Contacts of the helix formed by residues 131 - 142 (chain G) in PDB entry 5TJ4
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 GLU 131 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354C ARG* 3.5 23.6 - - + +
126G PRO* 3.3 25.0 - - + +
127G LYS 3.4 14.2 + - - -
128G THR* 3.0 33.0 + - + +
129G TRP 3.2 0.6 - - - -
130G GLU* 1.3 77.2 - - - +
132G ILE* 1.3 61.4 + - - +
133G PRO* 3.4 0.7 - - - -
134G ALA* 3.4 10.4 + - - +
135G LEU* 3.0 37.6 + - + +
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Residues in contact with ILE 132 (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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115G LEU* 6.4 0.2 - - + -
126G PRO* 3.9 14.8 - - + -
128G THR 4.0 3.4 - - - +
129G TRP* 3.0 34.8 - - + +
131G GLU* 1.3 73.9 - - - +
133G PRO* 1.4 70.9 - - + +
135G LEU* 3.2 7.8 + - - +
136G ASP* 3.0 23.2 + - + +
146G ALA* 4.2 18.4 - - + -
147G LEU* 4.3 28.0 - - + -
198G LEU* 4.7 14.4 - - + -
203G HIS* 6.1 2.2 - - + -
224G MET* 3.6 26.2 - - + -
248G PRO* 4.5 10.8 - - + -
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Residues in contact with PRO 133 (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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129G TRP 3.6 6.3 - - - +
130G GLU 3.2 19.1 - - - +
131G GLU 3.4 0.9 - - - -
132G ILE* 1.4 94.1 - - + +
134G ALA* 1.3 60.6 + - - +
136G ASP 3.3 0.2 + - - -
137G LYS* 3.3 18.5 + - - +
194G PHE* 4.4 18.8 - - + -
198G LEU* 5.0 5.8 - - + -
201G ASN* 6.3 0.2 - - - +
203G HIS* 3.3 42.8 - - + +
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Residues in contact with ALA 134 (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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130G GLU 5.4 1.3 - - - +
131G GLU* 3.4 12.7 + - - +
132G ILE 3.3 0.4 - - - -
133G PRO* 1.3 79.6 - - - +
135G LEU* 1.3 64.5 + - + +
137G LYS* 3.2 18.6 + - - +
138G GLU* 3.2 12.1 + - - +
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Residues in contact with LEU 135 (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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122G LEU* 4.1 23.3 - - + -
124G ASN 5.7 1.3 - - - +
126G PRO* 3.9 27.8 - - + -
131G GLU* 3.0 44.3 + - + +
132G ILE* 3.2 9.3 + - - +
134G ALA* 1.3 77.7 - - + +
136G ASP* 1.3 60.6 + - - +
138G GLU* 3.3 8.0 + - - +
139G LEU* 2.8 45.4 + - + +
146G ALA* 4.4 4.3 - - + -
224G MET* 4.4 6.5 - - + -
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Residues in contact with ASP 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G ILE* 3.0 11.3 + - + +
133G PRO 3.6 3.4 - - - +
134G ALA 3.2 0.2 - - - -
135G LEU* 1.3 72.7 - - - +
137G LYS* 1.3 58.9 + - - +
139G LEU 3.2 0.2 + - - -
140G LYS* 2.7 43.0 + - - +
145G SER* 3.7 11.1 + - - -
146G ALA* 2.8 40.3 + - + +
147G LEU 4.4 0.5 + - - -
202G LYS 4.2 2.9 - - - +
203G HIS* 3.1 51.8 + - + +
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Residues in contact with LYS 137 (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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133G PRO 3.3 8.6 + - - +
134G ALA* 3.2 13.6 + - - +
136G ASP* 1.3 80.3 - - - +
138G GLU* 1.3 62.4 + - - +
140G LYS* 3.6 6.8 - - - +
141G ALA* 3.5 14.7 + - - +
203G HIS* 4.6 6.3 - - + -
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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
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1404C GLU* 5.2 15.0 - - + +
1405C GLY 4.9 5.0 - - - +
1407C THR 5.2 9.2 - - - +
134G ALA 3.2 8.8 + - - +
135G LEU* 3.6 10.8 - - - +
136G ASP 3.2 0.2 - - - -
137G LYS* 1.3 79.3 - - - +
139G LEU* 1.3 64.8 + - + +
141G ALA* 3.2 22.8 + - - +
142G LYS* 3.8 3.6 + - - +
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Residues in contact with LEU 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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121G LEU* 3.9 28.7 - - + +
122G LEU* 4.7 9.2 - - + -
135G LEU* 2.8 43.7 + - + +
136G ASP 4.2 0.9 - - - +
138G GLU* 1.3 72.7 - - + +
140G LYS* 1.3 62.8 + - - +
141G ALA 3.2 0.2 - - - -
142G LYS* 3.2 14.3 + - + +
144G LYS* 2.8 50.7 + - + +
145G SER 4.4 6.7 - - - -
146G ALA* 4.3 6.1 - - + -
223G ALA* 4.1 27.4 - - + -
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Residues in contact with LYS 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 ASP* 2.7 29.1 + - - +
137G LYS* 3.6 9.2 - - - +
138G GLU 3.3 0.2 - - - -
139G LEU* 1.3 72.6 - - - +
141G ALA* 1.3 56.9 + - - +
143G GLY* 3.0 18.9 + - - -
144G LYS 3.3 13.3 + - - +
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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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1265C GLU* 5.4 2.3 - - - +
1268C ARG* 5.7 2.3 + - - -
1405C GLY 4.8 0.7 - - - +
1406C PRO* 3.9 30.1 - - + +
137G LYS 3.5 7.3 + - - +
138G GLU* 3.2 16.9 + - - +
139G LEU 3.2 0.6 - - - -
140G LYS* 1.3 78.5 - - - +
142G LYS* 1.3 56.6 + - - +
143G GLY 3.3 1.1 + - - -
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Residues in contact with LYS 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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1265C GLU* 4.2 25.9 - - + +
1405C GLY 5.5 5.4 - - - +
138G GLU 3.8 2.3 + - - +
139G LEU* 3.2 17.1 + - + +
141G ALA* 1.3 75.9 - - - +
143G GLY* 1.3 59.3 + - - +
144G LYS* 3.3 19.6 + - + +
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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