Contacts of the helix formed by residues 103 - 109 (chain E) in PDB entry 2WJZ
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 103 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E SER* 5.4 0.4 - - - +
102E ILE* 1.3 76.7 - - - +
104E THR* 1.3 74.3 + - - +
105E ALA 3.2 1.6 - - - +
106E ALA* 2.9 14.5 + - - +
107E VAL* 3.0 18.3 + - - +
127E VAL* 5.3 0.6 - - - +
128E ALA* 2.9 42.8 + - + +
130E ASP* 3.4 27.3 + - - +
140E VAL* 5.9 1.4 - - - +
141E PHE 4.2 13.0 - - - +
142E THR* 4.5 4.7 - - - +
144E SER 6.3 0.9 - - - -
1252E PO4 3.0 26.1 + - - +
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Residues in contact with THR 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E HIS* 5.2 8.3 - - + +
103E ASN* 1.3 80.7 + - - +
105E ALA* 1.3 63.9 + - - +
107E VAL* 3.4 1.6 + - - +
108E GLU* 3.1 30.7 + - - +
142E THR* 3.7 14.1 - - - -
143E TYR* 2.8 69.0 + - + -
144E SER 4.3 0.2 + - - -
1252E PO4 2.9 26.6 + - - -
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Residues in contact with ALA 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E ILE 3.4 25.4 - - - +
84E HIS* 3.7 32.4 + - + +
102E ILE* 5.0 2.9 - - + -
103E ASN 3.2 1.4 - - - +
104E THR* 1.3 78.8 - - - +
106E ALA* 1.3 57.1 + - - +
108E GLU* 3.5 6.8 + - - +
109E ASN* 2.8 32.2 + - - +
112E LEU* 3.9 12.7 - - + +
1252E PO4 4.6 2.9 + - - +
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Residues in contact with ALA 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E ILE* 3.8 36.3 - - + +
103E ASN* 2.9 11.2 + - - +
105E ALA* 1.3 77.4 - - - +
107E VAL* 1.3 60.8 + - - +
109E ASN 4.0 6.3 - - - -
110E PRO* 2.9 34.0 - - - +
112E LEU* 4.6 1.9 - - - +
113E ILE* 4.2 13.0 - - + -
127E VAL* 4.6 4.7 - - + -
156E TRP* 3.6 11.2 - - + -
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Residues in contact with VAL 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E ASN* 3.0 14.3 + - - +
104E THR 3.8 2.0 - - - +
106E ALA* 1.3 76.8 - - - +
108E GLU* 1.3 66.1 + - + +
109E ASN 3.7 0.2 + - - -
110E PRO* 3.8 10.4 - - - +
140E VAL* 4.2 11.9 - - + -
142E THR* 3.5 34.5 - - + +
149E THR* 4.2 9.4 - - + -
151E ILE* 4.1 24.4 - - + +
156E TRP* 3.5 38.6 - - + +
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Residues in contact with GLU 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E HIS* 5.9 0.7 + - - -
104E THR* 3.1 22.6 + - + +
105E ALA* 4.0 5.8 - - - +
107E VAL* 1.3 85.3 - - + +
109E ASN* 1.3 62.4 + - + +
110E PRO* 3.8 3.8 - - - +
142E THR* 5.2 2.0 + - + +
143E TYR* 2.6 43.1 + - + -
147E LYS* 4.4 9.8 + - - +
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Residues in contact with ASN 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E ALA 2.8 12.4 + - - +
106E ALA* 3.0 5.2 - - - +
108E GLU* 1.3 81.6 + - + +
110E PRO* 1.3 67.5 - - - +
111E SER* 3.6 22.8 + - - +
112E LEU* 2.9 37.8 + - + +
115E GLN* 4.9 5.7 - - - +
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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