - -
188A ILE* 4.6 7.0 - - + +
191A TRP* 4.5 12.8 - - + -
192A LEU* 4.1 27.4 - - + -
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Residues in contact with HIS 148 (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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53A LYS* 6.2 1.3 - - - -
146A GLU* 3.1 41.3 + - + +
147A ILE* 1.3 75.4 - - - +
149A LEU* 1.3 71.5 + - + +
150A LEU* 2.8 16.1 + - - -
151A ASP* 3.1 19.4 + - - +
179A SER* 3.7 12.3 - - - +
180A ALA* 3.2 40.0 + - + +
182A ALA* 5.6 1.1 - - + -
188A ILE* 5.0 0.2 - - - -
405A ILE* 3.8 29.2 - - + +
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Residues in contact with LEU 149 (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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76A PRO* 3.5 38.4 - - + -
77A LEU* 5.3 2.5 - - + -
146A GLU* 3.0 26.7 + - + +
147A ILE 2.9 1.4 - - - -
148A HIS* 1.3 108.7 - - + +
150A LEU* 1.3 51.7 + - - +
151A ASP* 2.9 6.7 - - - +
152A SER* 2.8 38.7 + - - +
155A ARG* 4.1 13.2 - - + +
156A GLY* 3.3 8.8 + - - -
159A LEU* 4.2 11.4 - - + -
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Residues in contact with LEU 150 (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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147A ILE* 3.0 24.9 + - + +
148A HIS 2.8 0.2 + - - -
149A LEU* 1.3 77.9 - - - +
151A ASP* 1.3 59.5 + - - +
152A SER 3.5 0.3 + - - +
156A GLY* 3.7 14.5 - - - +
159A LEU* 3.6 25.3 - - + +
160A GLU* 3.3 34.3 - - + +
188A ILE* 4.5 9.2 - - + -
191A TRP* 3.6 28.5 - - + -
405A ILE* 4.1 11.9 - - + -
407A SER* 3.9 16.2 - - - -
408A LYS 4.1 2.1 + - - -
442A PHE* 3.9 32.5 - - + -
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Residues in contact with ASP 151 (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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148A HIS 3.1 12.9 + - - +
149A LEU* 5.2 0.2 - - - -
150A LEU* 1.3 79.6 - - - +
152A SER* 1.3 61.6 + - - +
153A GLU 3.3 3.1 + - - -
359A LYS* 4.6 5.2 + - - +
404A ARG 3.4 1.8 - - - +
405A ILE* 3.8 18.4 - - + +
406A THR 2.9 25.9 + - - -
408A LYS* 3.1 24.3 + - - +
706A PO4 2.6 33.7 + - - -
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Residues in contact with SER 152 (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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149A LEU* 2.8 29.8 + - - +
151A ASP* 1.3 76.9 - - - +
153A GLU* 1.3 61.0 + - - +
154A LYS* 2.9 12.0 + - - +
155A ARG* 3.0 28.7 + - - +
156A GLY* 2.7 27.7 + - - -
157A ALA 4.5 0.5 + - - -
408A LYS* 4.5 3.1 - - - +
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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