Contacts of the helix formed by residues 130 - 139 (chain D) in PDB entry 1FBA
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 LEU 130 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108D VAL* 3.7 32.8 - - + -
126D GLY 3.8 19.1 - - - +
127D LEU* 3.1 17.5 + - + +
128D ASP 3.1 3.1 - - - -
129D ASP* 1.3 77.8 - - - +
131D ALA* 1.3 52.6 + - - +
133D ARG* 3.1 16.7 + - + +
134D CYS* 2.8 45.6 + - - +
147D TRP* 4.5 5.2 - - + -
173D TYR* 4.3 28.9 - - + +
176D ILE* 3.7 32.1 - - + +
177D CYS* 4.9 0.2 - - - -
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Residues in contact with ALA 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C VAL* 6.5 1.8 - - + -
129D ASP 3.3 1.0 - - - -
130D LEU* 1.3 75.9 - - - +
132D ALA* 1.3 58.8 + - - +
135D ALA* 3.0 26.5 + - - +
176D ILE* 3.4 22.1 - - + +
179D SER* 5.0 1.3 - - - +
180D GLN* 3.4 31.8 - - - +
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Residues in contact with ALA 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ASP* 3.2 16.0 + - + +
131D ALA* 1.3 75.5 - - - +
133D ARG* 1.3 64.3 + - - +
135D ALA* 3.5 7.4 + - - +
136D GLN* 3.2 22.0 + - - +
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Residues in contact with ARG 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D HIS* 5.0 2.4 + - - +
107D LYS 4.3 3.2 + - - -
108D VAL* 2.9 36.8 + - - +
109D ASP 5.5 0.6 + - - -
110D LYS* 4.0 25.7 - - - +
126D GLY 4.3 2.8 + - - -
128D ASP 4.4 11.0 - - - -
129D ASP* 3.0 23.5 + - + +
130D LEU* 3.1 19.7 + - + +
132D ALA* 1.3 75.8 - - + +
134D CYS* 1.3 57.3 + - - +
136D GLN* 3.3 7.1 + - - +
137D TYR* 2.9 73.7 + - + -
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Residues in contact with CYS 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D ILE* 6.4 0.4 - - - -
108D VAL* 4.8 9.9 - - - -
130D LEU* 2.8 39.2 + - - +
131D ALA 3.6 4.7 - - - +
133D ARG* 1.3 75.3 - - - +
135D ALA* 1.3 58.4 + - - +
137D TYR* 3.2 7.6 + - - +
138D LYS* 2.9 31.9 + - - +
176D ILE* 4.9 0.4 - - - -
177D CYS* 4.1 28.5 - - - -
180D GLN* 3.8 20.9 - - + -
182D ILE* 4.2 15.6 - - + +
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Residues in contact with ALA 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ALA 3.0 16.3 + - - +
132D ALA* 3.8 8.1 - - - +
133D ARG 3.4 0.2 - - - -
134D CYS* 1.3 76.5 - - - +
136D GLN* 1.3 61.2 + - - +
138D LYS* 3.5 6.0 + - - +
139D LYS* 3.2 34.3 + - - +
180D GLN* 3.6 19.9 - - - +
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Residues in contact with GLN 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D TYR* 4.3 5.8 - - - +
132D ALA 3.2 11.0 + - - +
133D ARG* 3.6 9.4 - - - +
134D CYS 3.2 0.6 - - - -
135D ALA* 1.3 76.3 - - - +
137D TYR* 1.3 61.2 + - + +
139D LYS* 3.2 24.5 + - - +
140D ASP* 2.9 61.2 + - - +
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Residues in contact with TYR 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D HIS* 2.5 44.6 + + - +
83D LEU* 3.7 19.5 - - + -
84D TYR* 3.9 9.4 - - - -
106D ILE* 3.7 46.2 - - + +
107D LYS 4.8 0.3 + - - -
108D VAL* 3.9 11.7 - - + -
133D ARG* 2.9 66.5 + - + +
134D CYS* 3.2 8.0 + - - +
136D GLN* 1.3 78.3 - - + +
138D LYS* 1.3 59.5 + - - +
140D ASP* 3.2 11.5 + - - +
141D GLY 3.2 1.2 + - - -
142D CYS* 2.9 28.4 + - + +
182D ILE* 5.0 2.5 - - + -
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Residues in contact with LYS 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D GLU* 2.9 26.7 + - - -
18D ILE* 4.0 4.9 - - - +
134D CYS 2.9 16.8 + - - +
135D ALA* 3.7 6.7 - - - +
137D TYR* 1.3 72.4 - - - +
139D LYS* 1.3 67.4 - - - +
141D GLY* 3.0 15.4 + - - -
142D CYS 3.4 20.1 + - - +
143D ASP* 2.9 23.2 + - - +
180D GLN 4.0 11.0 - - - +
181D ARG* 2.8 57.6 + - + +
182D ILE* 4.0 6.7 - - + +
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Residues in contact with LYS 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D ALA* 3.2 20.6 + - - +
136D GLN* 3.3 25.7 + - - +
138D LYS* 1.3 80.7 - - - +
140D ASP* 1.3 64.1 + - - +
141D GLY 3.4 2.8 + - - -
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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