Contacts of the helix formed by residues 132 - 145 (chain C) in PDB entry 4BSX
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 ARG 132 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C TRP* 3.4 36.0 - - + -
98C ARG* 4.6 9.3 - - - +
125C LEU* 4.0 3.5 - - + +
130C ASP* 2.8 16.1 + - - +
131C HIS* 1.3 101.4 - - + +
133C LEU* 1.3 66.7 + - - +
134C GLY 3.4 2.2 - - - -
135C GLU* 3.2 44.0 + - - +
136C LEU* 3.1 19.2 + - - +
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Residues in contact with LEU 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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122C VAL* 3.7 12.8 - - + +
125C LEU* 3.7 30.2 - - + +
126C SER* 3.5 32.5 - - - +
129C ASP* 5.8 4.5 - - - +
130C ASP 3.0 19.6 + - - +
131C HIS 3.2 1.6 - - - -
132C ARG* 1.3 77.6 - - - +
134C GLY* 1.3 64.3 + - - +
136C LEU* 3.0 7.3 + - + +
137C GLN* 2.9 49.6 + - + +
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Residues in contact with GLY 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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131C HIS 4.7 2.4 + - - -
132C ARG 3.4 0.6 - - - -
133C LEU* 1.3 77.6 - - - +
135C GLU* 1.3 56.8 + - - +
137C GLN* 3.2 16.6 + - - +
138C ASP* 2.8 40.8 + - - +
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Residues in contact with GLU 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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94C TRP* 3.8 11.3 - - + -
98C ARG* 4.7 4.9 + - - -
131C HIS 5.5 0.2 + - - -
132C ARG* 3.2 56.6 + - - +
134C GLY* 1.3 74.6 - - - +
136C LEU* 1.3 57.7 + - - +
138C ASP* 3.3 10.1 + - - +
139C GLU* 2.9 29.1 + - + +
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Residues in contact with LEU 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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94C TRP* 3.4 47.1 - - + +
118C TYR* 3.9 20.4 - - + -
121C ALA* 3.4 39.7 - - + +
122C VAL* 3.8 14.6 - - + -
125C LEU* 3.7 21.5 - - + -
132C ARG 3.1 7.4 + - - +
133C LEU* 3.0 9.9 + - + +
135C GLU* 1.3 75.9 - - - +
137C GLN* 1.3 55.1 + - - +
139C GLU* 3.2 3.1 + - - +
140C ALA* 2.7 34.0 + - - +
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Residues in contact with GLN 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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122C VAL* 4.4 19.8 - - + +
126C SER* 5.3 0.6 + - - -
133C LEU* 2.9 43.1 + - + +
134C GLY* 3.6 18.6 + - - +
136C LEU* 1.3 75.9 - - - +
138C ASP* 1.3 66.8 + - - +
140C ALA* 3.7 7.7 - - - +
141C ARG* 3.0 25.3 + - - +
148C ILE* 5.7 1.9 + - + -
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Residues in contact with ASP 138 (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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134C GLY 2.8 22.9 + - - +
135C GLU* 3.4 10.7 + - - +
137C GLN* 1.3 76.6 - - - +
139C GLU* 1.3 62.7 + - - +
141C ARG* 3.1 22.6 + - - +
142C ASN* 3.1 24.1 + - - +
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Residues in contact with GLU 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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38C GLN* 5.1 0.7 - - - +
94C TRP* 3.1 20.5 + - - -
98C ARG* 2.9 43.7 + - - +
118C TYR* 2.4 33.7 + - + +
135C GLU* 2.9 14.1 + - - +
136C LEU 3.5 7.4 - - - +
138C ASP* 1.3 75.8 - - - +
140C ALA* 1.3 64.8 + - - +
142C ASN* 3.8 5.3 - - - +
143C ARG* 3.0 41.5 + - + +
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Residues in contact with ALA 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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118C TYR* 3.7 27.8 - - + -
122C VAL* 4.4 8.5 - - + -
136C LEU 2.7 21.1 + - - +
137C GLN* 3.7 9.4 - - - +
138C ASP 3.2 0.4 - - - -
139C GLU* 1.3 72.9 - - - +
141C ARG* 1.3 57.4 + - - +
144C CYS* 2.9 37.4 + - - +
148C ILE* 3.6 25.1 - - - +
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Residues in contact with ARG 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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137C GLN 3.0 17.2 + - - +
138C ASP* 3.1 19.3 + - - +
140C ALA* 1.3 75.3 - - - +
142C ASN* 1.3 63.2 + - - +
145C GLY* 3.2 24.1 + - - -
146C TRP* 3.3 32.9 + - - +
147C ASP* 4.3 18.4 - - - +
148C ILE 4.6 5.1 - - - +
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Residues in contact with ASN 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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138C ASP 3.1 15.3 + - - +
139C GLU* 3.8 6.3 - - - +
141C ARG* 1.3 86.0 - - - +
143C ARG* 1.3 73.2 + - + +
145C GLY* 4.2 5.0 + - - -
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Residues in contact with ARG 143 (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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36C GLY* 3.4 21.1 + - - -
37C CYS* 5.2 0.4 - - - +
38C GLN* 2.6 38.8 + - - +
98C ARG* 4.2 9.3 - - - +
101C HIS* 3.4 51.2 + - - +
114C ARG* 3.2 22.9 + - - -
118C TYR* 3.1 40.7 + - + +
139C GLU* 3.0 35.3 + - + +
142C ASN* 1.3 88.6 + - - +
144C CYS* 1.3 63.4 + - - +
145C GLY 3.4 0.4 + - - -
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Residues in contact with CYS 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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114C ARG* 3.7 21.0 + - - +
115C ASP* 3.3 28.7 - - - +
118C TYR* 3.6 37.2 - - - -
140C ALA 2.9 19.9 + - - +
143C ARG* 1.3 80.7 - - - +
145C GLY* 1.3 51.5 + - - +
146C TRP* 2.6 41.8 + - - +
148C ILE 4.2 9.2 - - - -
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Residues in contact with GLY 145 (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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141C ARG 3.2 9.5 + - - -
142C ASN 4.2 4.0 + - - -
143C ARG 3.4 2.8 - - - -
144C CYS* 1.3 77.1 - - - +
146C TRP* 1.3 64.6 + - - +
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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