Contacts of the helix formed by residues 126 - 137 (chain C) in PDB entry 5JKL
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 ASP 126 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C ASN* 3.2 25.8 + - - +
12C TYR* 3.6 11.4 - - - -
13C HIS* 4.7 0.8 + - + +
16C SER* 4.7 3.2 + - - +
76C ARG* 3.0 32.2 + - - -
121C ALA* 2.9 18.5 + - - +
122C THR* 5.1 0.2 - - - +
124C LYS* 4.3 8.1 - - + +
125C ASN* 1.3 74.6 - - - +
127C PRO* 1.3 65.5 - - - +
128C HIS* 3.5 4.2 + - - +
129C LEU* 3.1 25.5 + - + +
130C CYS* 3.0 26.0 + - - -
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Residues in contact with PRO 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ASN* 3.9 8.5 - - - +
125C ASN* 3.2 15.0 - - + +
126C ASP* 1.3 84.9 - - - +
128C HIS* 1.3 58.9 + - + +
130C CYS* 3.7 9.3 - - + +
131C ASP* 3.0 29.6 + - - +
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Residues in contact with HIS 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C LEU* 3.8 28.0 - - + -
75C GLN* 5.3 6.1 - - + -
76C ARG* 3.1 40.0 + - - +
126C ASP* 3.3 2.5 + - - +
127C PRO* 1.3 81.0 - - + +
129C LEU* 1.3 59.1 + - - +
131C ASP* 3.3 11.5 + - - +
132C PHE* 2.9 30.7 + + + +
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Residues in contact with LEU 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C TYR* 4.4 7.0 - - + -
16C SER* 3.8 30.1 - - - +
20C ILE* 4.0 28.5 - - + -
72C LEU* 4.2 17.9 - - + -
76C ARG* 4.1 3.6 - - - +
117C LEU* 5.0 5.2 - - + -
121C ALA* 3.7 21.5 - - + -
126C ASP* 3.1 27.8 + - - +
128C HIS* 1.3 77.2 + - - +
130C CYS* 1.3 65.0 + - - +
132C PHE* 3.2 10.3 + - + +
133C ILE* 3.0 41.4 + - + +
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Residues in contact with CYS 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C HIS* 3.6 23.1 - - + +
121C ALA* 3.7 6.7 - - - -
122C THR* 3.6 40.8 - - - -
126C ASP 3.0 20.4 + - - +
127C PRO* 3.7 12.8 - - + +
129C LEU* 1.3 76.4 - - - +
131C ASP* 1.3 58.8 + - - +
133C ILE* 3.4 3.8 + - - +
134C GLU* 3.0 38.5 + - - +
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Residues in contact with ASP 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C PRO 3.0 17.7 + - - +
128C HIS* 3.7 11.9 - - + +
130C CYS* 1.3 76.6 - - - +
132C PHE* 1.3 60.4 + - - +
134C GLU* 4.3 4.2 + - - -
135C THR* 2.7 43.3 + - - +
203C GOL 2.6 44.3 + - - -
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Residues in contact with PHE 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ILE* 5.2 0.2 - - + -
68C LYS* 3.8 24.7 - - + -
69C LEU* 3.6 19.3 - - + -
72C LEU* 3.7 47.1 - - + -
75C GLN* 5.2 3.6 - - - -
128C HIS* 2.9 22.0 + + + +
129C LEU* 3.5 11.9 - - + +
131C ASP* 1.3 79.6 + - - +
133C ILE* 1.4 69.4 + - + +
136C HIS* 3.0 58.5 + + - +
137C TYR* 3.4 29.2 - + - -
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Residues in contact with ILE 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C LEU* 6.3 0.2 - - + -
114C LEU* 4.1 17.0 - - + +
117C LEU* 3.8 36.1 - - + +
118C HIS* 4.0 26.2 - - + -
121C ALA* 4.5 1.1 - - + -
129C LEU* 3.0 31.7 + - + +
130C CYS 3.7 3.4 - - - +
132C PHE* 1.4 88.5 - - + +
134C GLU* 1.3 57.5 + - - +
137C TYR* 2.9 35.1 + - + +
138C LEU* 2.9 34.2 + - + -
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Residues in contact with GLU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A PRO* 4.1 7.4 - - - +
130A CYS* 5.9 1.3 - - - -
131A ASP* 3.6 44.5 + - + +
134A GLU* 4.6 5.7 - - - +
203A MG 3.9 10.7 - - - -
118C HIS* 2.7 34.7 + - + +
130C CYS* 3.0 25.5 + - - +
131C ASP* 3.8 5.0 - - - +
133C ILE* 1.3 77.7 - - - +
135C THR* 1.3 64.6 + - - +
138C LEU* 3.8 26.3 + - + +
139C ASN* 4.1 9.7 + - - +
203C GOL 3.8 15.3 - - - -
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Residues in contact with THR 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ASP* 5.5 0.2 - - - -
131C ASP* 2.7 37.8 + - - +
134C GLU* 1.3 75.9 - - - +
136C HIS* 1.3 86.3 + - + +
139C ASN* 5.7 3.3 + - - +
140C GLU* 5.7 1.2 - - - +
203C GOL 2.9 26.9 + - - +
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Residues in contact with HIS 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C HIS* 5.8 2.6 - - - -
68C LYS* 3.1 34.7 + - + +
131C ASP* 6.0 0.2 - - - -
132C PHE* 3.0 44.4 + + - +
135C THR* 1.3 99.0 + - + +
137C TYR* 1.3 83.3 + - + +
139C ASN 5.5 0.2 - - - -
140C GLU* 3.4 22.5 - - - +
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Residues in contact with TYR 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C GLU* 4.2 7.6 - - - -
65C HIS* 2.7 52.8 + + + -
68C LYS* 3.4 19.8 - - + +
69C LEU* 3.4 22.0 + - + +
114C LEU* 3.9 36.1 - - + -
132C PHE* 3.4 34.5 - + - -
133C ILE* 2.9 16.6 + - + +
136C HIS* 1.3 97.3 - - + +
138C LEU* 1.3 66.7 + - - +
139C ASN 3.4 1.8 - - - -
140C GLU* 3.3 5.8 + - + +
141C GLN* 2.9 28.8 + - - +
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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