Contacts of the helix formed by residues 127 - 135 (chain A) in PDB entry 1B3U
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 PHE 127 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 4.2 19.9 - - + +
111A LEU* 3.7 19.3 - - + -
114A ILE* 5.4 0.2 - - + -
115A SER* 3.6 28.3 - - - -
118A HIS* 4.2 19.2 + + - +
122A ASP 3.2 2.0 + - - -
123A LEU* 2.9 33.5 + - + +
126A HIS* 1.3 76.2 - - - +
128A VAL* 1.3 62.4 + - - +
130A LEU* 3.2 10.2 + - + +
131A VAL* 3.1 43.5 + - + +
149A LEU* 3.9 25.8 - - + -
152A VAL* 4.0 8.1 - - + -
153A CYS* 3.5 30.3 - - + -
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Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 2.7 26.6 + - + +
124A GLU* 4.1 7.0 - - - +
127A PHE* 1.3 69.1 - - - +
129A PRO* 1.3 74.8 - - + +
131A VAL* 3.0 9.5 + - + +
132A LYS* 2.8 53.6 + - + +
153A CYS* 4.9 12.8 - - - -
157A VAL* 4.5 8.3 - - + -
161A VAL* 4.0 27.6 - - + -
165A LEU* 4.6 13.5 - - + -
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Residues in contact with PRO 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLU 3.4 16.4 - - - +
125A ALA 3.7 17.3 - - - +
126A HIS* 3.3 15.0 - - - +
128A VAL* 1.3 96.9 - - + +
130A LEU* 1.3 55.1 - - - +
132A LYS* 3.3 9.9 + - + +
133A ARG* 2.9 48.1 + - + +
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Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 4.1 24.2 - - + +
93A GLU* 3.0 49.6 - - + +
111A LEU* 4.0 35.0 - - + -
126A HIS 3.4 9.8 + - - +
127A PHE* 3.2 17.9 + - + +
128A VAL 3.1 0.6 - - - -
129A PRO* 1.3 76.8 - - - +
131A VAL* 1.3 66.6 + - - +
133A ARG* 3.2 14.6 + - - +
134A LEU* 3.0 35.7 + - + +
149A LEU* 5.0 4.0 - - + -
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A PHE* 3.2 41.1 - - + +
128A VAL* 3.0 9.4 + - - +
130A LEU* 1.3 77.5 - - + +
132A LYS* 1.3 58.6 + - + +
134A LEU* 3.4 5.0 + - - +
135A ALA* 2.9 28.8 + - + +
146A ALA* 4.2 3.9 - - + +
149A LEU* 4.1 22.9 - - + -
150A PHE* 4.1 37.7 - - + -
153A CYS* 4.4 5.8 - - - -
165A LEU* 4.8 11.0 - - + -
168A TYR* 6.2 1.1 - - + -
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Residues in contact with LYS 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A VAL* 2.8 41.9 + - + +
129A PRO* 3.6 8.7 - - + +
131A VAL* 1.3 77.9 - - + +
133A ARG* 1.3 63.4 + - + +
135A ALA* 3.3 2.8 + - - +
136A GLY* 3.0 20.3 + - - -
161A VAL* 5.5 0.2 - - - +
164A GLU* 3.1 33.8 + - - +
165A LEU* 5.9 3.0 - - + +
168A TYR* 3.3 57.3 - - + +
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Residues in contact with ARG 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 5.6 4.8 - - - +
90A PRO* 6.0 2.4 - - - +
93A GLU* 2.6 41.0 + - - +
126A HIS 5.3 1.4 + - - -
129A PRO* 2.9 44.6 + - + +
130A LEU* 3.2 22.6 + - - +
132A LYS* 1.3 77.6 - - + +
134A LEU* 1.3 63.3 + - + +
136A GLY* 3.1 4.8 + - - -
137A GLY* 3.0 20.8 + - - -
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A GLU* 4.0 25.8 - - + +
96A ALA* 4.9 11.0 - - + +
97A THR* 4.3 11.0 - - - +
111A LEU* 5.1 2.5 - - + -
130A LEU* 3.0 32.4 + - + +
131A VAL 3.9 1.1 - - - +
133A ARG* 1.3 78.1 - - - +
135A ALA* 1.3 61.9 + - - +
137A GLY 3.1 10.7 + - - -
142A SER* 3.3 49.1 - - - +
143A ARG 3.4 1.4 + - - -
145A SER* 4.8 7.0 - - - -
146A ALA* 3.8 13.0 - - + +
149A LEU* 3.6 31.0 - - + -
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Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A VAL 2.9 18.8 + - - +
132A LYS 3.8 3.8 - - - +
134A LEU* 1.3 76.8 - - - +
136A GLY* 1.3 57.2 + - - +
137A GLY 3.4 0.2 - - - -
143A ARG* 3.1 25.8 - - - +
146A ALA* 3.6 15.8 - - + +
150A PHE* 4.8 4.3 - - + -
168A TYR* 4.0 21.8 - - + +
172A LEU* 4.1 22.0 - - + +
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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