Contacts of the helix formed by residues 128 - 138 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102I GLN* 2.9 35.1 + - - +
126I ASN* 3.4 24.5 - - - +
127I VAL* 1.3 72.6 - - - +
129I GLU* 1.3 74.1 + - - +
130I GLU 3.2 3.1 + - - -
131I HIS* 2.9 37.0 + - + +
132I VAL* 2.9 18.0 + - - +
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Residues in contact with GLU 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102I GLN* 5.2 1.0 - - - +
128I THR* 1.3 83.7 + - - +
130I GLU* 1.3 96.4 + - - +
132I VAL* 3.2 21.8 - - - +
133I GLU* 3.2 19.0 + - + +
151I THR* 5.7 4.9 - - + -
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Residues in contact with GLU 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102I GLN* 3.4 32.5 + - - +
103I ASP* 5.4 1.4 - - - +
106I LEU* 5.2 7.6 - - + +
129I GLU* 1.3 99.4 + - - +
131I HIS* 1.3 64.2 + - - +
133I GLU* 3.4 4.2 + - - +
134I GLU* 2.9 42.8 + - + +
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Residues in contact with HIS 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102I GLN* 3.2 39.8 + - - +
105I GLU* 2.9 38.7 + - + +
106I LEU* 4.7 11.0 + - + +
122I PHE* 4.7 8.4 - + + -
126I ASN 3.3 12.6 + - - -
127I VAL* 3.6 13.9 - - + -
128I THR* 2.9 47.2 + - + +
130I GLU* 1.3 79.2 - - - +
132I VAL* 1.3 51.8 + - - +
134I GLU* 2.9 9.0 + - - +
135I LEU* 2.5 43.8 + - + +
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Residues in contact with VAL 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127I VAL* 4.3 2.4 - - + +
128I THR 2.9 16.6 + - - +
129I GLU* 3.2 22.9 - - - +
131I HIS* 1.3 74.8 - - - +
133I GLU* 1.3 63.1 + - + +
135I LEU* 3.2 13.8 - - - +
136I LYS* 3.1 33.6 + - - +
149I GLU* 3.8 14.1 - - - +
151I THR* 3.7 30.1 - - + +
153I GLN* 3.8 13.9 - - + +
154I ILE* 4.1 18.2 - - + -
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Residues in contact with GLU 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129I GLU* 3.2 18.2 + - + +
130I GLU* 3.8 4.3 - - - +
132I VAL* 1.3 82.4 - - + +
134I GLU* 1.3 59.5 + - + +
136I LYS* 3.0 36.1 + - - +
137I LYS* 3.2 39.4 + - - +
153I GLN* 5.0 0.8 - - - +
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Residues in contact with GLU 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106I LEU* 3.6 41.4 - - + +
109I LEU* 4.3 5.4 - - + +
110I ASN* 5.3 6.1 + - - +
130I GLU* 2.9 33.2 + - + +
131I HIS 2.9 8.8 + - - +
133I GLU* 1.3 77.6 - - + +
135I LEU* 1.3 67.2 + - - +
137I LYS* 3.2 42.4 + - - +
138I SER* 3.4 8.0 + - - -
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Residues in contact with LEU 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I LEU* 3.2 40.4 - - + -
122I PHE* 4.4 13.5 - - + -
127I VAL* 4.1 12.8 - - + -
131I HIS* 2.5 16.6 + - + +
132I VAL* 3.2 16.8 - - - +
134I GLU* 1.3 73.7 - - - +
136I LYS* 1.3 61.8 + - - +
138I SER* 3.0 20.8 - - - -
142I VAL* 4.2 19.8 - - + +
144I LEU* 4.1 11.2 - - + -
154I ILE* 3.3 38.8 - - + -
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Residues in contact with LYS 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I VAL* 3.1 23.4 + - - +
133I GLU* 3.0 32.8 + - - +
134I GLU 3.3 0.2 - - - -
135I LEU* 1.3 75.2 - - - +
137I LYS* 1.3 60.8 + - + +
138I SER 2.8 15.9 + - - +
153I GLN* 3.1 46.1 + - - +
154I ILE* 4.6 9.8 - - + +
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Residues in contact with LYS 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I GLU* 3.2 33.8 - - - +
134I GLU* 3.2 33.6 + - - +
136I LYS* 1.3 74.8 - - + +
138I SER* 1.3 63.4 + - - +
139I PRO* 3.5 4.3 - - - +
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Residues in contact with SER 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I LEU* 3.7 29.2 + - - -
110I ASN* 4.9 4.7 - - - +
113I LEU* 3.8 5.5 - - - +
134I GLU 3.4 3.2 + - - -
135I LEU 3.0 18.5 + - - -
136I LYS 2.8 12.6 + - - +
137I LYS* 1.3 80.0 - - - +
139I PRO* 1.3 80.3 - - - +
140I VAL 3.6 15.9 + - - +
142I VAL* 4.0 8.2 - - - +
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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