Contacts of the helix formed by residues 146 - 152 (chain E) in PDB entry 2ZUQ
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 SER 146 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E PRO 3.2 7.0 + - - -
145E PRO* 1.3 73.4 - - - +
147E SER* 1.3 67.5 + - - +
148E GLU 2.9 3.3 + - - -
149E GLN* 2.9 31.7 + - - +
150E LEU* 3.5 5.2 + - - +
156E SER 4.7 0.2 + - - -
128F TYR* 3.1 25.3 - - - +
129F PRO* 3.0 40.0 - - - +
130F LEU* 4.6 3.8 - - - +
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Residues in contact with SER 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E PRO 3.5 2.4 + - - -
146E SER* 1.3 70.9 - - - +
148E GLU* 1.3 63.5 + - - +
150E LEU* 3.9 18.7 - - - +
151E THR* 3.9 7.8 + - - +
129F PRO* 6.0 3.4 - - - -
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Residues in contact with GLU 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E SER* 2.9 1.6 + - - +
147E SER* 1.3 74.7 - - - +
149E GLN* 1.3 69.7 + - - +
150E LEU 3.0 2.5 - - - -
151E THR* 2.8 22.4 + - - +
152E SER* 3.1 13.3 + - - +
127F VAL 5.0 3.5 - - - +
128F TYR* 4.2 20.8 - - + -
129F PRO* 4.2 24.6 - - + +
214F LYS* 5.1 10.8 + - - +
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Residues in contact with GLN 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E PRO 4.9 0.7 - - - -
146E SER* 2.9 27.2 + - - +
148E GLU* 1.3 80.2 - - - +
150E LEU* 1.3 58.9 + - - +
152E SER* 3.0 20.6 + - - -
154E GLY* 2.8 28.1 + - - +
155E ALA* 3.8 5.0 + - - -
156E SER* 2.8 51.8 + - - +
128F TYR* 3.3 49.4 - - + +
130F LEU* 5.8 0.8 - - - +
147F LEU* 3.9 6.1 - - - +
149F LYS* 4.3 4.7 - - - +
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Residues in contact with LEU 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E PRO* 3.5 24.9 - - + +
146E SER 3.9 9.2 - - - +
147E SER* 3.9 13.7 - - - +
148E GLU 3.0 1.0 + - - -
149E GLN* 1.3 71.5 - - - +
151E THR* 1.3 54.6 + - - +
152E SER 2.9 3.8 - - - -
153E GLY* 2.7 26.2 + - - -
154E GLY 3.3 4.3 - - - +
155E ALA* 3.7 25.4 - - + -
208E LYS* 3.4 36.7 - - + +
211E TYR* 3.9 24.7 - - + -
212E GLU* 5.1 2.9 - - - +
236E ARG* 5.6 1.1 - - - +
239E CYS* 5.4 11.0 - - - +
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Residues in contact with THR 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E SER 3.9 3.7 + - - +
148E GLU* 2.8 24.4 + - - +
150E LEU* 1.3 75.2 - - - +
152E SER* 1.3 58.3 + - - +
153E GLY 3.2 1.5 + - - -
208E LYS* 4.2 13.5 + - - +
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Residues in contact with SER 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E GLU* 3.1 14.9 + - - +
149E GLN* 3.1 14.1 + - - -
150E LEU 2.8 0.6 + - - -
151E THR* 1.3 77.1 + - - +
153E GLY* 1.3 57.0 + - - +
154E GLY* 3.4 1.1 - - - -
128F TYR* 4.2 17.2 + - - -
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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