Contacts of the helix formed by residues 136 - 149 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134B SER* 3.3 22.7 - - - +
135B ASN* 1.3 81.7 - - - +
137B PRO* 1.3 75.9 - - + +
138B LYS* 4.4 6.5 - - + +
139B GLN* 3.0 18.1 + - + +
140B LYS* 3.2 7.8 + - - +
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Residues in contact with PRO 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ASN 3.5 2.9 - - - +
136B ARG* 1.3 88.4 - - + +
138B LYS* 1.3 64.0 + - + +
140B LYS* 3.1 10.4 + - + +
141B GLU* 2.9 38.9 + - - +
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Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ARG* 3.2 5.6 + - + +
137B PRO* 1.3 80.9 - - + +
139B GLN* 1.3 69.8 + - + +
141B GLU* 3.4 14.4 + - - +
142B LYS* 3.0 28.1 + - - +
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Residues in contact with GLN 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B GLN* 3.2 23.1 - - + +
133B ASN* 2.8 58.3 + - - +
134B SER* 3.3 29.8 - - - +
136B ARG* 3.0 10.0 + - + +
138B LYS* 1.3 85.9 + - + +
140B LYS* 1.3 59.3 + - - +
142B LYS* 3.3 29.6 + - - +
143B TRP 3.0 24.9 + - - -
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Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B GLN* 3.7 30.2 - - - +
135B ASN* 3.7 20.0 - - + +
136B ARG 3.2 12.5 + - - +
137B PRO* 3.1 10.7 + - + +
139B GLN* 1.3 77.3 - - - +
141B GLU* 1.3 58.1 + - + +
143B TRP* 4.0 2.0 - - - +
144B LYS* 3.0 28.9 + - - +
2C C 4.1 30.0 + - - -
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Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B PRO* 2.9 33.5 + - - +
138B LYS* 3.7 13.2 + - - +
140B LYS* 1.3 75.8 - - - +
142B LYS* 1.3 57.3 + - - +
143B TRP 3.2 0.2 - - - -
144B LYS* 4.5 5.2 - - + -
145B SER* 2.8 38.2 + - - -
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Residues in contact with LYS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 3.6 8.7 - - - +
129B GLU* 2.7 39.2 + - + +
130B ASN* 3.4 25.2 - - - +
131B GLN 3.3 18.5 + - - -
133B ASN* 5.0 0.8 + - - -
138B LYS 3.0 17.7 + - - +
139B GLN* 3.4 32.0 + - - +
141B GLU* 1.3 76.4 - - - +
143B TRP* 1.3 57.2 + - - +
145B SER* 3.7 5.4 - - - -
146B TYR* 3.1 27.0 + - - +
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Residues in contact with TRP 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASN* 5.8 0.2 - - - -
110A SER* 3.9 20.9 - - - -
12B ASN* 3.3 33.9 + - + +
14B VAL* 5.1 4.3 - - + -
130B ASN 3.4 22.6 + - - +
131B GLN* 3.1 35.2 - - - -
132B GLN* 3.5 30.3 - - + +
139B GLN 3.0 16.0 + - - +
140B LYS* 4.1 2.2 - - - +
142B LYS* 1.3 73.8 - - - +
144B LYS* 1.3 73.6 + - + +
145B SER 3.1 1.6 - - - -
146B TYR* 3.1 14.9 + + - +
147B VAL* 3.0 47.3 + - + +
1C C 4.1 14.3 + - - -
2C C 3.9 18.5 + - - -
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Residues in contact with LYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LYS 3.0 21.7 + - - +
141B GLU* 3.9 5.8 - - + +
143B TRP* 1.3 82.0 - - + +
145B SER* 1.3 65.3 + - - +
147B VAL* 3.3 8.4 - - + +
148B ASP* 2.9 55.0 + - - +
1C C 5.2 9.4 - - - +
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Residues in contact with SER 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B GLU 2.8 24.4 + - - -
142B LYS* 3.7 6.3 - - - -
144B LYS* 1.3 75.7 - - - +
146B TYR* 1.3 62.4 + - - +
148B ASP* 3.8 4.6 - - - +
149B ASN* 3.2 24.1 + - - +
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Residues in contact with TYR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 5.3 0.2 - - - -
6B LEU* 5.1 1.2 - - - +
14B VAL* 3.7 30.3 - - + +
123B VAL* 4.9 3.8 + - - +
126B GLN* 4.2 13.2 - - + +
127B TYR* 3.5 37.8 + + - +
130B ASN* 3.5 40.8 - - + +
142B LYS 3.1 11.9 + - - +
143B TRP* 3.1 17.2 + + - +
145B SER* 1.3 79.0 - - - +
147B VAL* 1.3 75.2 + - + +
149B ASN* 3.1 22.2 + - - +
150B LEU* 3.7 24.1 - - + +
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LYS* 3.7 26.1 - - + +
12B ASN* 4.8 1.3 - - - +
14B VAL* 5.3 2.5 - - + -
143B TRP* 3.0 49.3 + - + +
144B LYS* 3.3 12.6 - - - +
146B TYR* 1.3 80.8 - - + +
148B ASP* 1.3 71.3 + - - +
149B ASN 3.1 1.8 - - - -
150B LEU* 3.2 29.7 + - + +
152B THR* 6.0 0.2 - - - +
1C C 3.5 29.6 - - - +
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Residues in contact with ASP 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LYS* 6.0 0.2 - - - -
144B LYS* 2.9 56.0 + - - +
145B SER* 3.8 5.5 - - - +
147B VAL* 1.3 84.8 - - - +
149B ASN* 1.3 56.5 + - - +
150B LEU 3.1 10.0 + - - +
1C C 4.7 8.1 + - - +
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Residues in contact with ASN 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B SER 3.2 16.0 + - - +
146B TYR* 3.1 7.0 + - - +
147B VAL 3.1 1.0 - - - -
148B ASP* 1.3 76.6 - - - +
150B LEU* 1.3 69.6 + - - +
151B GLN* 5.6 2.1 + - - -
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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