Contacts of the helix formed by residues 127 - 135 (chain E) in PDB entry 2H46
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 SER 127 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125E PHE* 3.2 10.9 + - - +
126E ASN* 1.3 82.7 - - - +
128E LEU* 1.3 65.2 + - - +
129E ASN* 3.6 9.8 + - - +
130E GLU* 2.7 37.2 + - - +
131E LEU* 3.1 17.5 + - - +
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Residues in contact with LEU 128 (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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127E SER* 1.3 74.5 - - - +
129E ASN* 1.3 57.6 + - - +
131E LEU* 3.1 19.4 + - + +
132E VAL* 2.8 39.4 + - + +
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Residues in contact with ASN 129 (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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127E SER* 3.7 10.7 - - - +
128E LEU* 1.3 78.6 - - - +
130E GLU* 1.3 57.9 + - + +
132E VAL* 3.5 6.3 + - - +
133E ASP* 3.0 44.4 + - - +
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Residues in contact with GLU 130 (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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125E PHE* 3.8 14.8 - - + -
126E ASN* 3.5 22.0 + - - +
127E SER* 2.7 41.5 + - - +
129E ASN* 1.3 74.5 - - + +
131E LEU* 1.3 66.8 + - - +
133E ASP* 3.9 5.6 - - - +
134E TYR* 3.0 26.3 + - - +
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Residues in contact with LEU 131 (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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125E PHE* 3.5 38.1 - - + -
127E SER 3.1 13.8 + - - +
128E LEU* 3.5 22.2 - - + +
130E GLU* 1.3 77.0 - - - +
132E VAL* 1.3 77.9 + - + +
134E TYR* 3.6 1.0 - - - +
135E HIS* 3.1 44.1 + - + +
140E VAL* 6.3 0.4 - - + -
148E LEU* 5.4 3.1 - - + -
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Residues in contact with VAL 132 (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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128E LEU* 2.8 24.6 + - + +
129E ASN* 3.7 7.0 - - - +
131E LEU* 1.3 87.8 - - + +
133E ASP* 1.3 67.9 + - - +
135E HIS 3.1 10.6 + - - -
136E ARG* 3.4 34.6 + - - +
148E LEU* 3.6 24.5 - - + +
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Residues in contact with ASP 133 (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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129E ASN* 3.0 33.8 + - - +
130E GLU* 4.1 5.5 - - - +
132E VAL* 1.3 78.2 - - - +
134E TYR* 1.3 63.2 + - - +
136E ARG* 2.9 50.2 + - - +
137E SER* 4.4 2.6 + - - -
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Residues in contact with TYR 134 (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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123E VAL* 3.7 34.1 - - + +
125E PHE* 3.3 33.0 - + + -
130E GLU 3.0 18.4 + - - +
131E LEU 3.6 1.3 - - - +
133E ASP* 1.3 76.6 - - - +
135E HIS* 1.3 77.0 + + - +
136E ARG 3.1 4.7 + - - -
137E SER* 3.2 19.0 + - - -
138E THR* 3.2 48.0 + - + +
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Residues in contact with HIS 135 (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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125E PHE* 4.0 10.5 - + - -
131E LEU* 3.1 45.8 + - + +
132E VAL 3.1 3.2 + - - -
134E TYR* 1.3 98.2 - + - +
136E ARG* 1.3 60.0 + - - +
137E SER 3.1 1.6 - - - -
138E THR* 3.0 28.8 + - + +
139E SER 3.3 20.3 + - - -
140E VAL* 3.6 25.8 - - + +
147E PHE* 3.7 3.1 - - - -
148E LEU* 2.9 31.5 + - + +
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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