Contacts of the helix formed by residues 149 - 155 (chain A) in PDB entry 4ILW
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 MET 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A CYS* 3.7 22.0 - - - -
136A ILE* 3.4 33.0 - - + -
138A CYS* 3.9 10.3 - - - -
147A LEU* 3.5 26.7 - - + +
148A TRP* 1.3 72.3 - - - +
150A ASP* 1.3 64.5 + - - +
151A TRP 3.2 3.1 + - - -
152A VAL* 3.4 10.8 + - + -
153A THR* 2.9 38.4 + - + +
161A GLN* 2.6 23.1 + - - +
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Residues in contact with ASP 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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148A TRP* 3.1 27.3 + - + +
149A MET* 1.3 78.9 - - - +
151A TRP* 1.3 57.3 + - - +
153A THR* 4.2 5.1 + - - -
154A GLU* 2.8 35.3 + - - +
155A LYS 3.3 0.9 + - - -
156A ASN 3.3 17.1 - - - +
157A ILE 4.2 0.4 - - - +
159A GLY* 3.0 24.9 + - - +
160A HIS* 3.6 3.7 + - - +
161A GLN* 3.0 27.4 + - - +
162A ALA* 3.0 25.5 + - - +
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Residues in contact with TRP 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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132A ARG* 3.6 37.2 - - + +
133A CYS 5.0 2.0 - - - +
134A PRO 4.7 9.2 - - - -
148A TRP* 5.2 2.2 + - - +
149A MET 3.2 0.8 - - - -
150A ASP* 1.3 78.4 - - - +
152A VAL* 1.3 63.6 + - - +
155A LYS* 2.7 82.2 + - + +
156A ASN* 3.3 26.5 - - - +
157A ILE* 4.1 20.0 - - + -
242D PHE* 3.7 38.9 - + - -
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Residues in contact with VAL 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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133A CYS* 3.9 16.4 + - - +
134A PRO 4.0 3.1 - - - +
135A MET* 3.4 34.5 - - + -
136A ILE* 3.4 23.7 - - + +
149A MET* 3.4 36.3 - - + +
151A TRP* 1.3 84.7 - - - +
153A THR* 1.3 71.4 + - + +
155A LYS 4.9 0.2 + - - -
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Residues in contact with THR 153 (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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136A ILE* 5.6 1.6 - - + -
149A MET* 2.9 39.0 + - + +
150A ASP* 3.9 2.6 + - - -
152A VAL* 1.3 88.4 - - + +
154A GLU* 1.3 76.5 + - - +
160A HIS* 6.0 0.2 - - - +
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Residues in contact with GLU 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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150A ASP* 2.8 16.7 + - - +
153A THR* 1.3 92.4 + - - +
155A LYS* 1.3 66.5 + - - +
156A ASN* 3.3 21.3 + - + +
159A GLY* 3.6 13.3 - - - -
160A HIS* 2.8 42.1 + - - +
163A LYS* 5.4 3.1 + - - -
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Residues in contact with LYS 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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151A TRP* 2.7 71.8 + - + +
152A VAL 4.9 0.2 + - - -
153A THR 3.8 0.4 - - - -
154A GLU* 1.3 73.2 - - - +
156A ASN* 1.3 58.2 + - - +
242D PHE* 6.0 1.4 - - - -
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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