Contacts of the helix formed by residues 120 - 135 (chain E) in PDB entry 4P9U
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 120 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116E ALA 3.1 12.3 + - - +
119E LEU* 1.3 86.7 - - - +
121E LYS* 1.3 64.3 + - - +
122E GLU 3.5 1.8 - - - -
123E SER* 4.0 22.1 + - - +
124E ALA* 3.0 16.1 + - - +
195E HIS* 3.6 43.0 + - + +
197E GLY* 5.2 4.4 - - - +
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Residues in contact with LYS 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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116E ALA 3.7 2.8 + - - -
117E PHE 3.4 24.6 + - - +
118E LYS 4.6 4.5 - - - +
119E LEU 3.5 4.0 + - - -
120E ASN* 1.3 72.2 - - - +
122E GLU* 1.3 72.7 + - - +
124E ALA* 3.0 8.1 - - - +
125E GLU* 2.9 54.4 + - - +
240E CYS* 3.1 14.2 + - - +
241E GLN 4.2 13.1 + - - -
243E GLY* 6.1 1.7 - - - -
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Residues in contact with GLU 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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121E LYS* 1.3 89.7 - - + +
123E SER* 1.3 60.1 + - - +
125E GLU* 3.2 32.2 - - + +
126E ARG* 3.0 27.6 + - - +
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Residues in contact with SER 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E ASN* 3.6 16.7 + - - +
121E LYS 3.5 0.4 - - - -
122E GLU* 1.3 74.2 - - - +
124E ALA* 1.3 64.5 + - - +
126E ARG* 3.0 31.1 - - - +
127E ILE* 3.1 17.8 + - - +
195E HIS* 3.5 30.2 - - - -
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Residues in contact with ALA 124 (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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116E ALA* 4.0 4.7 - - + +
117E PHE* 3.9 23.1 - - + -
120E ASN 3.0 14.5 + - - +
121E LYS 3.0 15.0 - - - +
123E SER* 1.3 79.3 - - - +
125E GLU* 1.3 61.2 + - - +
127E ILE* 3.2 2.0 - - - +
128E MET* 2.9 30.8 + - - +
192E LEU* 3.7 26.5 - - + -
195E HIS* 4.9 3.3 - - + -
240E CYS* 4.0 0.4 - - - -
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Residues in contact with GLU 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E LYS* 2.9 35.2 + - - +
122E GLU* 3.2 31.8 - - + +
123E SER 3.5 0.2 - - - -
124E ALA* 1.3 71.7 - - - +
126E ARG* 1.3 57.1 + - - +
128E MET* 3.8 2.0 - - - +
129E ILE* 2.9 41.2 + - + +
237E LEU* 4.0 16.2 - - + -
240E CYS* 3.4 11.6 - - + +
241E GLN* 3.1 45.1 + - + +
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Residues in contact with ARG 126 (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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122E GLU 3.0 22.2 + - - +
123E SER* 3.0 35.7 + - - +
125E GLU* 1.3 77.2 - - - +
127E ILE* 1.3 77.7 + - - +
129E ILE* 3.9 5.4 - - - +
130E ASN* 2.9 29.0 + - - +
195E HIS* 5.1 5.1 + - - -
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Residues in contact with ILE 127 (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 SER 3.1 20.1 + - - +
124E ALA* 3.2 9.9 - - - +
126E ARG* 1.3 97.7 - - - +
128E MET* 1.3 57.8 + - + +
130E ASN* 3.4 8.6 - - - +
131E VAL* 2.9 34.5 + - + +
187E MET* 5.7 1.3 - - + +
188E LEU* 5.0 3.1 - - + +
191E ARG* 3.6 54.3 - - + +
192E LEU* 3.8 26.2 - - + +
195E HIS* 4.6 12.8 - - + +
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Residues in contact with MET 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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117E PHE* 3.8 28.3 - - - -
