Contacts of the helix formed by residues 132 - 144 (chain B) in PDB entry 2QB0
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 LEU 132 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B ILE* 4.2 16.8 - - + -
118B TYR* 4.0 31.9 - - + +
130B PRO 3.8 1.8 + - - -
131B SER* 1.3 74.1 + - - +
133B ASN* 1.3 70.9 + - - +
134B ALA 3.3 0.7 - - - -
135B ALA* 3.2 16.5 + - + +
136B LYS* 3.2 43.8 + - + +
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Residues in contact with ASN 133 (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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131B SER* 3.5 12.3 + - - +
132B LEU* 1.3 83.1 - - - +
134B ALA* 1.3 57.1 + - - +
136B LYS* 3.5 8.2 + - - +
137B SER* 3.1 27.2 + - - -
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Residues in contact with ALA 134 (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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127B THR* 4.0 6.8 - - + +
129B SER* 4.0 28.9 - - - +
131B SER* 4.1 6.7 + - - +
132B LEU 3.3 0.6 - - - -
133B ASN* 1.3 76.3 - - - +
135B ALA* 1.3 61.8 + - - +
137B SER* 3.7 7.8 - - - -
138B GLU* 3.3 29.5 + - - +
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Residues in contact with ALA 135 (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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110B ILE* 5.1 3.1 - - + -
118B TYR* 3.8 36.8 - - + -
126B LEU* 3.6 20.6 - - + +
127B THR* 3.8 15.5 - - + +
131B SER 4.1 1.0 + - - +
132B LEU* 3.2 16.6 + - + +
134B ALA* 1.3 79.3 - - - +
136B LYS* 1.3 61.7 + - - +
138B GLU 3.7 0.3 + - - -
139B LEU* 3.3 22.0 + - - +
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Residues in contact with LYS 136 (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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110B ILE* 5.0 5.8 - - + -
132B LEU* 3.2 42.7 + - + +
133B ASN* 3.5 9.2 + - - +
135B ALA* 1.3 75.2 - - + +
137B SER* 1.3 60.2 + - - +
138B GLU 3.4 0.2 - - - -
139B LEU* 4.2 7.6 - - + -
140B ASP* 3.0 43.0 + - - +
146B ASN* 6.2 0.4 - - - +
148B ASN* 3.2 46.2 + - - +
149B GLY* 4.2 16.2 - - - +
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Residues in contact with SER 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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133B ASN 3.1 18.0 + - - -
134B ALA* 3.7 10.1 - - - -
135B ALA 3.3 0.4 - - - -
136B LYS* 1.3 76.5 - - - +
138B GLU* 1.3 64.3 + - - +
140B ASP* 3.7 5.5 + - - +
141B LYS* 3.3 26.8 + - - +
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Residues in contact with GLU 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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126B LEU* 3.7 29.4 - - + +
127B THR* 4.7 5.6 - - - -
134B ALA* 3.3 17.0 + - + +
135B ALA 4.1 3.4 - - - +
137B SER* 1.3 78.2 + - - +
139B LEU* 1.3 63.0 + - - +
141B LYS* 3.5 29.4 + - - +
142B ALA* 3.2 22.9 + - - +
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Residues in contact with LEU 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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110B ILE* 3.5 30.5 - - + -
120B ILE* 3.9 30.7 - - + -
126B LEU* 3.8 12.1 - - + +
135B ALA 3.3 16.0 + - - +
136B LYS* 3.7 7.4 - - - +
137B SER 3.3 0.2 - - - -
138B GLU* 1.3 78.0 - - - +
140B ASP* 1.3 59.4 + - - +
142B ALA* 3.1 4.0 + - - +
143B ILE* 2.8 53.4 + - + +
147B THR* 3.3 24.7 - - - +
149B GLY* 4.4 3.6 - - - +
151B ILE* 4.0 9.6 - - + -
159B LEU* 4.2 7.6 - - + -
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Residues in contact with ASP 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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136B LYS* 3.0 26.4 + - - +
137B SER* 4.1 5.4 - - - +
139B LEU* 1.3 75.0 - - - +
141B LYS* 1.3 57.7 + - - +
143B ILE* 4.0 1.6 - - - +
144B GLY* 3.0 26.3 + - - -
145B ARG 3.1 24.4 + - - +
146B ASN* 3.0 24.7 + - - +
147B THR* 2.9 28.1 + - - -
148B ASN 4.3 0.7 + - - -
206D GLY 5.6 0.2 - - - +
209D ASN* 3.7 11.4 + - - +
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Residues in contact with LYS 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 SER* 3.3 20.5 + - - +
138B GLU* 3.7 30.9 + - - +
139B LEU 3.2 0.4 - - - -
140B ASP* 1.3 79.0 - - - +
142B ALA* 1.3 59.9 + - - +
143B ILE 3.9 0.2 + - - -
144B GLY* 4.4 4.0 + - - -
209D ASN* 5.0 6.1 + - - +
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Residues in contact with ALA 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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124B HIS* 5.2 6.5 - - + +
126B LEU* 6.1 0.2 - - + -
138B GLU 3.2 16.1 + - - +
139B LEU* 3.1 7.4 + - - +
141B LYS* 1.3 78.2 - - - +
143B ILE* 1.3 63.2 + - - +
158B LYS* 3.8 17.2 - - - -
159B LEU* 3.8 25.0 - - + +
162B GLN* 4.4 11.4 + - - +
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Residues in contact with ILE 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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139B LEU* 2.8 30.7 + - + +
142B ALA* 1.3 81.4 - - - +
144B GLY* 1.3 59.1 + - - +
145B ARG* 3.7 21.3 - - + +
147B THR* 3.9 15.0 - - + -
151B ILE* 4.2 3.8 - - + -
155B GLU* 3.5 50.3 - - + +
158B LYS* 4.3 17.5 - - + +
159B LEU* 3.8 35.2 - - + -
225D ASN* 5.3 1.7 + - - -
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Residues in contact with GLY 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 ASP 3.0 7.4 + - - -
141B LYS 4.4 2.4 + - - -
142B ALA 3.7 0.8 - - - -
143B ILE* 1.3 78.2 - - - +
145B ARG* 1.3 54.6 + - - +
209D ASN* 3.2 32.0 - - - +
213D MET* 4.3 6.1 - - - +
225D ASN* 2.7 32.6 + - - +
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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