Contacts of the helix formed by residues 106 - 111 (chain J) in PDB entry 5DST
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 ASN 106 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101J ASN 4.3 1.0 - - - +
102J SER* 2.8 25.2 - - - +
103J MET 3.1 7.9 + - - -
105J HIS* 1.3 96.5 + - - +
107J LYS* 1.3 63.1 + - - +
108J HIS* 3.1 21.0 - - + -
109J VAL* 3.0 25.5 + - + +
110J PHE* 3.5 9.5 - - + -
215J PHE* 5.5 1.1 - - + -
318J CYS* 3.1 25.3 - - - +
319J HIS* 3.2 26.8 - - - +
322J MET* 5.0 0.7 - - - +
303L TYR* 3.1 13.3 + - - -
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Residues in contact with LYS 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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103J MET 3.4 2.2 + - - -
104J TYR* 3.3 38.9 + - - +
105J HIS 3.8 1.4 - - - -
106J ASN* 1.3 75.5 - - - +
108J HIS* 1.3 58.4 + - - +
109J VAL 3.1 0.2 - - - -
110J PHE 3.1 1.0 + - - +
111J LYS* 3.0 34.2 + - + +
131J LYS 4.2 15.0 - - - -
132J ALA* 3.5 29.6 - - + +
345L TYR* 3.8 20.2 + - + +
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Residues in contact with HIS 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105J HIS 4.8 0.4 + - - -
106J ASN* 3.7 37.0 - - + -
107J LYS* 1.3 79.3 - - - +
109J VAL* 1.3 76.0 + - + +
110J PHE 3.4 0.2 - - - -
111J LYS* 4.4 8.6 + - - +
113J LYS* 5.5 1.0 - - - +
317J LYS 5.2 3.6 + - - -
319J HIS* 4.5 4.6 - - + +
347L THR* 4.2 27.7 + - + +
382L LEU* 3.1 55.9 - - + +
383L CYS* 5.4 1.3 - - + -
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Residues in contact with VAL 109 (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 ASN* 3.0 19.1 + - + +
108J HIS* 1.3 103.3 - - + +
110J PHE* 1.3 63.7 + - + +
111J LYS 3.6 0.2 - - - -
113J LYS* 2.9 27.7 - - - +
181J ILE* 3.6 13.8 - - + +
213J LEU* 3.3 33.7 - - + -
215J PHE* 4.3 16.6 - - + -
317J LYS 4.8 11.4 - - - +
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Residues in contact with PHE 110 (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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102J SER 4.4 0.4 - - - -
103J MET* 3.8 43.3 - - + -
106J ASN 3.5 15.7 - - - -
107J LYS 3.1 2.0 + - - +
109J VAL* 1.3 82.3 - - + +
111J LYS* 1.3 66.0 + - - +
112J ASP 3.1 1.2 + - - -
113J LYS* 3.0 17.1 + - - +
115J VAL* 3.9 18.8 - - + -
129J ALA* 4.6 8.1 - - + -
132J ALA* 3.5 26.7 - - + +
133J GLY 4.1 1.1 - - - -
134J ALA* 3.4 12.6 - - - +
181J ILE* 3.5 31.4 - - + -
183J ILE* 4.3 8.1 - - + -
215J PHE* 3.8 39.5 - + - -
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Residues in contact with LYS 111 (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 LYS* 3.0 18.6 + - + +
108J HIS* 4.4 7.2 + - - +
109J VAL 3.6 1.8 - - - -
110J PHE* 1.3 74.7 - - - +
112J ASP* 1.3 90.8 + - - +
113J LYS* 3.3 11.1 + - - +
132J ALA 4.4 1.3 - - - +
133J GLY* 3.4 15.9 - - - +
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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