124E ALA 2.9 26.9 + - - +
125E GLU 3.8 3.1 - - - +
127E ILE* 1.3 75.4 - - + +
129E ILE* 1.3 60.3 + - - +
131E VAL* 3.1 7.6 + - - +
132E ILE* 2.9 34.9 + - + +
188E LEU* 4.7 11.6 - - + +
192E LEU* 4.0 20.6 - - + -
233E TYR 3.6 8.7 - - - +
236E LEU* 3.4 22.2 - - + +
237E LEU* 3.2 45.8 - - + +
240E CYS* 4.6 3.4 - - - -
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Residues in contact with ILE 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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125E GLU* 2.9 25.9 + - + +
126E ARG* 3.9 4.7 - - - +
128E MET* 1.3 75.2 - - - +
130E ASN* 1.3 63.4 + - - +
132E ILE* 3.2 8.6 + - + +
133E GLU* 2.9 40.4 + - + +
237E LEU* 3.6 30.1 - - + -
241E GLN* 4.5 8.7 - - - +
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Residues in contact with ASN 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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126E ARG 2.9 19.3 + - - +
127E ILE* 3.4 10.5 - - + +
129E ILE* 1.3 78.0 - - - +
131E VAL* 1.3 58.0 + - - +
133E GLU* 4.2 6.0 - - - +
134E SER* 2.9 45.1 + - - -
184E TYR* 4.5 4.2 - - - -
187E MET* 4.2 20.0 - - - +
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Residues in contact with VAL 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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127E ILE* 2.9 20.3 + - + +
128E MET 3.4 7.2 - - - +
130E ASN* 1.3 78.1 - - - +
132E ILE* 1.3 58.4 + - - +
134E SER* 3.3 2.1 + - - -
135E CYS* 2.8 36.4 + - - +
184E TYR* 3.8 37.2 - - + +
187E MET* 4.6 11.9 - - + -
188E LEU* 3.7 38.6 - - + +
191E ARG* 6.2 0.4 - - - -
233E TYR* 4.1 19.3 - - + -
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Residues in contact with ILE 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 MET* 2.9 20.2 + - + +
129E ILE* 3.8 4.9 - - - +
131E VAL* 1.3 75.7 - - + +
133E GLU* 1.3 61.2 + - - +
135E CYS* 3.2 13.5 + - - +
136E GLU* 2.9 27.1 - - - +
230E MET* 5.0 4.4 - - + +
233E TYR* 3.6 46.2 - - + +
234E ARG* 3.9 34.3 - - + +
237E LEU* 4.0 23.1 - - + -
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Residues in contact with GLU 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 ILE* 2.9 29.5 + - + +
130E ASN* 4.6 5.0 - - - +
132E ILE* 1.3 72.8 - - - +
134E SER* 1.3 68.9 + - - +
135E CYS 3.1 1.3 - - - -
136E GLU* 3.3 26.1 + - + +
147E PHE* 4.4 25.2 - - + -
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Residues in contact with SER 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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130E ASN* 2.9 31.7 + - - -
131E VAL 3.6 1.3 - - - -
133E GLU* 1.3 76.2 - - - +
135E CYS* 1.3 57.4 + - - +
136E GLU 3.0 9.0 + - - -
137E ALA* 4.0 1.0 + - - +
144E TRP* 3.1 34.0 - - - -
147E PHE* 4.9 7.6 - - - -
148E ILE* 5.2 4.4 - - - +
184E TYR* 3.4 41.0 + - - -
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Residues in contact with CYS 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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131E VAL* 2.8 28.5 + - - +
132E ILE* 3.4 10.1 - - - +
133E GLU 3.1 1.2 - - - -
134E SER* 1.3 75.5 - - - +
136E GLU* 1.3 64.9 + - - +
137E ALA* 3.1 7.4 - - - +
138E LEU* 3.2 21.3 - - - +
181E PHE* 3.8 33.9 - - + -
184E TYR* 3.8 28.9 - - - -
230E MET* 3.4 12.1 - - + +
233E TYR* 4.3 5.6 - - + -
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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