Contacts of the helix formed by residues 134 - 143 (chain B) in PDB entry 2BKU
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 GLU 134 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B ASN* 5.4 5.3 + - - -
97B LYS* 4.9 2.3 + - - +
132B TRP* 3.2 25.8 + - + +
133B PRO* 1.3 101.6 - - + +
135B LEU* 1.3 62.4 - - - +
137B LYS* 3.4 10.0 + - - +
138B ILE* 3.1 33.7 + - + +
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Residues in contact with LEU 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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101B LEU* 4.4 4.3 - - + -
119B ILE* 4.0 7.9 - - + -
123B ALA* 3.8 22.7 - - + -
127B LEU* 4.3 5.8 - - + -
132B TRP* 3.5 66.3 + - + +
133B PRO 3.2 1.0 - - - -
134B GLU* 1.3 77.8 - - - +
136B MET* 1.3 70.1 + - + +
138B ILE* 3.0 8.1 + - + +
139B MET* 2.8 58.6 + - + +
162B MET* 3.9 13.2 - - - -
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Residues in contact with MET 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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127B LEU* 4.1 17.7 - - + -
132B TRP 5.0 0.4 + - - -
133B PRO 4.3 6.3 + - - +
134B GLU 3.5 0.6 - - - -
135B LEU* 1.3 90.7 - - + +
137B LYS* 1.3 57.2 + - - +
139B MET* 3.2 4.8 + - + +
140B VAL* 2.8 36.9 + - + +
159B LEU* 4.8 2.9 - - - -
162B MET* 3.7 29.4 - - - -
172B ALA* 4.8 15.7 - - + -
173B LEU* 4.9 12.1 - - + +
176B SER* 3.4 28.9 - - - +
180B ILE* 3.7 27.8 - - - -
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Residues in contact with LYS 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 PRO 5.0 2.6 + - - +
134B GLU* 3.4 11.1 + - - +
135B LEU 3.3 0.4 - - - -
136B MET* 1.3 78.3 - - - +
138B ILE* 1.3 61.5 + - + +
140B VAL* 4.0 3.3 - - - -
141B ASP* 2.9 72.2 + - + +
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Residues in contact with ILE 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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101B LEU* 4.2 24.9 - - + -
132B TRP* 6.0 0.4 - - - +
134B GLU* 3.1 29.8 - - + +
135B LEU* 3.0 8.9 + - - +
137B LYS* 1.3 80.2 - - + +
139B MET* 1.3 69.2 + - + +
141B ASP* 3.7 3.7 - - - +
142B ASN* 2.9 54.5 + - - +
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Residues in contact with MET 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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101B LEU* 3.8 22.2 - - + -
104B LEU* 3.6 25.6 - - + -
119B ILE* 4.8 1.8 - - + -
135B LEU* 2.8 41.5 + - + +
136B MET* 3.6 6.1 - - + +
138B ILE* 1.3 84.1 - - + +
140B VAL* 1.3 61.6 + - - +
142B ASN* 3.5 9.5 + - - +
143B THR* 3.3 20.8 + - - -
155B SER* 4.2 12.3 - - - +
158B ALA* 4.2 14.6 - - - -
159B LEU* 3.8 23.8 - - + +
162B MET* 3.8 26.2 - - + -
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Residues in contact with VAL 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 MET 2.8 25.1 + - - +
137B LYS* 4.1 3.8 - - - +
139B MET* 1.3 72.1 - - + +
141B ASP* 1.3 65.8 + - - +
143B THR* 3.0 26.9 + - - +
144B GLY* 3.6 3.5 + - - -
159B LEU* 5.3 1.1 - - + -
176B SER* 4.9 1.6 - - - +
179B ASN* 4.0 48.0 - - + +
180B ILE* 4.3 14.6 - - + -
183B ALA* 4.6 8.5 - - + -
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Residues in contact with ASP 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 LYS* 2.9 59.3 + - + +
138B ILE* 3.7 4.3 - - - +
140B VAL* 1.3 84.2 - - - +
142B ASN* 1.3 63.6 + - - +
143B THR 3.1 0.2 - - - -
144B GLY* 3.1 13.1 + - - +
146B GLU* 4.9 1.0 - - - +
147B GLN* 3.4 19.7 + - - +
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Residues in contact with ASN 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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101B LEU* 5.7 0.4 - - - +
104B LEU* 4.3 5.9 - - - +
105B VAL* 4.7 8.4 - - - +
138B ILE* 2.9 39.1 + - - +
139B MET* 3.7 10.8 - - - +
140B VAL 3.3 0.2 - - - -
141B ASP* 1.3 78.6 - - - +
143B THR* 1.3 55.9 + - - +
144B GLY 3.2 1.3 - - - -
147B GLN* 3.5 16.7 + - - +
151B VAL* 3.7 17.0 - - + +
152B LYS* 3.3 27.1 + - - +
155B SER* 3.0 31.3 + - - +
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Residues in contact with THR 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 MET 3.3 11.2 + - - -
140B VAL 3.0 13.9 + - - -
142B ASN* 1.3 75.1 - - - +
144B GLY* 1.3 67.4 + - - +
145B ALA* 3.6 1.2 + - - -
152B LYS* 3.9 14.6 - - + +
155B SER* 4.6 4.3 - - - -
156B LEU* 3.8 22.8 - - + +
159B LEU* 4.2 4.9 - - - +
183B ALA* 3.1 44.7 - - + +
186B GLN* 4.6 13.4 - - + +
187B GLY* 5.1 4.3 - - - +
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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