Contacts of the helix formed by residues 131 - 137 (chain D) in PDB entry 1LBI
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 GLN 131 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129D ASP 2.4 11.3 + - - +
130D ASP* 1.3 86.8 + - + +
132D ASP* 1.3 57.7 + - - +
134D ILE* 2.9 53.9 + - - +
135D ALA* 3.1 6.4 + - - +
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Residues in contact with ASP 132 (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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103D GLY* 6.2 0.2 - - - -
104D VAL* 3.1 39.9 - - + +
128D LEU* 4.2 6.1 - - + -
129D ASP* 3.0 33.3 + - - +
131D GLN* 1.3 76.8 - - - +
133D ALA* 1.3 56.8 + - - +
135D ALA* 3.3 6.6 + - - +
136D VAL* 2.9 35.0 + - - +
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Residues in contact with ALA 133 (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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128D LEU* 3.8 12.1 - - + +
130D ASP* 2.9 18.2 + - - +
132D ASP* 1.3 75.5 - - - +
134D ILE* 1.3 56.2 + - - +
137D GLU* 2.8 35.3 + - - +
147D PHE* 3.3 11.9 - - + -
150D VAL* 3.7 21.1 - - + -
154D THR* 4.4 0.7 - - + -
156D ILE* 3.5 28.2 - - + +
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Residues in contact with ILE 134 (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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130D ASP* 3.3 11.0 - - - +
131D GLN* 3.0 47.1 - - - +
133D ALA* 1.3 78.6 - - - +
135D ALA* 1.3 54.9 + - - +
137D GLU* 3.6 11.3 - - - +
138D ALA* 3.2 27.4 + - + +
154D THR* 4.2 16.2 - - + -
155D PRO* 4.5 14.8 - - + -
156D ILE* 4.6 4.9 - - + -
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Residues in contact with ALA 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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104D VAL* 3.7 15.5 - - + -
108D LYS* 3.5 21.3 + - - +
131D GLN 3.1 6.8 + - - +
132D ASP* 3.4 15.3 - - - +
133D ALA 3.2 0.4 - - - -
134D ILE* 1.3 78.1 - - - +
136D VAL* 1.3 59.5 + - - +
138D ALA* 3.3 6.7 + - - +
139D ALA 2.9 21.0 + - - -
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Residues in contact with VAL 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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104D VAL* 3.1 20.2 - - + +
107D CYS* 4.0 24.5 - - + -
108D LYS* 4.4 6.1 - - - +
111D VAL* 3.9 24.5 - - + -
124D ILE* 4.7 3.4 - - + -
128D LEU* 4.1 15.5 - - + -
132D ASP 2.9 19.0 + - - +
133D ALA 4.1 2.2 - - - +
135D ALA* 1.3 70.2 - - - +
137D GLU* 1.3 67.1 + - - +
138D ALA 3.0 1.6 - - - -
139D ALA* 4.1 5.4 - - + -
140D CYS* 2.9 30.9 + - - -
147D PHE* 4.2 11.4 - - + -
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Residues in contact with GLU 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 ALA 2.8 22.9 + - - +
134D ILE* 3.6 10.8 - - - +
135D ALA 3.3 0.2 - - - -
136D VAL* 1.3 74.9 - - - +
138D ALA* 1.3 61.7 + - - +
140D CYS* 3.6 6.6 - - - +
141D THR* 2.8 30.8 + - - +
145D ALA* 5.0 7.2 - - + +
147D PHE* 3.4 20.1 - - + -
155D PRO 4.0 10.0 - - - +
156D ILE* 3.4 30.8 - - + +
157D ASN* 4.8 5.6 + - - +
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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