Contacts of the helix formed by residues 139 - 146 (chain E) in PDB entry 3UF2
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 CYS 139 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47E VAL 4.6 0.2 - - - -
48E CYS* 2.0 61.5 - - + -
51E LYS* 3.6 21.5 - - - -
94E ASP* 3.3 17.2 + - - +
137E LYS* 4.4 7.6 - - - -
138E ASN* 1.3 75.9 + - - +
140E ASN* 1.3 60.7 + - - +
141E ASN 3.2 2.7 - - - +
142E SER* 3.3 3.1 + - - +
143E PHE* 2.9 42.2 + - + -
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Residues in contact with ASN 140 (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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93E LYS 5.6 0.2 + - - -
94E ASP* 3.0 16.2 + - - +
95E TYR* 2.8 44.0 + - + +
138E ASN* 2.8 33.9 + - - +
139E CYS* 1.3 78.1 - - - +
141E ASN* 1.3 64.2 + - - +
143E PHE* 3.5 6.7 + - - +
144E ALA* 3.2 24.4 + - - +
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Residues in contact with ASN 141 (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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138E ASN* 4.2 24.9 + - - +
139E CYS 3.2 0.8 - - - -
140E ASN* 1.3 79.5 - - - +
142E SER* 1.3 57.9 - - - +
144E ALA* 3.4 5.3 + - - +
145E GLU* 2.9 30.9 + - - +
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Residues in contact with SER 142 (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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42E GLN 5.3 0.3 - - - +
43E LEU* 4.0 19.1 - - - +
44E LYS* 5.7 4.7 - - - -
45E ASP* 4.2 11.4 + - - +
48E CYS* 3.5 26.3 - - - -
137E LYS* 5.2 2.9 + - - -
138E ASN 5.3 0.7 + - - -
139E CYS* 3.3 8.8 + - - -
141E ASN* 1.3 78.6 - - - +
143E PHE* 1.3 64.5 + - - +
145E GLU* 3.7 11.3 + - - +
146E CYS* 3.2 24.1 + - - +
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Residues in contact with PHE 143 (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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43E LEU* 3.8 19.7 - - + -
48E CYS* 3.7 25.6 - - + -
51E LYS* 4.7 3.6 - - + -
52E LYS* 4.0 33.7 - - + -
55E LEU* 6.4 1.6 - - + -
94E ASP* 4.0 24.2 - - + -
95E TYR 4.7 16.2 - - - +
101E ALA* 4.2 11.6 - - + +
102E CYS* 4.4 4.9 - - - -
139E CYS* 2.9 41.8 + - + +
140E ASN* 3.9 4.9 - - - +
142E SER* 1.3 78.6 - - - +
144E ALA* 1.3 59.0 + - - +
146E CYS* 2.9 27.0 - - - +
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Residues in contact with ALA 144 (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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140E ASN 3.2 17.8 + - - +
141E ASN* 3.8 5.2 - - - +
142E SER 3.3 0.2 - - - -
143E PHE* 1.3 75.7 - - - +
145E GLU* 1.3 66.2 + - - +
146E CYS 3.5 6.6 - - - +
147E SER* 5.2 0.5 - - - -
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Residues in contact with GLU 145 (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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42E GLN 6.1 0.2 - - - +
44E LYS* 2.9 39.6 + - - +
141E ASN 2.9 18.6 + - - +
142E SER* 3.7 11.8 + - - +
144E ALA* 1.3 76.0 - - - +
146E CYS* 1.3 65.9 + - - +
147E SER* 3.2 11.1 + - - -
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Residues in contact with CYS 146 (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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42E GLN* 3.4 31.8 + - + +
101E ALA* 4.3 3.2 - - - +
102E CYS* 2.0 55.6 - - - -
142E SER 3.2 7.0 + - - +
143E PHE 2.9 21.7 - - - +
144E ALA* 3.5 8.1 - - - +
145E GLU* 1.3 80.2 - - - +
147E SER* 1.3 60.4 + - - +
148E SER 3.6 2.9 + - - -
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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