Contacts of the helix formed by residues 133 - 150 (chain A) in PDB entry 6CNB
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 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A GLY 3.5 5.1 + - - +
132A VAL* 1.3 75.4 - - - +
134A ASN* 1.3 92.3 + - - +
135A LEU* 3.3 8.8 + - + +
136A ARG* 3.2 14.8 + - + +
137A ARG* 2.9 26.9 + - - +
1365A LYS* 5.0 4.0 + - - -
1379A MET* 3.9 33.5 - - - +
1381A ASP* 4.5 11.9 - - - +
177E ARG* 5.1 16.2 + - - +
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Residues in contact with ASN 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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133A ASP* 1.3 92.9 + - - +
135A LEU* 1.3 64.0 + - - +
137A ARG* 3.0 13.0 + - - +
138A MET* 2.9 27.4 + - - +
1379A MET 5.5 2.5 - - - +
1380A ARG 6.0 0.2 - - - +
1381A ASP* 2.8 35.4 + - + +
1404A LYS* 2.8 46.1 + - - +
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Residues in contact with LEU 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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133A ASP* 3.3 7.4 - - + +
134A ASN* 1.3 80.7 - - - +
136A ARG* 1.3 70.6 + - + +
138A MET* 3.2 8.6 + - + -
139A GLY* 2.9 21.6 + - - +
1365A LYS* 4.1 12.1 - - + +
1367A GLU* 5.3 8.5 - - - +
1377A SER* 5.4 9.6 - - - +
1378A LYS* 3.3 29.2 - - - +
1379A MET* 5.7 1.3 + - - +
177E ARG* 6.0 1.8 - - - +
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Residues in contact with ARG 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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126A GLU* 3.4 14.7 + - - -
129A ARG* 3.0 32.1 - - - +
131A GLY 5.4 2.7 + - - +
132A VAL* 3.6 19.1 - - + +
133A ASP* 3.2 24.7 + - + +
135A LEU* 1.3 80.6 - - + +
137A ARG* 1.3 67.7 + - - +
139A GLY* 3.2 2.8 + - - -
140A ILE* 2.9 33.5 + - + +
177E ARG* 5.5 9.6 - - - +
192E ARG* 5.2 5.5 - - - +
215E MET* 4.5 24.4 - - - +
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Residues in contact with ARG 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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127A LEU* 4.2 30.9 - - - +
132A VAL* 3.8 16.8 - - + +
133A ASP 2.9 21.6 + - - +
134A ASN* 3.1 16.4 - - - +
136A ARG* 1.3 73.0 - - - +
138A MET* 1.3 66.8 + - + +
140A ILE* 2.9 18.8 + - - +
141A LEU* 2.9 26.5 + - + +
240A GLU* 5.0 2.8 + - - +
243A GLY* 4.0 28.5 + - - -
245A ASP* 5.1 11.9 + - - -
1402A TYR* 4.4 13.7 + - - +
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Residues in contact with MET 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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101A GLN* 5.9 2.0 - - - +
134A ASN* 2.9 26.7 + - - +
135A LEU* 3.7 11.9 - - + +
137A ARG* 1.3 78.3 - - - +
139A GLY* 1.3 58.4 + - - +
141A LEU* 3.3 15.0 + - + +
142A LYS* 2.9 27.6 + - - +
1398A ASP* 4.8 8.3 - - - +
1402A TYR* 3.4 47.1 - - + +
1404A LYS* 4.3 7.6 - - - +
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Residues in contact with GLY 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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135A LEU* 2.9 15.0 + - - +
136A ARG* 3.6 3.6 - - - -
138A MET* 1.3 78.2 - - - +
140A ILE* 1.3 64.5 + - - +
142A LYS* 2.9 22.3 + - - +
143A LYS* 2.9 11.8 + - - +
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Residues in contact with ILE 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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123A PHE* 4.4 17.0 - - + -
126A GLU* 3.1 45.8 - - + +
127A LEU* 3.5 23.1 - - + -
132A VAL* 5.9 1.8 - - + -
136A ARG* 2.9 26.1 + - + +
137A ARG* 2.9 12.8 + - - +
139A GLY* 1.3 71.2 - - - +
141A LEU* 1.3 60.0 + - + +
143A LYS* 2.9 17.4 + - + +
144A ILE* 2.8 27.4 + - + +
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Residues in contact with LEU 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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127A LEU* 5.4 9.0 - - + -
137A ARG* 2.9 28.4 + - + +
138A MET* 3.5 24.5 - - + +
140A ILE* 1.3 78.4 - - + +
142A LYS* 1.3 61.7 + - - +
144A ILE* 3.2 7.0 - - + +
