Contacts of the strand formed by residues 131 - 136 (chain C) in PDB entry 3LUE
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 ALA 131 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C PRO* 3.3 12.7 - - + +
103C VAL 3.1 19.8 + - - -
124C PHE* 4.0 4.9 - - - -
129C THR* 3.1 10.8 - - - +
130C PRO* 1.4 81.3 - - + +
132C MET* 1.3 67.9 + - - +
353C GLN* 4.9 4.0 - - - +
356C TRP* 3.8 24.9 - - + -
357C ILE 3.2 15.7 - - - +
358C SER* 4.2 4.7 - - - -
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Residues in contact with MET 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C VAL* 3.3 19.3 - - + +
105C LEU* 3.5 35.4 - - + -
119C MET 3.9 6.1 - - - +
120C THR* 4.1 21.3 - - - -
123C MET* 3.8 21.3 - - + -
124C PHE* 3.6 26.9 - - + -
129C THR* 4.8 2.0 - - + -
131C ALA* 1.3 79.3 - - - +
133C TYR* 1.3 60.9 + - - +
134C VAL* 4.0 23.3 - - + -
356C TRP* 3.4 5.4 - - - -
357C ILE* 2.9 45.4 + - - +
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Residues in contact with TYR 133 (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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103C VAL 3.1 5.3 + - - +
104C LEU* 3.4 10.4 - - + -
105C LEU* 2.8 32.2 + - - +
132C MET* 1.3 77.3 - - - +
134C VAL* 1.3 84.3 + - - +
135C ALA* 3.9 13.0 - - + -
346C LEU* 5.1 2.0 - - + -
352C PHE* 3.5 23.6 - + + -
355C MET* 3.1 44.1 - - + +
356C TRP* 3.4 20.4 - - + -
357C ILE* 5.1 0.4 - - + -
373C LYS 3.7 17.6 + - - -
374C CYS* 3.7 31.8 - - - -
375C PHE* 4.5 12.6 - - - -
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Residues in contact with VAL 134 (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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105C LEU* 3.4 11.4 - - + +
107C GLU* 3.4 39.8 - - + +
116C ARG* 4.4 9.2 - - + +
119C MET* 3.9 25.4 - - + -
132C MET* 4.0 21.1 - - + -
133C TYR* 1.3 85.9 - - - +
135C ALA* 1.3 58.5 + - - +
370C VAL* 3.8 23.8 - - + -
374C CYS* 3.7 22.9 - - - +
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Residues in contact with ALA 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C LEU* 4.4 15.3 - - + -
105C LEU 3.4 5.1 + - - -
106C THR* 3.2 6.6 - - - -
107C GLU* 2.7 33.2 + - - -
133C TYR* 3.9 19.4 + - + -
134C VAL* 1.3 75.1 - - - +
136C ILE* 1.3 57.4 + - - +
139C VAL* 6.1 2.0 - - + -
140C LEU* 3.4 26.2 - - + -
346C LEU* 5.3 3.6 - - + -
375C PHE* 6.6 0.4 - - - -
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Residues in contact with ILE 136 (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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107C GLU* 3.3 27.5 + - - +
108C ALA 4.4 6.3 - - - +
109C PRO* 3.8 27.1 - - + -
110C LEU 5.3 0.2 - - - +
134C VAL 4.3 0.2 + - - -
135C ALA* 1.3 70.6 - - - +
137C GLN* 1.3 64.1 + - - +
138C ALA* 3.9 10.3 - - + +
139C VAL* 3.5 23.8 + - + +
140C LEU* 2.9 19.6 - - - +
161C HIS* 4.2 25.4 - - + +
163C VAL* 5.4 0.7 - - + -
175C ILE* 5.6 2.5 - - + -
374C CYS 6.1 0.7 - - - +
375C PHE* 4.2 32.1 - - + -
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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