Contacts of the helix formed by residues 131 - 142 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119C LYS* 4.2 14.6 - - - +
241C ASN* 5.9 0.2 + - - -
315C PRO* 5.6 2.2 - - + -
126F PRO* 3.4 27.6 - - + +
127F LYS* 3.4 14.8 + - - +
128F THR* 3.1 32.8 + - + +
129F TRP 3.2 0.4 - - - -
130F GLU* 1.3 77.8 - - - +
132F ILE* 1.3 62.0 + - - +
133F PRO* 3.4 0.4 - - - -
134F ALA* 3.4 11.6 + - - +
135F LEU* 3.2 26.5 + - + +
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Residues in contact with ILE 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F PRO* 4.3 7.9 - - + -
128F THR 3.6 7.4 - - - +
129F TRP* 3.2 55.5 + - + +
131F GLU* 1.3 75.3 - - - +
133F PRO* 1.3 71.8 - - + +
135F LEU* 3.1 5.7 + - - +
136F ASP* 2.9 22.4 + - + +
146F ALA* 4.2 17.7 - - + -
147F LEU* 4.4 18.4 - - + -
198F LEU* 4.7 16.2 - - + -
203F HIS* 5.9 2.7 - - + -
224F MET* 4.0 20.6 - - + -
248F PRO* 4.3 12.1 - - + -
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Residues in contact with PRO 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F TRP 3.6 8.5 - - - +
130F GLU 3.2 18.2 - - - +
131F GLU 3.4 1.1 - - - -
132F ILE* 1.3 93.8 - - + +
134F ALA* 1.3 61.5 + - - +
136F ASP 3.3 0.2 + - - -
137F LYS* 3.3 17.5 + - - +
194F PHE* 4.4 18.2 - - + -
198F LEU* 5.0 7.0 - - + -
203F HIS* 3.3 42.8 - - + +
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Residues in contact with ALA 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F GLU 5.0 1.5 + - - +
131F GLU* 3.4 11.8 + - - +
132F ILE 3.2 0.2 - - - -
133F PRO* 1.3 79.8 - - - +
135F LEU* 1.3 63.2 + - + +
137F LYS* 3.2 18.3 + - - +
138F GLU* 3.2 12.0 + - - +
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Residues in contact with LEU 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F LEU* 4.7 14.6 - - + -
124F ASN 5.7 2.0 - - - +
126F PRO* 3.8 39.7 - - + -
131F GLU* 3.2 18.3 + - + +
132F ILE* 3.1 11.3 + - + +
134F ALA* 1.3 80.3 - - + +
136F ASP* 1.3 57.5 + - - +
138F GLU* 3.3 9.6 + - + +
139F LEU* 2.8 49.4 + - + +
146F ALA* 4.1 5.4 - - + -
224F MET* 4.9 3.1 - - + -
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Residues in contact with ASP 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F ILE* 2.9 12.7 + - + +
133F PRO 3.6 3.4 - - - +
135F LEU* 1.3 73.2 - - - +
137F LYS* 1.3 57.6 + - - +
140F LYS* 2.7 42.4 + - - +
144F LYS 5.6 0.2 - - - -
145F SER* 3.7 10.4 + - - -
146F ALA* 2.8 39.2 + - + +
147F LEU 4.4 0.2 + - - -
202F LYS 4.2 3.1 - - - +
203F HIS* 3.1 52.5 + - + +
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Residues in contact with LYS 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F PRO 3.3 8.4 + - - +
134F ALA* 3.2 14.5 + - - +
136F ASP* 1.3 80.1 + - - +
138F GLU* 1.3 62.6 + - - +
140F LYS* 3.6 7.0 - - - +
141F ALA* 3.5 14.7 + - - +
203F HIS* 4.6 6.3 - - + -
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Residues in contact with GLU 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F ALA 3.2 8.3 + - - +
135F LEU* 3.6 17.0 - - + +
136F ASP 3.2 0.2 - - - -
137F LYS* 1.3 78.5 - - - +
139F LEU* 1.3 63.8 + - + +
141F ALA* 3.2 22.8 + - - +
142F LYS* 3.8 3.5 + - - +
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Residues in contact with LEU 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F LEU* 3.9 29.2 - - + +
122F LEU* 4.7 7.9 - - + -
135F LEU* 2.8 48.8 + - + +
136F ASP 4.2 1.3 - - - +
138F GLU* 1.3 71.4 - - + +
140F LYS* 1.3 63.0 + - - +
141F ALA 3.2 0.2 - - - -
142F LYS* 3.2 13.4 + - + +
144F LYS* 2.8 50.5 + - + +
145F SER 4.4 6.5 - - - -
146F ALA* 4.3 6.5 - - - +
223F ALA* 4.1 27.4 - - + -
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Residues in contact with LYS 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F ASP* 2.7 28.4 + - - +
137F LYS* 3.6 9.0 - - - +
139F LEU* 1.3 71.8 - - - +
141F ALA* 1.3 56.7 + - - +
143F GLY* 3.0 18.9 + - - -
144F LYS 3.3 13.3 + - - +
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Residues in contact with ALA 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F LYS 3.5 6.9 + - - +
138F GLU* 3.2 16.3 + - - +
139F LEU 3.2 0.4 - - - -
140F LYS* 1.3 79.1 - - - +
142F LYS* 1.3 56.5 + - - +
143F GLY 3.3 1.0 + - - -
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Residues in contact with LYS 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F GLU 3.8 1.9 + - - +
139F LEU* 3.2 17.2 + - + +
141F ALA* 1.3 76.7 - - - +
143F GLY* 1.3 60.0 + - - +
144F LYS* 3.3 16.6 + - + +
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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