Contacts of the strand formed by residues 131 - 136 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F PRO* 3.3 12.3 - - + +
103F VAL 3.1 20.8 + - - -
124F PHE* 4.0 4.5 - - - -
129F THR* 3.1 9.7 - - - +
130F PRO* 1.4 82.8 - - + +
132F MET* 1.3 67.7 + - - +
353F GLN* 4.9 4.0 - - - +
356F TRP* 3.8 25.1 - - + -
357F ILE 3.2 15.9 - - - +
358F SER* 4.2 5.2 - - - -
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Residues in contact with MET 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F VAL* 3.3 18.6 - - + +
105F LEU* 3.5 35.4 - - + -
119F MET 3.9 5.8 - - - +
120F THR* 4.1 21.3 - - - -
123F MET* 3.8 21.1 - - + -
124F PHE* 3.6 26.5 - - + -
129F THR* 4.8 2.0 - - + -
131F ALA* 1.3 80.0 - - - +
133F TYR* 1.3 61.2 + - - +
134F VAL* 4.0 23.6 - - + -
356F TRP* 3.4 5.1 - - - -
357F ILE* 2.9 44.3 + - - +
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Residues in contact with TYR 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F VAL 3.1 4.9 + - - +
104F LEU* 3.4 10.2 - - + -
105F LEU* 2.8 32.6 + - - +
132F MET* 1.3 78.5 - - - +
134F VAL* 1.3 82.9 + - - +
135F ALA* 3.9 13.7 - - + -
346F LEU* 5.1 1.8 - - + -
352F PHE* 3.5 23.6 - + + -
355F MET* 3.1 44.5 - - + +
356F TRP* 3.4 20.8 - - + -
357F ILE* 5.1 0.7 - - + -
373F LYS 3.7 16.6 + - - -
374F CYS* 3.7 32.0 - - - -
375F PHE* 4.5 12.8 + - - -
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Residues in contact with VAL 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F LEU* 3.4 11.4 - - + +
106F THR 4.4 0.2 - - - -
107F GLU* 3.4 40.6 - - + +
116F ARG* 4.4 10.0 + - + +
119F MET* 3.9 25.1 - - + -
120F THR* 4.8 0.2 - - - +
132F MET* 4.0 20.9 - - + -
133F TYR* 1.3 84.6 - - - +
135F ALA* 1.3 57.3 + - - +
370F VAL* 3.8 23.8 - - + -
374F CYS* 3.7 22.6 - - - +
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Residues in contact with ALA 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F LEU* 4.4 16.1 - - + +
105F LEU 3.4 5.5 + - - -
106F THR* 3.2 7.3 - - - -
107F GLU* 2.7 32.8 + - - -
133F TYR* 3.9 19.8 - - + -
134F VAL* 1.3 74.1 - - - +
136F ILE* 1.3 56.8 + - - +
139F VAL* 6.1 1.8 - - + -
140F LEU* 3.4 26.0 - - + -
346F LEU* 5.3 3.4 - - + -
375F PHE* 6.6 0.4 - - - -
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Residues in contact with ILE 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F GLU* 3.3 26.8 + - + +
108F ALA 4.4 6.5 - - - +
109F PRO* 3.8 26.9 - - + -
135F ALA* 1.3 72.0 - - - +
137F GLN* 1.3 64.0 + - - +
138F ALA* 3.9 10.3 - - + +
139F VAL* 3.5 23.5 + - + +
140F LEU* 2.9 19.9 - - - +
161F HIS* 4.2 24.9 - - + +
163F VAL* 5.4 0.4 - - + -
175F ILE* 5.6 2.2 - - + -
375F PHE* 4.2 30.8 - - + -
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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