Contacts of the helix formed by residues 128 - 137 (chain D) in PDB entry 1SXG
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 THR 128 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102D GLN* 3.7 21.0 + - - +
126D ASN* 2.8 28.9 - - - +
127D VAL* 1.3 79.3 - - - +
129D GLU* 1.3 77.6 + - - +
130D GLU* 3.5 21.0 + - - +
131D HIS* 2.8 50.9 + - - +
132D VAL* 3.3 10.5 + - - +
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Residues in contact with GLU 129 (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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126D ASN* 5.9 0.2 + - - -
127D VAL 4.4 2.3 - - - +
128D THR* 1.3 88.9 - - - +
130D GLU* 1.3 78.5 + - - +
131D HIS 3.2 0.4 - - - -
132D VAL* 3.0 29.6 - - + +
133D GLU* 3.1 19.3 - - - +
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Residues in contact with GLU 130 (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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102D GLN* 3.9 15.5 + - - +
128D THR* 3.2 20.4 + - - +
129D GLU* 1.3 107.2 - - - +
131D HIS* 1.3 62.5 + - + +
133D GLU* 3.2 18.4 - - - +
134D GLU* 3.0 33.6 + - + +
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Residues in contact with HIS 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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102D GLN* 3.7 24.3 + - + +
105D GLU* 2.9 39.2 + - + +
106D LEU* 5.5 6.7 - - + -
109D LEU* 5.5 8.8 - - + +
122D PHE* 5.0 10.0 - + + -
124D SER* 4.6 0.9 - - - -
126D ASN 3.2 16.8 + - - -
127D VAL* 3.4 14.3 - - + +
128D THR* 2.8 38.9 + - - +
130D GLU* 1.3 78.7 - - + +
132D VAL* 1.3 56.3 + - - +
133D GLU 3.1 0.3 + - - -
134D GLU* 3.2 5.8 + - - +
135D LEU* 2.7 44.1 + - + +
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Residues in contact with VAL 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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127D VAL* 4.1 11.9 - - + +
128D THR 3.3 11.6 + - - +
129D GLU* 3.0 22.4 - - + +
131D HIS* 1.3 75.2 - - - +
133D GLU* 1.3 69.4 + - + +
135D LEU* 3.8 7.8 - - - +
136D LYS* 2.8 48.2 + - - +
149D GLU* 3.7 31.9 - - + +
151D THR* 4.8 1.8 - - + +
153D GLN* 4.7 10.3 - - + +
154D ILE* 4.7 11.1 - - + +
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Residues in contact with GLU 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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129D GLU* 3.1 27.4 + - - +
130D GLU* 3.2 20.2 - - - +
131D HIS 3.0 0.4 - - - -
132D VAL* 1.3 90.6 - - + +
134D GLU* 1.3 61.2 + - + +
136D LYS* 2.9 33.8 + - - +
137D LYS* 3.4 15.5 + - - +
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Residues in contact with GLU 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 LEU* 3.6 40.3 - - + +
109D LEU* 5.2 11.4 - - + +
110D ASN* 4.7 5.2 - - - +
130D GLU* 3.0 14.7 + - + +
131D HIS* 3.9 3.4 - - - +
133D GLU* 1.3 80.9 - - + +
135D LEU* 1.3 60.9 + - - +
137D LYS* 3.3 49.6 + - - +
138D SER* 3.9 3.6 + - - -
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Residues in contact with LEU 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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109D LEU* 3.5 35.0 - - + +
120D ILE* 6.1 0.2 - - + -
122D PHE* 3.9 12.8 - - + -
127D VAL* 5.1 4.9 - - + -
131D HIS* 2.7 25.6 + - + +
132D VAL* 3.8 6.7 - - - +
134D GLU* 1.3 72.5 - - - +
136D LYS* 1.3 62.2 + - - +
138D SER* 3.3 21.4 + - - -
142D VAL* 3.7 33.7 - - + +
144D LEU* 3.9 29.4 - - + -
154D ILE* 4.0 23.5 - - + +
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Residues in contact with LYS 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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132D VAL* 2.8 34.7 + - - +
133D GLU* 2.9 22.8 + - - +
135D LEU* 1.3 74.4 - - - +
137D LYS* 1.3 56.6 + - + +
138D SER 3.0 14.7 + - - +
153D GLN* 3.3 38.6 + - - +
154D ILE* 4.9 10.8 - - + -
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Residues in contact with LYS 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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113D LEU* 5.6 1.2 - - - +
133D GLU* 3.8 12.3 - - - +
134D GLU* 3.3 53.3 + - - +
135D LEU 3.2 0.6 - - - -
136D LYS* 1.3 78.1 - - + +
138D SER* 1.3 61.4 + - - +
139D PRO* 3.3 9.4 - - - +
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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