Contacts of the strand formed by residues 133 - 137 (chain U) in PDB entry 3J0S
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 HIS 133 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56F ASP* 4.9 15.8 + - - -
98U ASP* 4.1 34.0 - - + +
99U LEU 3.9 2.7 + - - +
100U VAL* 3.5 32.2 - - + -
101U PHE 3.5 3.1 + - - -
131U ILE* 4.1 8.2 - - - +
132U LYS* 1.3 102.4 + - + +
134U GLU* 1.3 64.7 + - - +
152U LYS* 4.1 28.4 + - + +
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Residues in contact with GLU 134 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149H THR* 3.9 11.8 + - - -
166H TYR* 5.2 2.1 - - - -
167H GLU* 3.6 15.5 - - - +
100U VAL* 4.8 1.1 - - - -
101U PHE 3.6 13.7 - - - +
103U PHE* 3.2 16.6 - - + -
121U LYS* 3.0 39.4 + - - -
125U LYS* 5.6 2.2 - - - +
131U ILE* 5.0 9.8 - - + +
133U HIS* 1.3 78.0 - - - +
135U LEU* 1.3 72.5 + - - +
136U GLN* 4.4 4.1 + - + +
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Residues in contact with LEU 135 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68U TYR* 4.9 6.5 - - + +
100U VAL* 4.9 3.1 - - + +
101U PHE 3.3 5.3 + - - +
102U ILE* 3.5 31.6 - - + +
103U PHE* 3.0 24.6 + - - +
134U GLU* 1.3 82.8 - - - +
136U GLN* 1.3 61.7 + - - +
148U THR* 3.3 39.3 - - + +
149U LEU* 3.9 26.0 - - + +
151U GLU* 5.6 3.1 - - + +
152U LYS* 3.2 35.0 - - + +
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Residues in contact with GLN 136 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146H GLY 2.9 22.8 + - - -
147H ARG* 3.0 46.8 + - - +
148H THR 4.0 1.4 + - - -
149H THR 5.2 0.2 + - - -
296H ASN* 5.9 0.9 + - - -
102U ILE* 5.8 0.4 - - - -
103U PHE* 3.3 42.1 - - + +
105U ALA* 4.6 4.6 - - + +
121U LYS* 3.9 21.5 + - - +
134U GLU* 4.2 4.0 - - + -
135U LEU* 1.3 75.8 - - - +
137U ALA* 1.3 69.0 + - - +
142U GLU* 4.1 5.2 - - - +
148U THR* 5.6 6.0 - - - +
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Residues in contact with ALA 137 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H ARG* 4.7 2.0 - - - +
102U ILE* 6.1 0.2 - - - +
103U PHE 3.4 4.3 + - - +
104U TRP* 3.1 20.8 - - - -
105U ALA 3.6 11.8 + - - -
136U GLN* 1.3 79.5 - - - +
138U ASN* 1.3 58.6 + - - +
139U CYS 3.4 3.4 - - - +
142U GLU* 3.4 37.5 - - + +
143U VAL* 3.5 25.3 - - + +
148U THR* 6.0 2.5 - - + -
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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