Contacts of the helix formed by residues 131 - 146 (chain C) in PDB entry 4KZX
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C PHE* 4.3 2.9 - - - -
129C SER 4.7 0.4 - - - -
130C LYS* 1.3 108.4 - - + +
132C VAL* 1.3 63.2 + - - +
133C ALA* 4.4 3.4 - - + +
134C THR* 2.7 37.8 - - + +
135C ALA* 2.8 8.7 + - - +
116D ARG* 3.3 35.8 + - - +
120D TYR* 3.5 19.8 + - + +
152D PHE* 6.5 0.9 - - - -
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Residues in contact with VAL 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ILE* 4.5 19.3 - - + -
109C PHE* 2.9 38.5 - - + -
131C GLU* 1.3 73.1 - - - +
133C ALA* 1.3 65.8 + - - +
135C ALA* 3.0 7.1 + - + +
136C ILE* 2.8 45.6 + - + +
116D ARG* 4.2 10.4 - - - +
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Residues in contact with ALA 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C GLU* 3.2 1.8 - - - +
132C VAL* 1.3 79.9 - - - +
134C THR* 1.3 52.9 + - - +
136C ILE* 3.2 6.9 + - - +
137C ARG* 2.7 53.5 + - - +
116D ARG* 4.9 3.8 - - - +
120D TYR* 5.1 15.5 - - + +
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Residues in contact with THR 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C LYS* 5.6 0.2 - - - +
129C SER* 3.1 25.5 + - - -
130C LYS* 4.3 2.0 - - + +
131C GLU* 2.7 40.6 + - + +
133C ALA* 1.3 75.5 - - - +
135C ALA* 1.3 61.5 + - - +
137C ARG* 3.7 26.1 + - - +
138C GLY* 2.7 34.3 + - - -
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Residues in contact with ALA 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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109C PHE* 3.8 24.0 - - + +
111C ALA* 3.9 18.4 - - + +
127C LYS* 3.6 9.7 - - - +
129C SER* 3.8 16.6 - - - +
131C GLU 2.8 9.7 + - - +
132C VAL* 3.4 11.9 - - + +
134C THR* 1.3 81.5 - - - +
136C ILE* 1.3 57.8 + - - +
139C ALA* 3.0 28.6 + - - +
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Residues in contact with ILE 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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91C VAL* 3.7 31.6 - - + -
94C ILE* 4.7 7.2 - - + -
111C ALA* 4.1 16.2 - - + -
113C VAL* 4.4 0.7 - - + -
132C VAL* 2.8 40.9 + - + +
133C ALA* 3.6 6.7 - - - +
135C ALA* 1.3 74.0 - - - +
137C ARG* 1.3 65.8 + - - +
139C ALA* 3.1 5.5 + - - +
140C ILE* 2.9 39.7 + - + +
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Residues in contact with ARG 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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133C ALA* 2.7 49.6 + - - +
134C THR* 3.6 25.5 + - - +
136C ILE* 1.3 75.4 - - - +
138C GLY* 1.3 61.8 + - - +
140C ILE* 3.6 13.2 + - + +
141C ILE* 3.4 17.3 + - - +
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Residues in contact with GLY 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C LYS* 4.3 9.2 - - - -
134C THR* 2.7 20.4 + - - -
135C ALA 4.2 0.4 - - - -
137C ARG* 1.3 70.9 - - - +
139C ALA* 1.3 58.9 + - - +
141C ILE* 2.1 39.3 - - - +
142C LEU* 2.8 12.4 + - - +
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Residues in contact with ALA 139 (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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111C ALA* 4.0 10.3 - - + +
113C VAL* 3.1 31.4 - - + -
125C GLY* 3.9 12.7 - - - +
127C LYS* 4.0 11.1 - - + +
135C ALA 3.0 20.4 + - - +
