Contacts of the helix formed by residues 126 - 138 (chain B) in PDB entry 3ISL
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 ASP 126 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B VAL 3.8 0.8 + - - -
125B PHE* 1.3 74.9 - - - +
127B PRO* 1.4 76.3 - - - +
128B GLU* 2.9 28.6 + - - +
129B ASP* 3.0 36.7 + - - +
130B ILE 3.7 2.6 + - - -
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Residues in contact with PRO 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B PHE 3.5 8.7 - - - +
126B ASP* 1.4 86.8 - - - +
128B GLU* 1.3 56.0 + - - +
130B ILE* 2.9 10.2 + - + +
131B ILE* 2.9 31.1 + - + +
155B HIS* 4.8 1.6 - - - +
156B PRO* 4.5 32.1 - - + +
159B ALA* 4.3 20.9 - - + -
160B ILE* 4.0 25.4 - - + +
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ASP* 2.9 22.3 + - - +
127B PRO* 1.3 78.9 - - - +
129B ASP* 1.3 61.8 + - - +
131B ILE* 4.0 23.5 - - - +
132B ARG* 3.0 46.0 + - - +
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Residues in contact with ASP 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LEU* 4.3 6.9 - - + +
125B PHE* 5.1 12.6 - - + -
126B ASP* 3.0 29.3 + - - +
128B GLU* 1.3 77.8 - - - +
130B ILE* 1.3 61.9 + - - +
132B ARG* 3.0 36.3 + - - +
133B GLU* 3.3 21.7 + - - +
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Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU* 4.1 5.6 - - + +
94B PRO* 3.7 31.4 - - + -
117B LEU* 3.9 20.9 - - + -
125B PHE* 3.5 36.6 - - + -
126B ASP 3.7 2.2 + - - +
127B PRO 2.9 8.6 + - - +
129B ASP* 1.3 75.7 - - - +
131B ILE* 1.3 60.4 + - - +
133B GLU* 3.1 4.9 + - - +
134B ILE* 2.9 44.2 + - + +
142B VAL* 4.9 1.6 - - + -
144B MET* 4.0 4.9 - - + -
155B HIS* 4.0 1.1 - - - +
160B ILE* 3.8 35.0 - - + -
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B PRO 2.9 22.6 + - - +
128B GLU* 4.0 26.0 - - - +
130B ILE* 1.3 75.7 - - - +
132B ARG* 1.3 62.3 + - - +
134B ILE* 3.1 11.2 + - + +
135B LYS* 3.0 24.6 + - + +
159B ALA* 3.9 34.3 - - + +
160B ILE* 4.3 11.2 - - + -
163B ALA* 3.7 27.8 - - + -
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Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B GLU* 3.0 37.4 + - - +
129B ASP* 3.0 40.5 + - - +
130B ILE 3.3 0.4 - - - -
131B ILE* 1.3 77.8 - - - +
133B GLU* 1.3 61.5 + - - +
135B LYS* 2.8 41.7 + - + +
136B LYS* 3.0 14.6 + - + +
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Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU* 3.8 27.0 - - + +
115B HIS* 5.5 2.9 - - - +
116B MET 5.4 1.7 - - - +
117B LEU* 3.9 29.0 - - + +
129B ASP 3.3 11.0 + - - +
130B ILE 3.1 9.4 + - - +
132B ARG* 1.3 81.3 - - - +
134B ILE* 1.3 57.3 + - - +
136B LYS* 2.9 39.3 + - - +
137B VAL* 2.9 44.6 + - + +
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Residues in contact with ILE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU* 3.6 19.1 - - + -
130B ILE* 2.9 32.9 + - + +
131B ILE* 3.1 14.6 + - - +
133B GLU* 1.3 74.8 - - - +
135B LYS* 1.3 55.6 - - - +
138B LYS* 2.8 33.1 + - - +
139B PRO* 4.1 12.1 - - + -
142B VAL* 3.9 9.2 - - + -
160B ILE* 4.2 12.3 - - + +
163B ALA* 4.4 13.7 - - + +
164B CYS* 3.9 28.0 - - - -
167B GLU* 3.8 26.6 - - + +
169B ALA* 4.9 2.0 - - + -
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Residues in contact with LYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ILE* 3.0 17.6 + - + +
132B ARG* 2.8 45.7 + - + +
134B ILE* 1.3 77.6 - - - +
136B LYS* 1.3 73.8 + - - +
138B LYS* 3.1 34.9 + - - +
167B GLU* 4.1 21.1 - - - +
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Residues in contact with LYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ARG* 3.0 18.6 + - + +
133B GLU* 2.9 40.3 + - - +
135B LYS* 1.3 92.2 - - - +
137B VAL* 1.3 65.9 + - + +
138B LYS* 4.2 8.2 + - - +
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Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ASP* 4.2 9.4 - - + +
92B LEU* 4.8 3.1 - - + -
115B HIS* 3.9 48.0 - - + +
133B GLU* 2.9 44.1 + - + +
136B LYS* 1.3 78.7 - - + +
138B LYS* 1.3 69.8 + - - +
139B PRO* 3.7 22.9 - - + -
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Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ASP* 4.5 4.3 - - - +
134B ILE 2.8 17.8 + - - +
135B LYS* 3.1 25.4 + - - +
136B LYS* 4.2 7.2 + - - +
137B VAL* 1.3 75.9 - - - +
139B PRO* 1.4 69.8 - - - +
140B LYS 3.8 0.5 + - - -
167B GLU* 3.6 31.9 - - + +
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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