Contacts of the strand formed by residues 103 - 107 (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 VAL 103 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8J LEU* 3.6 18.6 - - + +
10J VAL* 5.5 1.6 - - + -
90J PHE* 4.0 28.7 - - + -
98J PRO* 5.6 2.5 - - + +
101J HIS 4.2 2.5 - - - +
102J PRO* 1.3 79.3 - - - +
104J LEU* 1.3 62.5 + - - +
105J LEU* 4.4 13.0 - - + -
123J MET* 3.8 19.5 - - - -
129J THR* 3.8 19.3 - - + -
131J ALA 3.1 4.9 + - - -
132J MET* 3.3 20.4 - - + -
133J TYR 3.1 23.4 + - - +
356J TRP* 3.3 4.5 - - - -
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Residues in contact with LEU 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J ALA* 5.1 0.4 - - - +
8J LEU 3.2 8.8 + - - +
9J VAL* 3.7 26.3 - - + -
10J VAL* 3.0 25.3 + - - +
102J PRO 4.3 0.4 + - - -
103J VAL* 1.3 72.9 - - - +
105J LEU* 1.3 61.5 + - - +
106J THR* 4.0 7.9 - - + -
133J TYR* 3.4 14.8 - - + +
135J ALA* 4.4 9.2 - - + -
140J LEU* 3.9 24.2 - - + -
343J GLY* 4.1 4.0 - - - +
346J LEU* 3.5 31.2 - - + -
347J ALA* 4.4 12.3 - - + +
352J PHE* 3.5 21.5 - - + -
356J TRP* 4.0 9.7 - - + -
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Residues in contact with LEU 105 (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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10J VAL* 3.4 29.2 - - + -
12J ASN* 4.3 2.7 - - - +
86J TRP* 4.4 12.3 - - + +
90J PHE* 5.6 0.2 - - + -
103J VAL* 4.4 10.3 - - + -
104J LEU* 1.3 75.0 - - - +
106J THR* 1.3 66.5 + - - +
119J MET* 3.5 32.5 - - + -
123J MET* 3.8 34.8 - - + -
132J MET* 3.5 27.4 - - + -
133J TYR 2.8 9.9 + - - +
134J VAL* 3.4 20.1 - - + -
135J ALA 3.4 2.9 + - - -
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Residues in contact with THR 106 (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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9J VAL* 5.1 2.5 - - + -
10J VAL 2.9 14.2 + - - +
11J ASP* 2.7 33.5 + - + +
12J ASN* 3.4 19.8 + - - +
104J LEU* 4.0 8.5 - - + -
105J LEU* 1.3 79.3 - - - +
107J GLU* 1.3 63.8 + - - +
119J MET* 4.7 4.2 - - - +
134J VAL* 4.4 0.6 - - - +
135J ALA 3.2 8.5 - - - +
137J GLN* 3.8 12.9 + - - +
140J LEU* 3.2 35.4 - - + -
339J VAL* 4.0 9.2 - - + +
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Residues in contact with GLU 107 (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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106J THR* 1.3 77.0 - - - +
108J ALA* 1.3 69.1 + - - +
111J ASN* 3.1 31.5 + - - +
116J ARG* 3.0 37.9 + - - +
119J MET* 4.4 4.0 - - + -
134J VAL* 3.4 20.1 - - + +
135J ALA 2.7 21.6 + - - +
136J ILE* 3.3 24.7 + - - +
137J GLN* 3.0 34.6 + - - +
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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