136C ILE* 3.1 1.5 + - - +
138C GLY* 1.3 75.5 - - - +
140C ILE* 1.3 53.4 + - - +
142C LEU* 3.0 8.3 + - - +
143C ALA* 2.7 35.3 + - - +
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Residues in contact with ILE 140 (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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89C ASP* 3.5 20.4 - - + +
91C VAL* 5.8 0.7 - - + -
113C VAL* 4.0 17.9 - - + -
115C ILE* 3.2 26.2 - - + +
136C ILE* 2.9 36.3 + - + +
137C ARG* 3.8 11.4 - - + +
138C GLY 3.1 0.2 - - - -
139C ALA* 1.3 75.6 - - - +
141C ILE* 1.3 61.9 + - - +
143C ALA 3.0 1.6 + - - -
144C LYS* 3.0 41.6 + - + +
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Residues in contact with ILE 141 (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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76C SER* 3.6 34.3 + - - +
137C ARG 3.4 6.9 + - - +
138C GLY* 2.1 44.6 + - - +
140C ILE* 1.3 78.9 - - - +
142C LEU* 1.3 75.7 + - + +
144C LYS* 3.2 6.2 + - - +
145C LEU* 2.9 27.0 + - + +
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Residues in contact with LEU 142 (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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124C LEU 4.3 0.3 - - - +
125C GLY* 4.2 9.2 - - - -
126C MET 3.2 16.6 - - - +
127C LYS* 3.1 42.8 - - + -
138C GLY* 2.8 9.8 + - - +
139C ALA* 3.4 6.1 - - - +
141C ILE* 1.3 82.0 - - + +
143C ALA* 1.3 60.9 + - - +
145C LEU* 2.3 59.7 - - + +
146C SER* 3.3 5.9 + - - -
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Residues in contact with ALA 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C VAL 3.9 9.0 - - - +
115C ILE* 3.5 23.6 - - + -
123C GLY* 3.5 7.1 - - - -
124C LEU 3.7 13.9 - - - +
125C GLY* 3.7 13.9 - - - +
139C ALA 2.7 16.4 + - - +
140C ILE* 3.0 8.9 + - - +
142C LEU* 1.3 74.7 - - - +
144C LYS* 1.3 62.7 + - - +
146C SER* 2.6 25.2 + - - -
147C ILE 3.3 5.5 + - - -
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Residues in contact with LYS 144 (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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73C ILE* 5.3 0.5 - - - +
76C SER* 4.0 13.2 - - - +
79C ILE* 3.5 36.6 - - + +
80C ASP* 4.1 20.8 + - + +
84C GLY* 5.5 7.2 + - - -
87C LEU* 5.1 7.6 - - + -
89C ASP* 3.9 8.8 + - - -
115C ILE* 3.1 23.6 - - + -
140C ILE* 3.0 34.9 + - + +
141C ILE* 3.7 7.2 - - - +
143C ALA* 1.3 74.1 - - - +
145C LEU* 1.3 65.7 + - - +
147C ILE* 2.9 29.1 + - + +
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Residues in contact with LEU 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ILE* 3.4 38.5 - - - +
74C LYS* 6.2 1.8 - - - +
76C SER* 5.2 4.9 + - - +
79C ILE* 4.6 5.3 - - - +
141C ILE* 2.9 15.5 + - + +
142C LEU* 2.3 68.0 - - + +
144C LYS* 1.3 77.4 - - - +
146C SER* 1.3 64.5 + - - +
147C ILE 3.4 2.9 + - - +
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Residues in contact with SER 146 (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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122C VAL 4.2 0.7 - - - +
124C LEU 3.0 30.3 + - - -
142C LEU 3.9 5.8 - - - -
143C ALA 2.6 19.6 + - - -
145C LEU* 1.3 85.0 - - - +
147C ILE* 1.3 66.3 + - - +
148C VAL* 2.8 19.6 - - - +
226C PHE* 4.4 6.6 - - - -
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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