Contacts of the helix formed by residues 135 - 146 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96G HIS* 5.6 1.3 - - + -
132G ARG* 4.1 12.2 - - - -
133G ALA 3.8 6.7 - - - +
134G VAL* 1.3 89.0 - - - +
136G THR* 1.3 67.7 + - - +
137G ASP* 3.1 9.6 + - + +
138G GLU* 3.2 37.4 + - + +
139G ALA 3.5 6.4 + - - -
356H GLU* 3.6 22.2 - - + +
357H PRO* 5.0 14.1 - - + +
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Residues in contact with THR 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132G ARG* 3.3 13.9 + - - +
134G VAL 3.3 2.4 + - - -
135G PRO* 1.3 71.0 - - - +
137G ASP* 1.3 60.5 + - - +
139G ALA* 3.1 5.3 + - - +
140G ARG* 2.8 56.5 + - - +
150G PHE* 3.8 13.0 - - + -
152G GLU* 2.9 33.8 + - + +
356H GLU* 4.7 4.1 + - - -
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Residues in contact with ASP 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135G PRO* 3.1 6.5 + - + +
136G THR* 1.3 78.7 - - - +
138G GLU* 1.3 57.8 + - - +
140G ARG* 3.9 15.3 + - - +
141G ALA* 3.0 30.3 + - - +
400H TYR* 5.5 6.2 + - - -
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Residues in contact with GLU 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G HIS* 4.5 12.6 + - - -
99G TYR* 3.4 34.4 + - + +
134G VAL* 5.2 2.2 - - + -
135G PRO* 3.2 35.5 + - + +
137G ASP* 1.3 79.4 - - - +
139G ALA* 1.3 57.6 + - - +
141G ALA* 3.5 5.6 + - - +
142G PHE* 2.9 23.6 + - + +
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Residues in contact with ALA 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G TYR* 3.2 27.8 - - + +
99G TYR* 3.8 20.9 - - + -
121G LEU* 4.2 2.9 - - + +
134G VAL* 4.3 3.6 - - + -
135G PRO 3.5 7.2 + - - +
136G THR* 3.1 6.6 + - - +
138G GLU* 1.3 78.2 - - - +
140G ARG* 1.3 66.6 + - - +
142G PHE* 3.2 2.6 + - - +
143G ALA* 3.0 24.4 + - - +
150G PHE* 3.3 18.8 - - + -
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Residues in contact with ARG 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G THR* 2.8 50.0 + - - +
137G ASP* 3.9 14.4 + - - +
139G ALA* 1.3 75.7 - - - +
141G ALA* 1.3 62.3 + - - +
143G ALA* 3.3 2.4 + - - +
144G GLU* 3.1 44.1 + - + +
150G PHE* 3.6 29.7 - - + -
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Residues in contact with ALA 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G ASP 3.0 20.0 + - - +
138G GLU* 3.5 7.2 - - - +
140G ARG* 1.3 75.6 - - - +
142G PHE* 1.3 66.2 + - - +
143G ALA 3.3 0.3 + - - -
144G GLU* 3.4 8.1 + - - +
145G LYS* 3.3 22.5 + - - +
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Residues in contact with PHE 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G TYR* 3.2 28.9 - + - +
102G VAL* 3.8 26.2 - - + -
103G GLU* 3.1 30.5 - - - -
106G LEU* 3.8 21.5 - - + -
121G LEU* 3.9 15.3 - - + -
138G GLU 2.9 9.9 + - - +
139G ALA 3.7 2.2 - - - +
141G ALA* 1.3 75.7 - - - +
143G ALA* 1.3 64.6 + - - +
145G LYS* 3.6 8.9 + - + +
146G ASN* 3.2 48.1 + - - +
148G LEU* 4.2 7.6 - - + -
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Residues in contact with ALA 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G LEU* 4.3 7.0 - - + -
139G ALA 3.0 17.3 + - - +
140G ARG 3.5 5.8 - - - +
141G ALA 3.1 0.2 - - - -
142G PHE* 1.3 79.4 - - - +
144G GLU* 1.3 62.8 + - + +
146G ASN 3.1 3.1 + - - -
147G GLY 3.1 5.0 + - - -
148G LEU* 2.9 50.1 + - + +
149G SER 4.2 0.9 - - - +
150G PHE* 3.6 26.5 - - + -
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Residues in contact with GLU 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G ARG* 3.1 35.6 + - + +
141G ALA* 3.4 6.7 + - - +
143G ALA* 1.3 76.7 - - + +
145G LYS* 1.3 63.8 + - - +
147G GLY* 3.2 12.7 + - - +
148G LEU 4.4 7.2 - - - +
150G PHE* 6.3 0.9 - - + -
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Residues in contact with LYS 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G ALA 3.3 12.1 + - - +
142G PHE* 3.6 11.0 - - + +
143G ALA 3.3 0.4 - - - -
144G GLU* 1.3 78.9 - - - +
146G ASN* 1.3 80.3 + - - +
147G GLY 3.4 0.4 + - - -
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Residues in contact with ASN 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G GLU* 4.2 8.2 + - - +
106G LEU* 3.8 14.4 - - + +
142G PHE* 3.2 49.5 + - - +
143G ALA 3.1 4.2 + - - +
145G LYS* 1.3 97.0 - - - +
147G GLY* 1.3 61.7 + - - +
148G LEU* 3.4 23.8 + - + +
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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