Contacts of the helix formed by residues 115 - 126 (chain A) in PDB entry 1SIW
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 LYS 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A MET 3.2 1.0 + - - -
114A ARG* 1.3 70.9 - - - +
116A ARG* 1.3 58.3 + - - +
118A MET* 3.1 10.7 + - + +
119A LYS* 2.8 37.9 + - + +
156A GLY* 2.7 25.2 + - - +
158A VAL* 3.8 24.0 - - + -
116B GLU* 4.1 33.9 + - + +
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Residues in contact with ARG 116 (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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114A ARG* 3.3 8.3 - - + +
115A LYS* 1.3 79.4 - - - +
117A LEU* 1.3 63.3 + - - +
119A LYS* 3.3 33.5 + - - +
120A MET* 3.1 45.3 + - + +
123A GLU* 5.7 0.2 + - - -
143A ASP 5.1 0.8 + - - -
144A LYS* 5.0 7.3 - - - +
147A SER* 2.9 56.7 + - - +
148A PHE* 4.0 4.9 - - + -
151A ALA* 4.8 4.7 - - + -
116B GLU* 3.8 18.8 + - - +
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Residues in contact with LEU 117 (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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113A MET* 4.1 18.8 - - + -
114A ARG* 3.0 16.0 + - + +
116A ARG* 1.3 78.4 - - - +
118A MET* 1.3 57.9 + - - +
120A MET* 3.6 9.9 + - + -
121A TRP* 2.9 27.0 + - - +
135A TRP* 4.3 14.4 - - + -
138A ILE* 4.9 7.6 - - + -
148A PHE* 3.8 41.1 - - + +
168A LEU* 4.3 12.3 - - + -
767A LEU* 4.1 14.8 - - + -
783A ASP* 3.9 27.6 - - + +
784A ILE* 4.7 1.1 - - + -
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Residues in contact with MET 118 (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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113A MET* 3.6 24.2 - - + +
114A ARG 3.0 9.9 + - - +
115A LYS* 3.5 19.3 - - + +
117A LEU* 1.3 75.6 - - - +
119A LYS* 1.3 67.3 + - - +
121A TRP* 3.2 3.2 + - - +
122A ARG* 3.0 71.9 + - - +
158A VAL* 3.6 39.9 - - + -
159A ARG 4.5 5.6 - - - +
160A SER* 5.2 3.6 - - - -
164A GLU* 4.4 5.2 - - - +
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Residues in contact with LYS 119 (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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115A LYS* 2.8 25.0 + - + +
116A ARG* 3.6 32.5 - - - +
118A MET* 1.3 81.2 - - - +
120A MET* 1.3 62.2 + - - +
122A ARG* 3.6 3.9 + - - +
123A GLU* 3.1 53.1 + - + +
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Residues in contact with MET 120 (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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116A ARG* 3.1 48.8 + - + +
117A LEU* 4.1 4.7 - - - +
119A LYS* 1.3 73.8 - - - +
121A TRP* 1.3 60.8 + - - +
123A GLU* 3.8 12.3 - - - +
124A ALA* 2.9 32.2 + - - +
138A ILE* 3.5 20.6 - - + +
144A LYS* 3.5 41.1 - - - +
147A SER* 3.3 27.8 - - - +
148A PHE* 3.7 20.4 - - + -
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Residues in contact with TRP 121 (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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113A MET* 4.9 1.8 - - + -
117A LEU* 2.9 20.3 + - + +
118A MET* 3.2 6.9 + - - +
120A MET* 1.3 77.2 - - - +
122A ARG* 1.3 58.3 + - + +
124A ALA* 3.3 2.4 + - - +
125A LYS* 2.9 56.5 + - + +
131A PRO* 3.7 20.2 - - + -
134A ALA* 4.1 6.7 - - + -
135A TRP* 3.8 33.7 - + + -
138A ILE* 3.7 16.3 - - + +
164A GLU* 3.7 41.0 + - + +
167A GLU* 3.8 13.7 + - + -
168A LEU* 3.7 53.6 - - + +
171A ALA* 4.0 7.4 - - + -
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Residues in contact with ARG 122 (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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118A MET* 3.0 52.0 + - - +
119A LYS* 4.2 4.0 - - - +
121A TRP* 1.3 74.7 - - + +
123A GLU* 1.3 64.5 + - + +
125A LYS* 3.8 9.1 + - + +
126A ALA* 3.3 20.8 + - - +
159A ARG 5.0 5.1 + - - -
160A SER* 4.9 1.8 + - - +
164A GLU* 2.6 44.5 + - - +
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Residues in contact with GLU 123 (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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116A ARG* 5.7 0.2 + - - -
119A LYS* 3.1 50.0 + - + +
120A MET* 3.9 15.0 - - - +
122A ARG* 1.3 76.5 - - + +
124A ALA* 1.3 64.9 + - - +
126A ALA* 3.4 14.0 + - - +
127A LEU* 3.5 20.1 + - - +
144A LYS* 5.4 4.3 + - - -
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Residues in contact with ALA 124 (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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120A MET 2.9 18.7 + - - +
121A TRP 3.6 4.5 - - - +
123A GLU* 1.3 75.7 - - - +
125A LYS* 1.3 60.1 + - - +
127A LEU* 3.0 4.6 + - - -
128A HIS* 2.8 36.1 + - - +
134A ALA* 3.6 28.7 - - + +
137A SER* 3.6 11.7 - - - +
138A ILE* 3.9 10.3 - - + -
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Residues in contact with LYS 125 (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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121A TRP* 2.9 55.8 + - + +
122A ARG* 4.1 8.7 - - + +
123A GLU 3.4 0.2 - - - -
124A ALA* 1.3 76.1 - - - +
126A ALA* 1.3 62.2 + - - +
128A HIS 3.0 24.0 + - - +
129A SER* 4.1 11.4 + - - -
131A PRO* 5.0 4.1 - - + +
134A ALA* 4.0 9.9 - - + -
164A GLU* 5.8 0.4 - - - +
167A GLU* 2.6 32.2 + - - +
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Residues in contact with ALA 126 (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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122A ARG 3.3 15.9 + - - +
123A GLU* 3.5 10.1 - - - +
124A ALA 3.1 0.8 - - - -
125A LYS* 1.3 78.2 - - - +
127A LEU* 1.3 66.6 + - + +
128A HIS 3.6 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