Contacts of the helix formed by residues 130 - 140 (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 ASP 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A HIS* 3.2 5.5 - - - +
129A SER* 1.3 82.2 + - - +
131A PRO* 1.3 74.2 - - - +
132A VAL* 2.8 21.7 + - - +
133A GLU* 3.0 35.5 + - - +
134A ALA 3.0 16.6 + - - -
836A VAL* 5.1 1.4 - - - +
840A HIS* 2.8 25.8 + - - -
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Residues in contact with PRO 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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121A TRP* 3.7 6.8 - - + -
125A LYS* 5.0 4.0 - - + +
128A HIS 5.1 0.4 - - - +
129A SER 3.5 8.9 - - - +
130A ASP* 1.3 88.0 - - - +
132A VAL* 1.3 56.5 + - - +
134A ALA* 3.6 9.1 - - + +
135A TRP* 2.9 23.6 + - - +
167A GLU* 3.7 41.3 - - + +
171A ALA* 3.4 18.2 - - + +
836A VAL* 3.9 23.6 - - + -
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Residues in contact with VAL 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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130A ASP* 2.8 13.4 + - - +
131A PRO* 1.3 73.1 - - - +
133A GLU* 1.3 56.9 + - + +
135A TRP* 3.5 4.0 + - - +
136A ALA* 3.1 23.4 + - - +
171A ALA* 4.1 9.4 - - - +
174A VAL* 3.8 16.2 - - + -
175A TYR* 4.1 29.6 - - + -
178A LYS* 5.4 4.0 - - + -
836A VAL* 3.7 26.5 - - + -
840A HIS* 3.7 41.7 - - + +
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Residues in contact with GLU 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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128A HIS* 4.0 22.2 + - + +
129A SER* 5.2 1.6 + - - -
130A ASP* 3.0 40.1 + - + +
132A VAL* 1.3 74.6 - - + +
134A ALA* 1.3 66.7 + - - +
135A TRP 3.2 0.2 - - - -
136A ALA* 3.2 8.9 + - + +
137A SER* 3.0 23.2 + - - -
840A HIS* 4.4 10.7 - - + -
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Residues in contact with ALA 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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121A TRP* 4.1 11.4 - - + -
124A ALA* 3.6 31.6 - - + +
125A LYS* 3.9 10.5 - - + +
128A HIS* 3.7 13.6 - - + +
130A ASP 3.0 12.5 + - - +
131A PRO* 3.3 12.8 + - + +
133A GLU* 1.3 78.1 - - - +
135A TRP* 1.3 59.8 + - - +
137A SER* 2.7 23.2 + - - -
138A ILE* 3.4 6.4 + - - +
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Residues in contact with TRP 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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117A LEU* 4.3 19.1 - - + -
121A TRP* 3.8 18.1 - + + -
131A PRO 2.9 15.7 + - - +
132A VAL* 3.7 4.7 - - - +
133A GLU 3.2 0.2 - - - -
134A ALA* 1.3 75.1 - - - +
136A ALA* 1.3 64.1 + - - +
138A ILE* 3.1 12.6 + - + +
139A ILE* 3.0 54.2 + - + +
148A PHE* 4.2 5.4 - + - -
168A LEU* 4.0 24.5 - - + -
171A ALA* 4.4 7.4 - - + -
172A SER* 3.3 42.7 + - - +
175A TYR* 3.5 33.9 - + + -
176A THR* 4.9 1.8 + - - -
766A ASP* 3.6 29.2 + - + +
767A LEU* 4.2 9.6 - - + -
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Residues in contact with ALA 136 (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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132A VAL* 3.1 15.4 + - + +
133A GLU* 3.2 13.9 + - - +
135A TRP* 1.3 77.5 - - - +
137A SER* 1.3 63.8 - - - +
139A ILE* 4.2 0.9 - - - -
140A GLU* 3.0 43.3 + - - +
175A TYR* 3.6 29.2 - - + -
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Residues in contact with SER 137 (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 ALA* 3.6 14.9 - - - +
128A HIS* 3.6 28.4 - - - -
133A GLU 3.0 7.4 + - - -
134A ALA 2.7 22.1 + - - -
136A ALA* 1.3 75.7 - - - +
138A ILE* 1.3 59.9 + - - +
140A GLU* 4.9 2.4 - - - -
141A ASP* 3.7 9.8 + - - +
144A LYS* 3.6 17.5 - - - +
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Residues in contact with ILE 138 (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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117A LEU* 4.9 6.7 - - + +
120A MET* 3.5 46.4 - - + +
121A TRP* 3.7 22.7 - - + +
124A ALA* 3.9 13.5 - - + -
134A ALA 3.7 9.0 - - - +
135A TRP* 3.1 15.1 + - + +
136A ALA 3.1 0.8 - - - -
137A SER* 1.3 79.1 - - - +
139A ILE* 1.3 67.7 + - - +
141A ASP 3.3 12.0 + - - +
144A LYS* 3.4 33.6 - - + +
145A ALA 3.8 1.9 + - - -
148A PHE* 4.4 21.8 - - + -
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Residues in contact with ILE 139 (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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135A TRP* 3.0 41.2 + - + +
136A ALA 3.8 1.8 - - - +
138A ILE* 1.3 77.8 - - - +
140A GLU* 1.3 63.1 + - + +
141A ASP 3.2 2.1 + - - +
142A ALA* 4.9 0.5 + - - -
145A ALA* 4.0 24.5 - - + +
148A PHE* 4.3 10.3 - - + -
149A LYS* 4.6 0.4 - - - -
175A TYR* 3.6 37.9 - - + +
707A ARG* 5.0 4.0 - - - +
766A ASP* 3.4 50.7 - - + +
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Residues in contact with GLU 140 (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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136A ALA* 3.0 31.0 + - - +
137A SER* 4.9 2.2 - - - -
139A ILE* 1.3 74.2 - - + +
141A ASP* 1.3 58.5 + - - +
142A ALA 3.7 2.5 + - - -
175A TYR* 2.8 38.9 + - - +
179A ASN* 5.0 1.4 + - - -
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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