Contacts of the helix formed by residues 153 - 164 (chain A) in PDB entry 3ASZ
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 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A VAL* 4.4 3.4 - - - -
151A GLY 4.3 0.2 + - - -
152A ARG* 1.3 73.9 - - - +
154A LEU* 1.3 64.2 + - - +
155A GLU* 3.6 9.3 + - - +
156A GLY* 3.0 21.1 + - - -
157A VAL* 3.0 26.7 + - - +
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Residues in contact with LEU 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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139A PHE* 5.3 0.7 - - + -
143A LEU* 3.6 43.3 - - + -
147A VAL* 4.4 4.8 - - + +
153A SER* 1.3 73.2 - - - +
155A GLU* 1.3 60.0 + - - +
157A VAL* 3.2 2.8 + - - +
158A VAL* 2.9 48.1 + - + +
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Residues in contact with GLU 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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153A SER* 3.2 8.5 + - - +
154A LEU* 1.3 83.1 - - + +
156A GLY* 1.3 55.7 + - - +
158A VAL* 3.5 6.1 + - - +
159A ALA* 3.0 29.1 + - + +
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Residues in contact with GLY 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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152A ARG* 5.6 2.0 - - - -
153A SER* 3.0 19.9 + - - -
155A GLU* 1.3 75.6 + - - +
157A VAL* 1.3 63.3 + - - +
159A ALA* 3.8 5.2 - - - +
160A GLN* 3.0 27.5 + - - +
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Residues in contact with VAL 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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139A PHE* 4.0 14.1 - - + -
142A ARG* 4.6 7.0 - - + +
143A LEU* 3.9 37.9 - - + +
146A ASP* 3.6 37.5 - - + +
147A VAL* 4.6 1.8 - - + -
152A ARG* 3.8 10.5 - - + +
153A SER 3.0 22.5 + - - +
154A LEU 3.2 4.7 + - - +
156A GLY* 1.3 74.7 - - - +
158A VAL* 1.3 59.0 + - - +
160A GLN* 3.9 6.6 - - - +
161A TYR* 2.9 32.9 + - + +
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Residues in contact with VAL 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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139A PHE* 4.1 22.4 - - + -
154A LEU* 2.9 34.7 + - + +
155A GLU* 3.7 7.0 - - - +
157A VAL* 1.3 76.4 - - - +
159A ALA* 1.3 63.4 + - - +
161A TYR* 3.3 4.6 + - - +
162A LEU* 3.0 46.5 + - + +
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Residues in contact with ALA 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 GLU* 3.0 19.4 + - + +
156A GLY* 3.8 6.1 - - - +
157A VAL 3.4 0.2 - - - -
158A VAL* 1.3 78.6 - - - +
160A GLN* 1.3 61.9 + - - +
162A LEU* 4.2 2.2 - - - -
163A GLU* 3.0 47.3 + - - +
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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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59A TYR* 4.7 8.5 - - - -
60A ASP* 4.5 1.4 + - - -
93A TYR* 5.4 3.8 + - - -
142A ARG* 3.2 19.5 + - - -
146A ASP* 4.3 4.0 - - - +
152A ARG* 3.7 14.9 + - - +
156A GLY 3.0 17.8 + - - +
157A VAL* 4.0 5.0 - - - +
159A ALA* 1.3 77.3 - - - +
161A TYR* 1.3 57.5 + - - +
163A GLU* 5.0 1.1 - - - -
164A GLN* 2.8 49.8 + - - +
165A VAL* 3.1 11.9 + - + +
212A C5P 3.2 39.7 + - - -
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Residues in contact with TYR 161 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A THR* 5.5 2.2 - - + -
135A ALA* 3.7 29.3 + - - +
138A ARG* 4.8 10.9 + - - -
139A PHE* 3.7 45.8 - + + -
142A ARG* 5.2 8.1 - - + -
157A VAL* 2.9 21.8 + - + +
158A VAL* 3.7 3.4 - - - +
160A GLN* 1.3 78.3 - - - +
162A LEU* 1.3 77.0 + - + +
165A VAL* 3.3 34.5 + - + +
166A LYS* 2.8 63.0 + - + +
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Residues in contact with LEU 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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158A VAL* 3.0 37.3 + - + +
159A ALA* 4.3 2.5 - - - +
161A TYR* 1.3 96.8 - - + +
163A GLU* 1.3 65.0 + - + +
166A LYS* 4.7 15.7 - - + +
167A PRO* 3.5 15.9 - - - +
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Residues in contact with GLU 163 (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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58A ASN* 5.1 1.4 + - - -
159A ALA* 3.0 34.7 + - - +
160A GLN* 4.5 1.3 - - - +
162A LEU* 1.3 81.9 - - + +
164A GLN* 1.3 68.3 + - + +
167A PRO* 3.9 11.0 - - - +
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Residues in contact with GLN 164 (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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55A LEU 5.4 1.2 - - - +
56A ARG* 2.9 28.7 + - - +
57A VAL 3.4 10.6 - - - +
58A ASN* 3.5 42.9 - - - +
59A TYR 4.4 1.2 + - - -
60A ASP* 4.7 2.2 - - - +
160A GLN* 2.8 38.2 + - + +
162A LEU 3.5 1.0 - - - -
163A GLU* 1.3 84.3 - - + +
165A VAL* 1.3 67.1 + - - +
166A LYS 3.4 1.6 - - - -
167A PRO* 3.2 4.0 - - - +
168A MET* 3.0 31.0 + - - +
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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