Contacts of the helix formed by residues 119 - 123 (chain E) in PDB entry 2NX5
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 119 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14E GLU* 5.3 1.1 - - - -
117E LEU* 3.2 13.5 + - - +
118E GLU* 1.3 85.8 - - + +
120E LEU* 1.3 64.2 + - - +
121E ASN* 3.0 34.9 - - - +
122E LYS* 3.2 38.1 + - + +
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Residues in contact with LEU 120 (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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12E VAL 4.6 2.0 - - - +
13E THR* 3.9 29.4 - - - +
14E GLU* 3.9 30.0 - - + +
117E LEU* 4.6 11.2 - - + -
119E ASP* 1.3 69.9 + - - +
121E ASN* 1.3 58.9 + - - +
122E LYS 3.0 5.4 - - - -
123E VAL* 3.0 32.4 + - + +
220E LEU* 3.8 37.0 - - + +
224E ASP* 4.5 17.7 - - + +
225E GLU 5.2 7.0 - - - +
226E TRP* 3.7 12.6 - - + -
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Residues in contact with ASN 121 (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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119E ASP* 3.0 32.1 - - - +
120E LEU* 1.3 79.6 + - - +
122E LYS* 1.3 56.3 + - + +
123E VAL 3.2 2.0 - - - -
124E PHE* 3.8 6.2 - - - -
226E TRP* 3.9 17.5 - - + -
228E GLN* 3.2 37.6 + - - +
230E ARG* 2.8 24.2 + - - +
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Residues in contact with LYS 122 (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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117E LEU* 4.8 0.9 - - + -
119E ASP* 3.2 33.3 + - + +
120E LEU 3.0 0.8 - - - -
121E ASN* 1.3 79.4 - - + +
123E VAL* 1.3 57.3 + - - +
124E PHE* 3.2 24.6 - - + -
154E PHE* 3.3 30.1 - - + +
186E LEU* 6.0 3.0 - - - +
187E ASN 5.3 2.4 + - - -
188E ASP* 4.3 38.7 + - + +
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Residues in contact with VAL 123 (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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12E VAL* 5.3 4.3 - - + -
117E LEU* 3.9 23.6 - - + -
120E LEU* 3.0 23.0 + - + +
121E ASN 3.2 0.2 - - - -
122E LYS* 1.3 76.9 - - - +
124E PHE* 1.3 56.8 + - - +
154E PHE 3.4 18.8 - - - +
155E PRO* 4.6 4.5 - - + -
217E PHE* 3.8 12.3 - - + -
219E GLY* 4.5 7.6 - - - -
220E LEU* 4.5 15.7 - - + -
230E ARG* 2.7 32.1 + - - -
233E PRO* 3.4 33.0 - - + +
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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