Contacts of the strand formed by residues 122 - 126 (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 LYS 122 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C LYS* 1.3 73.3 - - - +
123C ALA* 1.3 64.0 - - - +
124C VAL* 3.8 21.5 - - - -
146C GLU* 3.4 36.2 + - - +
148C VAL* 3.8 22.5 - - - +
186C ALA 4.7 7.2 + - - -
188C LYS 5.1 5.1 + - - -
189C GLY 4.5 5.4 - - - +
190C ALA* 3.8 20.4 - - + +
191C HIS* 2.8 47.5 + - + +
192C PHE* 3.0 9.0 + - - +
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Residues in contact with ALA 123 (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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121C LYS 4.0 0.4 + - - -
122C LYS* 1.3 75.6 - - - +
124C VAL* 1.3 64.5 + - - +
125C VAL 4.2 0.2 - - - -
140C LEU* 4.2 29.6 - - + -
145C ALA* 4.5 8.5 - - + -
146C GLU 2.8 10.0 + - - +
147C VAL* 3.3 8.0 - - + +
148C VAL* 2.9 25.3 + - - +
192C PHE* 3.1 25.4 - - + +
194C PHE* 4.8 1.3 - - + -
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Residues in contact with VAL 124 (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 16.8 - - - -
123C ALA* 1.3 76.7 - - - +
125C VAL* 1.3 64.1 + - - +
126C LEU* 3.8 15.9 + - + -
148C VAL* 3.5 9.6 - - + +
150C CYS* 3.9 24.5 - - - -
186C ALA* 3.5 26.9 - - + +
187C VAL* 4.4 6.7 - - + -
190C ALA* 3.6 21.1 - - + -
192C PHE 2.9 8.8 + - - +
193C VAL* 3.4 8.7 - - + +
194C PHE* 3.0 26.0 + - - +
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Residues in contact with VAL 125 (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* 1.3 77.0 - - - +
126C LEU* 1.3 66.0 + - - +
128C GLY* 3.5 23.9 + - - -
133C GLY* 3.9 19.5 - - - +
136C SER* 4.9 2.9 - - - -
137C ALA* 4.3 12.6 - - + +
140C LEU* 4.1 25.1 - - + -
147C VAL* 4.3 16.4 - - + -
148C VAL 2.9 12.0 + - - +
149C LEU* 4.7 3.6 - - - -
150C CYS* 3.1 24.9 + - - +
194C PHE* 3.5 18.4 - - + +
196C ALA* 4.6 3.4 - - + -
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Residues in contact with LEU 126 (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* 4.1 8.7 - - + -
125C VAL* 1.3 68.7 - - - +
127C ALA* 1.3 70.1 + - - +
128C GLY 3.1 1.5 + - - -
150C CYS* 4.0 23.1 - - + -
177C THR* 4.9 0.2 - - + -
183C ARG* 4.1 33.7 - - + +
186C ALA* 4.5 1.3 - - + -
187C VAL* 3.9 18.8 - - + -
193C VAL* 4.1 8.5 - - + -
194C PHE 2.7 15.8 + - - +
195C THR* 4.0 18.6 - - + -
196C ALA* 3.0 26.3 + - - +
203C LEU* 4.1 22.4 - - + +
204C LEU* 4.0 20.0 - - + -
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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