Contacts of the strand formed by residues 145 - 150 (chain B) in PDB entry 4IJ3
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 ASN 145 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ILE* 1.3 81.5 - - - +
146B VAL* 1.3 71.7 + - - +
147B LYS* 4.8 3.3 + - - +
175B MET* 5.3 2.7 - - - -
195B GLU 3.9 0.7 - - - +
196B ALA* 3.6 1.7 - - - -
197B THR* 3.1 45.4 + - - +
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Residues in contact with VAL 146 (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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136B LEU* 3.4 37.7 - - + -
145B ASN* 1.3 82.0 - - - +
147B LYS* 1.3 61.0 + - - +
148B TRP* 4.0 13.7 + - + +
159B VAL* 5.3 0.9 - - + -
161B ASN* 4.1 10.1 - - - +
175B MET* 3.6 24.0 - - + +
177B SER* 3.4 26.7 - - - +
194B CYS* 5.1 6.1 - - - -
195B GLU 3.2 8.7 - - - +
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Residues in contact with LYS 147 (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 ASN* 4.3 4.2 + - - +
146B VAL* 1.3 76.1 - - - +
148B TRP* 1.3 69.4 + - - +
149B LYS* 3.6 28.7 - - - +
154B GLU* 3.5 40.5 + - + +
193B THR 4.0 0.2 - - - +
194B CYS* 3.7 2.8 - - - -
195B GLU* 2.8 50.1 + - + +
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Residues in contact with TRP 148 (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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117B ILE* 4.2 3.8 - - + -
132B VAL* 3.2 48.2 - - + -
133B VAL 4.3 0.2 - - - -
134B CYS* 3.7 25.1 - - + -
146B VAL* 4.0 9.6 - - + +
147B LYS* 1.3 79.3 - - - +
149B LYS* 1.3 63.9 + - - +
150B ILE 4.3 0.2 - - - -
154B GLU* 3.1 9.1 - - - +
155B ARG* 2.8 45.5 + - + +
159B VAL* 3.8 28.8 - - + +
177B SER* 2.8 43.2 + - - -
179B LEU* 3.9 25.6 - - + -
192B TYR* 5.4 2.0 - + + -
193B THR 3.1 25.6 - - - -
194B CYS* 4.1 10.5 - - + -
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Residues in contact with LYS 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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147B LYS* 3.6 21.8 + - + +
148B TRP* 1.3 81.6 - - - +
150B ILE* 1.3 63.7 + - - +
151B ASP 3.8 0.5 + - - -
152B GLY* 3.6 24.5 + - - +
153B SER 2.8 14.4 - - - +
154B GLU* 4.0 5.6 - - - +
191B SER 3.6 2.4 - - - +
192B TYR* 3.6 0.7 - - - -
193B THR* 2.8 52.3 + - + +
195B GLU* 3.2 40.7 + - + +
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Residues in contact with ILE 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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149B LYS* 1.3 71.2 - - - +
151B ASP* 1.3 72.2 + - - +
153B SER* 2.8 26.0 + - - +
155B ARG* 3.1 41.5 - - + +
179B LEU* 4.0 15.3 - - + -
181B LEU* 3.8 12.1 - - + -
185B GLU* 5.4 0.4 - - - +
189B HIS* 3.5 44.7 + - + +
191B SER 3.3 4.0 - - - +
192B TYR* 3.7 30.3 - - + -
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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