Contacts of the strand formed by residues 133 - 137 (chain W) 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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56H ASP* 4.9 15.6 + - - -
98W ASP* 4.1 34.5 + - + +
99W LEU 3.9 1.9 + - - +
100W VAL* 3.5 32.2 - - + -
101W PHE 3.5 3.3 + - - -
131W ILE* 4.1 8.5 - - - +
132W LYS* 1.3 101.3 + - + +
134W GLU* 1.3 64.2 + - - +
152W LYS* 4.1 29.7 + - + +
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Residues in contact with GLU 134 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149J THR* 3.9 12.1 + - - -
166J TYR* 5.2 2.1 - - - -
167J GLU* 3.7 15.3 - - - +
100W VAL* 4.8 1.1 - - - -
101W PHE 3.6 13.5 - - - +
103W PHE* 3.2 17.3 - - + -
121W LYS* 3.0 39.5 + - - -
125W LYS* 5.6 2.0 - - - +
131W ILE* 5.0 10.6 - - + +
133W HIS* 1.3 78.5 - - - +
135W LEU* 1.3 71.0 + - - +
136W GLN* 4.4 3.3 + - + +
152W LYS* 5.6 0.4 - - - -
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Residues in contact with LEU 135 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68W TYR* 4.9 6.5 - - + +
100W VAL* 4.9 3.1 - - + -
101W PHE 3.3 5.7 + - - +
102W ILE* 3.5 31.6 - - + +
103W PHE* 3.0 24.6 + - - +
134W GLU* 1.3 82.2 - - - +
136W GLN* 1.3 61.5 + - - +
148W THR* 3.3 37.9 - - + +
149W LEU* 3.9 24.9 - - + +
151W GLU* 5.6 2.2 - - - +
152W LYS* 3.2 36.3 - - + +
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Residues in contact with GLN 136 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146J GLY 2.9 22.1 + - - -
147J ARG* 3.0 47.6 + - - +
148J THR 4.0 1.2 + - - -
149J THR 5.2 0.2 + - - -
296J ASN* 5.9 0.7 + - - -
102W ILE* 5.8 0.2 - - - -
103W PHE* 3.3 42.2 - - + +
105W ALA* 4.6 4.6 - - + +
121W LYS* 3.9 21.0 + - - +
134W GLU* 4.4 3.7 + - + +
135W LEU* 1.3 76.3 - - - +
137W ALA* 1.3 68.6 + - - +
142W GLU* 4.1 5.5 - - - +
148W THR* 5.6 6.0 - - - +
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Residues in contact with ALA 137 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147J ARG* 4.7 2.0 - - - +
103W PHE 3.4 4.1 + - - +
104W TRP* 3.1 20.5 - - - -
105W ALA 3.6 12.0 + - - -
136W GLN* 1.3 79.3 - - - +
138W ASN* 1.3 59.5 + - - +
139W CYS 3.4 3.6 - - - +
142W GLU* 3.4 37.0 - - + +
143W VAL* 3.5 25.7 - - + +
148W 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