Contacts of the strand formed by residues 146 - 151 (chain C) in PDB entry 1LU9
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 146 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120C GLY* 4.9 6.3 - - - +
121C LYS 2.7 16.3 + - - +
122C LYS* 3.4 41.4 + - - +
123C ALA 2.8 25.8 + - - +
144C GLY 3.8 1.0 + - - -
145C ALA* 1.3 71.1 - - - +
147C VAL* 1.3 62.1 + - - +
148C VAL* 4.5 5.8 - - + +
173C THR* 5.8 3.4 - - - +
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Residues in contact with VAL 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C ALA* 3.3 9.2 - - + +
125C VAL* 4.3 8.5 - - + -
137C ALA* 3.8 29.4 - - + +
140C LEU* 3.8 14.4 - - + -
141C ALA* 3.7 32.1 - - + +
145C ALA* 3.5 11.4 + - + +
146C GLU* 1.3 79.0 - - - +
148C VAL* 1.3 75.1 - - - +
171C ASN 4.9 1.8 + - - +
172C VAL* 4.0 16.2 - - + +
173C THR* 3.1 28.6 + - - -
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Residues in contact with VAL 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LYS* 3.8 28.7 - - - +
123C ALA 2.9 11.1 + - - +
124C VAL* 3.5 10.7 - - + +
125C VAL* 2.9 28.2 + - - +
146C GLU* 4.5 8.3 - - + +
147C VAL* 1.3 79.5 - - - +
149C LEU* 1.3 61.5 + - - +
150C CYS* 3.7 11.3 + - - -
173C THR* 3.3 20.2 - - + +
174C ALA 4.6 1.1 - - - +
175C ALA* 3.6 30.5 - - + +
186C ALA* 6.1 1.8 - - + +
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Residues in contact with LEU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C VAL* 4.1 5.2 - - + -
128C GLY* 3.4 40.8 - - - +
129C THR* 3.8 13.5 - - + +
134C MET* 4.2 7.6 - - + -
137C ALA* 4.0 24.5 - - + -
147C VAL* 4.1 1.0 - - - -
148C VAL* 1.3 71.9 - - - +
150C CYS* 1.3 63.2 + - - +
157C ALA* 3.8 7.3 - - - +
160C ALA* 4.0 21.8 - - + +
161C ALA* 4.2 13.7 - - + +
164C VAL* 4.6 2.7 - - + -
172C VAL* 3.8 16.6 - - + -
173C THR 2.7 11.0 + - - +
174C ALA* 3.3 6.1 - - - -
175C ALA 3.0 20.9 + - - +
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Residues in contact with CYS 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C VAL* 3.9 27.4 - - - -
125C VAL 3.1 13.1 + - - +
126C LEU* 4.0 12.1 - - + -
127C ALA 3.4 4.6 + - - +
128C GLY* 2.8 30.7 + - - -
129C THR 3.9 0.3 + - - -
148C VAL* 4.0 14.4 - - - -
149C LEU* 1.3 79.9 - - - +
151C GLY* 1.3 57.7 + - - +
175C ALA* 3.2 11.0 - - - +
177C THR* 3.6 32.5 - - + +
186C ALA* 4.3 4.9 - - - -
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Residues in contact with GLY 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ALA* 5.0 4.5 - - - -
129C THR* 3.7 20.4 - - - -
150C CYS* 1.3 75.3 - - - +
152C ARG* 1.3 64.0 + - - -
153C LYS 3.2 5.6 + - - -
156C LYS* 5.9 0.4 - - - -
157C ALA* 3.7 7.1 - - - +
175C ALA 3.1 6.9 + - - -
176C GLU* 3.4 4.5 - - - -
177C THR* 2.9 27.9 + - - -
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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