Contacts of the helix formed by residues 135 - 146 (chain J) in PDB entry 4UJ3
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 PRO 135 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96J HIS* 5.6 0.2 - - + -
132J ARG* 4.2 11.1 - - - -
133J ALA 3.8 6.3 - - - +
134J VAL* 1.3 90.0 - - + +
136J THR* 1.3 65.8 + - - +
137J ASP* 3.2 6.5 - - + +
138J GLU* 3.1 43.4 + - + +
139J ALA* 3.5 7.1 + - - +
356K GLU* 4.5 15.3 - - - +
357K PRO* 4.0 24.7 - - + +
359K GLY 5.7 5.2 - - - +
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Residues in contact with THR 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J ARG* 3.1 22.7 + - - +
134J VAL 3.5 2.2 + - - -
135J PRO* 1.3 72.1 - - - +
137J ASP* 1.3 65.0 + - - +
139J ALA* 3.4 3.0 + - - +
140J ARG* 3.0 54.5 + - - +
150J PHE* 3.9 10.0 - - + -
152J GLU* 3.3 23.9 + - + +
356K GLU* 5.1 6.2 + - - -
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Residues in contact with ASP 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135J PRO* 3.2 5.3 - - + -
136J THR* 1.3 81.3 - - - +
138J GLU* 1.3 64.0 + - - +
140J ARG* 3.5 14.4 + - - +
141J ALA* 3.0 26.4 + - - +
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Residues in contact with GLU 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96J HIS* 4.2 18.9 + - - -
99J TYR* 3.5 23.2 + - + +
134J VAL* 5.3 2.2 - - + -
135J PRO* 3.1 39.4 + - + +
137J ASP* 1.3 78.4 - - - +
139J ALA* 1.3 57.7 + - - +
141J ALA* 3.6 5.5 - - - +
142J PHE* 3.2 22.4 + - + +
359K GLY* 5.7 4.3 - - - -
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Residues in contact with ALA 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91J TYR* 3.5 24.7 - - + +
99J TYR* 3.4 24.9 - - + -
121J LEU* 4.1 4.9 - - + +
134J VAL* 4.3 0.2 - - + -
135J PRO 3.5 6.4 + - - +
136J THR* 3.4 4.4 + - - +
137J ASP 3.2 0.2 - - - -
138J GLU* 1.3 76.0 - - - +
140J ARG* 1.3 56.2 + - - +
141J ALA 3.1 1.6 - - - -
142J PHE* 3.0 4.9 + - - +
143J ALA* 2.7 34.8 + - - +
150J PHE* 3.6 18.4 - - + -
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Residues in contact with ARG 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J THR* 3.0 44.7 + - - +
137J ASP* 4.0 15.1 + - - +
139J ALA* 1.3 76.7 - - - +
141J ALA* 1.3 62.2 + - - +
143J ALA* 3.3 2.8 + - - +
144J GLU* 3.1 39.9 + - + +
150J PHE* 3.8 34.8 + - + -
151J ILE* 6.0 1.2 - - - +
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Residues in contact with ALA 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137J ASP 3.0 18.9 + - - +
138J GLU* 3.6 7.2 - - - +
140J ARG* 1.3 74.6 - - - +
142J PHE* 1.3 60.2 + - - +
144J GLU* 3.3 9.0 + - - +
145J LYS* 3.0 29.5 + - - +
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Residues in contact with PHE 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99J TYR* 3.4 29.2 - + - +
102J VAL* 3.9 26.0 - - + -
103J GLU* 5.3 10.1 - - + -
106J LEU* 4.0 17.3 - - + -
121J LEU* 4.1 15.0 - - + -
138J GLU 3.2 5.3 + - - +
139J ALA 3.0 7.3 + - - +
141J ALA* 1.3 78.3 - - - +
143J ALA* 1.3 59.7 + - - +
145J LYS* 3.4 13.7 + - + +
146J ASN* 3.0 51.2 + - - +
148J LEU* 4.3 7.9 - - + -
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Residues in contact with ALA 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J LEU* 4.3 7.2 - - + -
139J ALA 2.7 15.0 + - - +
140J ARG 3.5 8.7 - - - +
141J ALA 3.2 0.2 - - - -
142J PHE* 1.3 76.4 - - - +
144J GLU* 1.3 65.9 + - + +
146J ASN 3.0 2.8 + - - -
147J GLY 2.9 5.7 + - - -
148J LEU* 2.9 47.4 + - + +
149J SER 4.2 3.1 - - - +
150J PHE* 3.6 24.7 - - + -
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Residues in contact with GLU 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J ARG* 3.1 32.3 + - + +
141J ALA* 3.8 6.9 - - - +
143J ALA* 1.3 80.6 - - + +
145J LYS* 1.3 60.3 - - - +
146J ASN 3.5 0.3 + - - -
147J GLY* 3.6 9.5 + - - +
148J LEU 4.6 3.8 - - - +
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Residues in contact with LYS 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LYS* 6.1 0.3 - - - -
141J ALA 3.0 17.2 + - - +
142J PHE* 3.6 13.2 - - + +
143J ALA 3.1 0.2 - - - -
144J GLU* 1.3 79.8 - - - +
146J ASN* 1.3 67.7 + - - +
147J GLY 3.5 0.2 - - - -
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Residues in contact with ASN 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LYS* 4.5 14.8 - - - +
106J LEU* 4.0 14.3 - - + +
142J PHE* 3.0 42.6 + - + +
143J ALA 3.0 3.2 + - - -
145J LYS* 1.3 86.6 + - - +
147J GLY* 1.3 64.3 + - - +
148J LEU* 3.4 27.7 + - + +
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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