Contacts of the helix formed by residues 132 - 145 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A TRP* 3.4 35.1 - - + -
98A ARG* 4.6 9.5 - - - +
125A LEU* 4.0 2.9 - - - -
130A ASP* 2.9 13.9 + - - +
131A HIS* 1.3 102.8 - - + +
133A LEU* 1.3 65.3 + - - +
134A GLY 3.3 2.2 - - - -
135A GLU* 3.1 44.4 + - - +
136A LEU* 3.1 20.6 + - - +
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A VAL* 3.7 21.8 - - + +
125A LEU* 3.7 30.7 - - + +
126A SER* 3.5 32.1 - - - +
129A ASP* 5.8 4.0 - - - +
130A ASP* 3.1 19.2 + - + +
131A HIS 3.2 1.4 - - - -
132A ARG* 1.3 78.4 - - - +
134A GLY* 1.3 62.4 + - - +
136A LEU* 3.2 4.7 + - + +
137A GLN* 3.0 41.9 + - + +
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Residues in contact with GLY 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A HIS 4.7 2.6 + - - -
132A ARG 3.3 0.6 - - - -
133A LEU* 1.3 76.0 - - - +
135A GLU* 1.3 56.8 + - - +
137A GLN* 3.2 16.5 + - - +
138A ASP* 2.8 39.2 + - - +
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Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A TRP* 3.8 11.5 - - + -
98A ARG* 4.6 4.9 + - - -
131A HIS 5.5 0.4 + - - -
132A ARG* 3.1 55.9 + - - +
134A GLY* 1.3 75.9 - - - +
136A LEU* 1.3 56.6 + - - +
138A ASP* 3.3 10.9 + - - +
139A GLU* 3.0 28.5 + - + +
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A TRP* 3.5 45.5 - - + +
118A TYR* 3.9 20.4 - - + -
121A ALA* 3.5 38.8 - - + +
122A VAL* 3.8 14.4 - - + -
125A LEU* 3.7 23.1 - - + -
132A ARG 3.1 8.9 + - - +
133A LEU* 3.2 8.5 + - + +
135A GLU* 1.3 76.7 - - - +
137A GLN* 1.3 56.5 + - - +
139A GLU* 3.3 3.3 + - - +
140A ALA* 2.6 32.4 + - - +
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Residues in contact with GLN 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A VAL* 4.4 18.7 - - + +
126A SER* 5.4 0.4 + - - -
133A LEU* 3.0 42.2 + - + +
134A GLY* 3.5 19.7 + - - +
136A LEU* 1.3 74.4 - - - +
138A ASP* 1.3 63.1 + - - +
140A ALA* 3.6 7.2 - - - +
141A ARG* 3.0 30.1 + - - +
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Residues in contact with ASP 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A GLY* 2.8 22.1 + - - +
135A GLU* 3.4 11.5 - - - +
137A GLN* 1.3 76.5 - - - +
139A GLU* 1.3 62.8 + - - +
141A ARG* 3.2 23.0 + - - +
142A ASN* 3.1 24.5 + - - +
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Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLN* 5.1 0.9 + - - +
94A TRP* 3.1 21.0 + - - -
98A ARG* 2.9 43.4 + - - +
118A TYR* 2.3 33.3 + - + +
135A GLU* 3.0 14.3 + - + +
136A LEU* 3.4 7.4 - - - +
138A ASP* 1.3 74.6 - - - +
140A ALA* 1.3 65.7 + - - +
142A ASN* 3.4 5.3 + - - +
143A ARG* 3.0 42.6 + - + +
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Residues in contact with ALA 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A TYR* 3.7 36.3 - - + -
122A VAL* 4.5 10.3 - - + -
136A LEU 2.6 20.9 + - - +
137A GLN* 3.6 9.2 - - - +
138A ASP 3.3 0.4 - - - -
139A GLU* 1.3 73.5 - - - +
141A ARG* 1.3 59.2 + - - +
144A CYS* 2.9 37.5 + - - +
146A TRP 4.7 0.7 - - - -
147A ASP 6.2 1.1 - - - -
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Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLN 3.0 17.4 + - - +
138A ASP* 3.6 19.8 + - - +
140A ALA* 1.3 76.2 - - - +
142A ASN* 1.3 62.9 - - - +
145A GLY* 3.2 23.9 + - - -
146A TRP* 3.3 33.0 + - - +
147A ASP* 4.3 20.6 - - - +
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Residues in contact with ASN 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ASP 3.1 15.5 + - - +
139A GLU* 3.8 6.5 - - - +
141A ARG* 1.3 86.2 - - - +
143A ARG* 1.3 72.3 + - + +
145A GLY* 4.1 5.7 + - - -
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Residues in contact with ARG 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLY* 3.4 21.6 + - - -
37A CYS* 5.2 0.4 - - - +
38A GLN* 2.6 38.5 + - - +
98A ARG* 4.2 8.9 - - - +
101A HIS* 3.4 51.1 + - - +
114A ARG* 3.2 22.5 + - - -
118A TYR* 3.1 40.1 + - + +
139A GLU* 3.0 35.9 + - + +
142A ASN* 1.3 86.6 + - - +
144A CYS* 1.3 62.2 + - - +
145A GLY 3.4 0.6 + - - -
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Residues in contact with CYS 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ARG* 3.7 21.7 + - - +
115A ASP* 3.1 32.5 - - - +
118A TYR* 3.7 33.0 - - - -
140A ALA* 2.9 20.3 + - - +
143A ARG* 1.3 78.0 - - - +
145A GLY* 1.3 53.5 + - - +
146A TRP* 2.7 43.0 + - + +
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Residues in contact with GLY 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ARG 3.2 9.0 + - - -
142A ASN 4.1 5.3 + - - -
143A ARG 3.4 3.2 - - - -
144A CYS* 1.3 76.9 - - - +
146A TRP* 1.3 64.8 + - - +
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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