Contacts of the strand formed by residues 131 - 136 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102J PRO* 3.3 13.0 - - + +
103J VAL 3.1 20.5 + - - -
124J PHE* 4.0 4.0 - - - -
129J THR* 3.1 9.7 - - - +
130J PRO* 1.4 82.6 - - + +
132J MET* 1.3 68.4 + - - +
353J GLN* 4.9 4.0 - - - +
356J TRP* 3.8 25.4 - - + -
357J ILE 3.2 15.5 - - - +
358J SER* 4.2 5.2 - - - -
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Residues in contact with MET 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103J VAL* 3.3 18.8 - - + +
105J LEU* 3.5 36.1 - - + -
119J MET 3.9 5.6 - - - +
120J THR* 4.1 21.3 - - - -
123J MET* 3.8 20.6 - - + -
124J PHE* 3.6 26.0 - - + -
129J THR* 4.8 2.2 - - + -
131J ALA* 1.3 80.0 - - - +
133J TYR* 1.3 62.2 + - - +
134J VAL* 4.0 24.2 - - + -
356J TRP* 3.4 4.9 - - - -
357J ILE* 2.9 44.0 + - - +
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Residues in contact with TYR 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103J VAL 3.1 4.7 + - - +
104J LEU* 3.4 9.6 - - + -
105J LEU* 2.8 32.4 + - - +
132J MET* 1.3 77.1 - - - +
134J VAL* 1.3 85.0 + - - +
135J ALA* 3.9 13.7 - - + -
346J LEU* 5.1 1.6 - - + -
352J PHE* 3.5 23.8 - + + -
355J MET* 3.1 43.8 - - + +
356J TRP* 3.4 21.3 - - + -
357J ILE* 5.1 0.2 - - + -
373J LYS 3.7 17.4 + - - -
374J CYS* 3.7 31.7 - - - -
375J PHE* 4.5 13.3 + - - -
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Residues in contact with VAL 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105J LEU* 3.4 11.7 - - + +
106J THR 4.4 0.2 - - - -
107J GLU* 3.4 40.5 - - + +
116J ARG* 4.4 10.0 + - + +
119J MET* 3.9 24.5 - - + -
120J THR* 4.8 0.2 - - - +
132J MET* 4.0 20.9 - - + -
133J TYR* 1.3 84.5 - - - +
135J ALA* 1.3 57.2 + - - +
136J ILE 4.3 0.2 + - - -
370J VAL* 3.8 24.2 - - + -
374J CYS* 3.7 22.8 - - - +
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Residues in contact with ALA 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104J LEU* 4.4 15.7 - - + +
105J LEU 3.4 5.3 + - - -
106J THR* 3.2 6.9 - - - -
107J GLU* 2.7 33.2 + - - -
133J TYR* 3.9 19.8 - - + -
134J VAL* 1.3 74.7 - - - +
136J ILE* 1.3 56.9 + - - +
139J VAL* 6.1 1.8 - - + -
140J LEU* 3.4 25.6 - - + -
346J LEU* 5.3 3.6 - - + -
375J PHE* 6.6 0.7 - - - -
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Residues in contact with ILE 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J GLU* 3.3 26.6 + - + +
108J ALA 4.4 6.3 - - - +
109J PRO* 3.8 27.8 - - + -
110J LEU 5.4 0.2 - - - +
134J VAL 4.3 0.2 + - - -
135J ALA* 1.3 71.6 - - - +
137J GLN* 1.3 64.6 + - - +
138J ALA* 3.9 10.3 - - + +
139J VAL* 3.5 23.6 + - + +
140J LEU* 2.9 19.6 - - - +
161J HIS* 4.2 24.9 - - + +
163J VAL* 5.4 1.1 - - + -
175J ILE* 5.6 2.2 - - + -
374J CYS 6.1 0.7 - - - +
375J PHE* 4.2 31.5 - - + -
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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