145A LEU* 2.9 29.8 + - - +
240A GLU 4.4 2.7 - - - +
241A LEU 3.2 22.0 - - - +
242A LEU* 3.2 30.3 - - - +
243A GLY* 4.2 5.2 - - - +
1402A TYR* 3.8 26.7 - - + +
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Residues in contact with LYS 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 MET 2.9 13.5 + - - +
139A GLY* 2.9 16.4 + - - +
141A LEU* 1.3 75.1 - - - +
143A LYS* 1.3 57.4 + - - +
145A LEU* 4.5 3.4 - - - +
146A ASP* 3.3 21.8 + - - +
55X A 5.8 4.0 - - - -
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Residues in contact with LYS 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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123A PHE* 3.8 23.1 - - + -
139A GLY 2.9 8.2 + - - +
140A ILE* 2.9 23.8 + - + +
142A LYS* 1.3 73.4 - - - +
144A ILE* 1.3 67.3 + - - +
145A LEU 3.0 1.9 + - - -
146A ASP* 2.6 24.5 - - - +
147A GLN* 2.9 13.8 + - + +
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Residues in contact with ILE 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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113A ILE* 6.0 4.9 - - + -
115A LEU* 3.4 17.9 - - + -
123A PHE* 3.1 58.7 - - + -
140A ILE* 2.8 11.4 + - + +
141A LEU* 3.2 26.9 - - + +
143A LYS* 1.3 72.2 - - - +
145A LEU* 1.3 69.4 + - + +
147A GLN* 3.5 2.1 + - - +
148A CYS* 3.2 19.3 + - - +
241A LEU* 3.6 36.8 - - + +
242A LEU* 5.5 6.5 - - + -
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Residues in contact with LEU 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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101A GLN* 3.6 51.4 - - + +
104A GLN* 3.8 14.1 - - + -
105A GLY* 5.4 1.8 - - - -
141A LEU 2.9 18.4 + - - +
142A LYS* 4.5 4.5 - - - +
143A LYS 3.0 0.8 + - - -
144A ILE* 1.3 77.7 - - + +
146A ASP* 1.3 61.7 + - + +
148A CYS* 2.8 37.6 + - - -
149A LYS* 3.1 33.2 + - - +
242A LEU* 6.3 3.6 - - + -
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Residues in contact with ASP 146 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A LYS* 3.3 14.1 + - - +
143A LYS* 2.6 31.6 + - - +
145A LEU* 1.3 81.2 - - + +
147A GLN* 1.3 66.1 + - - +
148A CYS 3.2 0.2 - - - -
149A LYS* 3.1 33.6 + - + +
150A LYS* 3.2 28.2 + - - +
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Residues in contact with GLN 147 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A LEU* 3.7 29.3 - - + +
119A ASP* 4.9 5.6 + - - -
123A PHE* 3.8 23.0 - - + -
143A LYS* 2.9 19.2 + - + +
144A ILE 3.5 7.2 - - - +
145A LEU 3.0 0.2 + - - -
146A ASP* 1.3 84.9 + - - +
148A CYS* 1.3 58.4 + - - +
150A LYS* 3.4 33.4 + - - +
151A GLN* 4.0 4.7 + - - +
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Residues in contact with CYS 148 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A GLN 4.6 3.1 - - - -
105A GLY* 3.4 36.8 - - - +
113A ILE* 5.5 3.1 - - + -
114A LEU* 3.1 41.5 - - + +
115A LEU* 4.4 16.6 - - + +
144A ILE* 3.2 13.3 + - + +
145A LEU* 2.8 37.6 + - - -
147A GLN* 1.3 72.0 - - - +
149A LYS* 1.3 65.7 + - - +
151A GLN* 3.2 8.6 + - - +
161A ASN* 5.5 0.9 - - - +
242A LEU* 6.1 1.6 - - - -
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Residues in contact with LYS 149 (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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104A GLN* 3.5 39.5 + - + +
145A LEU* 3.1 33.0 + - + +
146A ASP* 3.1 29.5 + - + +
148A CYS* 1.3 77.1 - - - +
150A LYS* 1.3 51.5 + - - +
151A GLN 2.7 22.7 - - - +
152A ARG* 2.7 10.6 + - - -
161A ASN* 5.3 0.9 - - - +
163A VAL* 6.3 3.8 - - + -
184A ARG* 5.3 4.5 + - - +
56X C 6.0 0.2 + - - -
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Residues in contact with LYS 150 (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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146A ASP* 3.2 21.3 + - - +
147A GLN* 3.4 38.4 + - - +
149A LYS* 1.3 74.2 - - - +
151A GLN* 1.3 62.1 + - - +
152A ARG* 3.0 30.7 + - - +
10Y T 3.8 39.7 + - - +
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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