Contacts of the helix formed by residues 136 - 149 (chain A) in PDB entry 2A6O
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 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A ASN* 5.8 0.2 - - - +
134A SER* 3.2 24.0 + - - +
135A ASN* 1.3 81.8 - - - +
137A PRO* 1.3 75.7 - - + +
138A LYS* 4.6 5.6 - - + +
139A GLN* 3.2 16.1 + - + +
140A LYS* 3.2 9.4 + - - +
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Residues in contact with PRO 137 (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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135A ASN 3.7 2.2 - - - +
136A ARG* 1.3 90.3 - - + +
138A LYS* 1.3 66.7 + - + +
140A LYS* 3.0 11.4 + - + +
141A GLU* 2.9 38.1 + - + +
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Residues in contact with LYS 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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136A ARG* 3.4 3.9 - - + +
137A PRO* 1.3 79.5 - - + +
139A GLN* 1.3 71.7 + - + +
141A GLU* 3.0 15.9 + - - +
142A LYS* 2.8 29.1 + - - +
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Residues in contact with GLN 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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132A GLN* 3.3 20.3 - - + +
133A ASN* 2.7 59.9 + - - +
134A SER* 3.4 25.1 - - - +
136A ARG* 3.2 11.8 + - + +
137A PRO 3.2 0.8 - - - -
138A LYS* 1.3 92.4 + - + +
140A LYS* 1.3 63.6 + - - +
142A LYS* 3.1 32.9 + - - +
143A TRP 3.0 19.4 + - - -
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Residues in contact with LYS 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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132A GLN* 3.6 27.9 + - - +
135A ASN* 3.6 28.5 - - - +
136A ARG 3.2 9.3 + - - +
137A PRO* 3.0 11.7 + - + +
139A GLN* 1.3 76.2 - - - +
141A GLU* 1.3 58.7 + - + +
143A TRP* 3.5 2.4 + - - +
144A LYS* 2.9 30.2 + - - +
2D C 4.6 21.2 + - - -
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Residues in contact with GLU 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 PRO* 2.9 32.3 + - + +
138A LYS* 3.3 13.3 + - - +
140A LYS* 1.3 77.1 - - + +
142A LYS* 1.3 65.2 + - - +
144A LYS* 3.9 7.2 - - + +
145A SER* 3.0 27.0 + - - -
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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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129A GLU* 2.6 34.4 + - + +
130A ASN* 3.3 29.4 - - - +
131A GLN 3.3 21.6 + - - -
133A ASN* 5.2 1.0 + - - -
138A LYS 2.8 12.9 + - - +
139A GLN* 3.4 33.1 + - - +
141A GLU* 1.3 78.0 - - - +
143A TRP* 1.3 61.3 + - - +
145A SER* 3.7 4.8 - - - -
146A TYR* 3.1 21.7 + - - +
28B ARG* 3.5 8.5 - - - +
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Residues in contact with TRP 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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12A ASN* 3.1 37.5 + - + +
14A VAL* 5.1 3.6 - - + -
130A ASN 3.5 26.2 + - - +
131A GLN* 3.0 39.3 - - - -
132A GLN* 3.6 31.2 - - + +
139A GLN 3.0 15.9 + - - +
140A LYS 3.9 2.0 - - - +
142A LYS* 1.3 75.5 - - - +
144A LYS* 1.3 72.3 + - + +
146A TYR* 3.0 14.7 + + - +
147A VAL* 3.0 48.4 + - + +
110B SER* 4.0 15.3 - - - -
1D C 4.2 11.7 + - - -
2D C 3.8 18.6 + - - -
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Residues in contact with LYS 144 (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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140A LYS 2.9 20.2 + - - +
141A GLU* 3.9 7.9 - - + +
143A TRP* 1.3 79.2 - - + +
145A SER* 1.3 58.1 + - - +
147A VAL* 4.1 7.0 - - - -
148A ASP* 2.7 64.0 + - - +
1D C 5.4 8.1 - - - +
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Residues in contact with SER 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 GLU 3.0 15.9 + - - -
142A LYS* 3.7 6.1 - - - -
144A LYS* 1.3 80.8 - - - +
146A TYR* 1.3 62.2 + - - +
148A ASP* 4.2 5.1 - - - +
149A ASN* 3.3 22.5 + - - +
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Residues in contact with TYR 146 (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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6A LEU* 5.4 1.0 - - - +
14A VAL* 3.7 29.8 - - + +
123A VAL* 4.7 3.8 + - - +
126A GLN* 4.1 18.8 - - + -
127A TYR* 3.5 39.7 + + - +
130A ASN* 3.7 33.0 - - + +
131A GLN* 4.7 0.4 - - - -
142A LYS 3.1 14.2 + - - +
143A TRP* 3.0 18.3 + + - +
145A SER* 1.3 77.0 - - - +
147A VAL* 1.3 83.7 + - + +
149A ASN* 3.1 21.3 + - - +
150A LEU* 3.8 21.5 + - + +
112B PHE* 5.5 0.3 - - - -
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Residues in contact with VAL 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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8A LYS* 3.8 28.5 - - + +
12A ASN* 4.7 0.7 - - - +
14A VAL* 5.2 2.5 - - + -
143A TRP* 3.0 57.9 + - + +
144A LYS* 3.4 6.5 - - - +
146A TYR* 1.3 84.1 - - + +
148A ASP* 1.3 73.1 + - - +
149A ASN 3.0 2.0 - - - -
150A LEU* 2.9 30.9 + - + +
1D C 3.5 30.1 - - - +
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Residues in contact with ASP 148 (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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8A LYS* 5.9 0.7 - - - -
144A LYS* 2.7 62.3 + - - +
145A SER* 4.2 4.9 - - - +
147A VAL* 1.3 82.5 - - - +
149A ASN* 1.3 56.4 + - - +
150A LEU 3.3 8.7 + - - +
1D C 4.5 11.1 + - - +
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Residues in contact with ASN 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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145A SER 3.3 18.7 + - - +
146A TYR* 3.1 9.3 + - - +
147A VAL 3.0 1.6 - - - -
148A ASP* 1.3 76.3 - - - +
150A LEU* 1.3 63.1 + - - +
151A GLN* 5.1 4.1 + - - -
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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