Contacts of the helix formed by residues 114 - 118 (chain E) in PDB entry 3LAW
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 ASP 114 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112E PRO 3.1 3.6 + - - -
113E ARG* 1.3 79.3 - - + +
115E PRO* 1.3 72.2 - - - +
116E GLU* 3.0 25.4 + - - +
117E ASN* 3.1 37.4 + - + +
118E PHE* 3.7 6.9 + - - +
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Residues in contact with PRO 115 (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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103E ARG* 4.8 4.5 + - - -
107E LEU* 3.6 45.3 - - + +
111E SER* 5.4 0.9 - - - -
112E PRO* 3.1 31.6 - - + +
114E ASP* 1.3 85.9 - - - +
116E GLU* 1.3 73.2 + - + +
117E ASN 3.3 1.0 + - - -
118E PHE* 3.3 11.8 + - - +
120E PHE* 4.9 0.2 - - - -
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Residues in contact with GLU 116 (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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103E ARG* 4.8 7.4 + - - +
107E LEU* 5.0 6.4 - - - +
114E ASP* 3.0 16.2 - - - +
115E PRO* 1.3 88.2 - - + +
117E ASN* 1.3 62.4 + - - +
118E PHE 3.6 0.9 - - - +
147E ASN* 2.9 49.5 + - - +
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Residues in contact with ASN 117 (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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114E ASP* 3.1 25.5 + - + +
116E GLU* 1.3 88.7 - - - +
118E PHE* 1.3 66.7 + - - +
119E PRO* 3.3 5.9 - - - +
147E ASN* 4.2 9.2 - - - +
176E GLN* 4.7 3.5 - - - +
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Residues in contact with PHE 118 (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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81E ALA 3.3 28.7 - - - -
82E ASP 3.6 14.1 - - - -
83E CYS* 3.6 3.1 - - - -
84E CYS 3.4 11.2 - - - -
103E ARG* 5.4 1.4 + - - -
106E PHE* 3.3 39.7 - + - -
107E LEU* 4.2 4.7 - - + -
110E ALA* 5.4 1.6 - - + -
112E PRO* 3.8 25.6 - - + -
113E ARG 5.9 0.7 - - - -
114E ASP 3.7 4.9 + - - +
115E PRO* 3.3 20.4 + - + +
116E GLU 4.9 1.4 - - - +
117E ASN* 1.3 77.5 - - - +
119E PRO* 1.4 99.6 - - + +
120E PHE* 3.1 22.9 + + + -
147E ASN* 6.0 0.9 - - - +
149E ILE* 4.7 6.6 - - - +
176E GLN* 4.0 20.0 - - - -
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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