Contacts of the helix formed by residues 130 - 141 (chain E) in PDB entry 1XFB
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 GLY 130 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128E LEU 3.1 0.2 + - - -
129E ASP* 1.3 70.7 - - - +
131E LEU* 1.3 64.6 + - - +
132E SER 3.2 3.1 - - - -
133E GLU* 3.1 23.1 + - - +
134E ARG* 3.1 26.9 + - - +
126F GLN* 3.1 22.1 + - - +
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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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109E VAL* 3.6 33.4 - - + +
127E GLY 3.7 7.0 - - - +
128E LEU* 3.1 22.2 + - + +
129E ASP 3.1 4.0 + - - -
130E GLY* 1.3 75.8 - - - +
132E SER* 1.3 58.6 + - - +
134E ARG* 3.5 21.6 - - + +
135E CYS* 2.8 44.1 + - - -
148E TRP* 4.4 3.6 - - + -
174E TYR* 4.0 29.6 - - + +
177E ILE* 4.0 30.1 - - + -
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Residues in contact with SER 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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130E GLY 3.2 0.8 - - - -
131E LEU* 1.3 78.5 - - - +
133E GLU* 1.3 74.6 + - - +
135E CYS 3.3 0.7 + - - -
136E ALA* 3.0 20.6 + - - +
177E ILE* 3.5 20.7 - - - +
180E GLN* 3.5 15.1 + - - -
181E ASN* 2.9 30.4 + - - +
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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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130E GLY* 3.3 27.0 - - - +
132E SER* 1.3 85.1 + - - +
134E ARG* 1.3 65.2 + - + +
136E ALA* 3.3 9.2 + - - +
137E GLN* 3.0 23.8 + - - +
126F GLN* 5.2 3.5 + - - +
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Residues in contact with ARG 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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108E LYS 4.5 1.2 + - - -
109E VAL* 3.0 41.7 + - - +
110E ASP 5.1 0.4 + - - -
111E LYS* 3.7 24.7 - - - +
127E GLY 3.4 20.0 + - - -
129E ASP 4.4 3.6 - - - -
130E GLY 3.1 19.0 + - - +
131E LEU* 3.5 16.6 - - + +
133E GLU* 1.3 75.4 - - + +
135E CYS* 1.3 60.4 + - - +
137E GLN* 3.1 9.0 + - - +
138E TYR* 2.8 63.0 + - + +
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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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107E ILE* 6.5 0.2 - - - -
109E VAL* 5.1 7.4 - - - -
131E LEU* 2.8 49.2 + - - +
132E SER 3.7 4.0 - - - +
134E ARG* 1.3 70.2 - - - +
136E ALA* 1.3 68.3 + - - +
137E GLN 3.0 0.3 + - - -
138E TYR* 3.0 5.6 + - - +
139E LYS* 2.8 26.5 + - - +
177E ILE* 4.8 0.2 - - - -
178E CYS* 4.0 29.4 - - - -
181E ASN* 3.7 20.2 - - + +
183E ILE* 3.6 17.1 - - + +
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Residues in contact with ALA 136 (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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132E SER 3.0 10.2 + - - +
133E GLU* 3.4 12.3 - - - +
135E CYS* 1.3 77.2 - - - +
137E GLN* 1.3 55.8 + - - +
139E LYS* 3.6 6.4 + - - +
140E LYS* 3.1 37.4 + - - +
181E ASN* 3.5 19.9 + - - +
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Residues in contact with GLN 137 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85E TYR* 4.6 1.9 + - - +
133E GLU 3.0 13.9 + - - +
134E ARG* 3.3 11.2 - - - +
135E CYS 3.0 0.2 - - - -
136E ALA* 1.3 73.9 - - - +
138E TYR* 1.3 70.8 + - + +
140E LYS* 2.9 37.1 + - - +
141E ASP* 2.9 51.5 + - - +
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Residues in contact with TYR 138 (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 HIS* 2.6 45.4 + + - +
84E LEU* 3.7 15.4 - - + +
85E TYR* 3.6 16.4 - - - -
107E ILE* 3.8 34.7 - - + +
108E LYS 4.9 1.5 + - - -
109E VAL* 4.0 22.4 - - + -
134E ARG* 2.8 58.1 + - + +
135E CYS* 3.6 6.7 - - - +
137E GLN* 1.3 75.3 - - + +
139E LYS* 1.3 62.9 + - - +
141E ASP* 2.9 14.0 + - - +
142E GLY 3.2 0.9 + - - -
143E ALA* 3.0 23.0 + - + +
183E ILE* 4.5 2.0 - - + -
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Residues in contact with LYS 139 (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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15E GLU* 2.9 28.8 + - - -
19E ILE* 3.7 5.9 - - - +
135E CYS 2.8 19.9 + - - +
136E ALA* 3.6 6.5 - - - +
138E TYR* 1.3 72.8 - - - +
140E LYS* 1.3 58.8 + - - +
142E GLY* 2.9 21.5 + - - -
143E ALA 3.2 21.4 + - - +
144E ASP* 2.9 22.2 + - - +
181E ASN 4.0 10.5 - - - +
182E GLY* 2.7 32.6 + - - +
183E ILE* 3.9 8.9 - - + +
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Residues in contact with LYS 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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136E ALA* 3.1 18.7 + - - +
137E GLN* 2.9 36.8 + - - +
139E LYS* 1.3 79.5 - - - +
141E ASP* 1.3 63.9 + - - +
142E GLY 3.4 0.6 + - - -
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Residues in contact with ASP 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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84E LEU* 4.7 8.0 - - + +
85E TYR* 2.6 43.4 + - + +
95E VAL* 3.8 20.3 - - - +
137E GLN* 2.9 31.5 + - - +
138E TYR* 2.9 12.4 + - - +
140E LYS* 1.3 87.0 - - - +
142E GLY* 1.3 55.8 + - - +
143E ALA 3.7 0.2 - - - -
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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