Contacts of the helix formed by residues 134 - 143 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94D ASN* 5.2 8.2 + - - -
97D LYS* 5.0 4.3 + - - +
132D TRP* 3.2 22.3 + - + +
133D PRO* 1.3 99.4 - - + +
135D LEU* 1.3 65.4 + - - +
137D LYS* 3.2 20.4 + - - +
138D ILE* 3.3 22.8 + - + +
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU* 4.4 3.6 - - + -
119D ILE* 4.1 6.5 - - + -
123D ALA* 3.9 12.3 - - + -
127D LEU* 4.4 4.0 - - + -
132D TRP* 3.3 64.7 + - + +
133D PRO 3.2 1.2 - - - -
134D GLU* 1.3 77.1 - - - +
136D MET* 1.3 85.5 + - + +
138D ILE* 2.9 19.6 + - + +
139D MET* 2.9 41.9 + - + +
162D MET* 3.7 17.5 - - + -
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Residues in contact with MET 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D LEU* 4.1 15.9 - - + -
132D TRP 4.9 0.4 + - - +
133D PRO 4.4 6.1 + - - +
134D GLU 3.3 1.0 + - - -
135D LEU* 1.3 106.2 - - + +
137D LYS* 1.3 58.1 + - - +
139D MET* 3.1 5.4 + - + +
140D VAL* 2.8 37.9 + - + +
159D LEU* 4.9 3.6 - - - -
162D MET* 3.8 16.2 - - - -
172D ALA* 4.6 17.7 - - + -
173D LEU* 4.6 16.8 - - + -
176D SER* 3.6 33.9 - - - +
180D ILE* 4.3 16.8 - - - -
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Residues in contact with LYS 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D PRO 5.0 2.2 + - - +
134D GLU* 3.2 12.2 + - - +
136D MET* 1.3 77.8 - - - +
138D ILE* 1.3 64.0 + - + +
140D VAL* 4.7 3.1 - - - -
141D ASP* 2.8 69.0 + - + +
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Residues in contact with ILE 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU* 4.0 25.6 - - + -
132D TRP* 5.7 0.7 - - - +
134D GLU* 3.4 28.7 - - + +
135D LEU* 2.9 10.6 + - - +
137D LYS* 1.3 83.2 - - + +
139D MET* 1.3 69.1 + - + +
141D ASP* 3.6 3.7 - - - +
142D ASN* 2.9 55.4 + - - +
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Residues in contact with MET 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU* 3.6 31.0 - - + -
104D LEU* 3.7 16.8 - - + -
119D ILE* 5.0 1.8 - - + -
135D LEU* 2.9 31.9 + - + +
136D MET* 3.7 8.1 - - + +
138D ILE* 1.3 87.8 - - + +
140D VAL* 1.3 62.0 + - - +
142D ASN* 3.5 10.8 + - - +
143D THR* 3.2 22.4 + - - -
155D SER* 4.0 10.5 - - - +
158D ALA* 4.1 15.7 - - - -
159D LEU* 3.7 24.5 - - + +
162D MET* 3.9 26.5 - - + -
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Residues in contact with VAL 140 (chain D).
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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136D MET 2.8 24.8 + - - +
137D LYS* 4.0 3.6 - - - +
139D MET* 1.3 72.6 - - + +
141D ASP* 1.3 62.7 + - - +
143D THR* 3.0 27.5 + - - -
144D GLY* 3.6 3.3 + - - -
159D LEU* 5.1 4.7 - - + -
176D SER* 4.8 4.0 - - - +
179D ASN* 4.3 33.9 - - + +
180D ILE* 4.2 24.5 - - + -
183D ALA* 5.3 6.5 - - + -
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Residues in contact with ASP 141 (chain D).
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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137D LYS* 2.8 64.2 + - + +
138D ILE* 3.6 4.3 - - - +
140D VAL* 1.3 79.7 - - - +
142D ASN* 1.3 60.5 + - - +
143D THR 3.1 0.2 - - - -
144D GLY* 3.0 18.8 + - - -
146D GLU* 4.7 1.2 - - - +
147D GLN* 3.5 15.0 + - - +
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Residues in contact with ASN 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU* 5.4 1.0 - - - +
104D LEU* 4.6 5.5 - - - +
105D VAL* 4.6 8.5 - - - +
138D ILE* 2.9 41.5 + - - +
139D MET* 3.7 8.6 - - - +
140D VAL 3.3 0.2 - - - -
141D ASP* 1.3 77.4 - - - +
143D THR* 1.3 57.3 + - - +
144D GLY 3.3 0.2 - - - -
147D GLN* 3.5 18.1 - - - +
151D VAL* 3.5 16.4 - - + +
152D LYS* 3.4 27.5 + - - +
155D SER* 3.0 30.0 + - - +
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Residues in contact with THR 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D MET 3.2 12.9 + - - -
140D VAL* 3.0 14.2 + - - -
142D ASN* 1.3 74.3 - - - +
144D GLY* 1.3 66.9 + - - +
145D ALA* 3.6 1.2 + - - -
152D LYS* 3.8 15.9 - - + +
155D SER* 4.4 4.5 - - - -
156D LEU* 3.9 25.5 - - + +
159D LEU* 4.4 6.9 - - - +
183D ALA* 3.7 37.7 - - + +
186D GLN* 6.1 1.6 - - + -
187D GLY* 5.8 1.1 - - - +
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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