Contacts of the helix formed by residues 106 - 116 (chain A) in PDB entry 1SAW
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 ARG 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ASN* 3.0 30.1 + - - +
69A HIS* 3.2 34.2 + - + +
71A GLU* 2.8 35.4 + - - +
104A THR* 3.1 17.2 + - - +
105A ALA* 1.3 70.6 - - - +
107A ASP* 1.3 59.3 + - - +
109A GLN* 3.0 31.5 + - - +
110A ASP* 3.1 38.0 + - - +
113A LYS* 5.8 0.6 - - - +
123A LYS* 4.7 0.4 - - - +
196A VAL* 3.2 25.7 - - - +
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Residues in contact with ASP 107 (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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64A TYR 4.3 4.2 - - - +
65A THR* 2.7 28.2 + - - -
66A ARG* 3.5 21.5 + - - +
67A ASN* 4.0 15.8 + - + +
105A ALA 4.0 0.5 - - - -
106A ARG* 1.3 75.4 - - - +
108A VAL* 1.3 71.5 + - - +
110A ASP* 3.6 9.6 + - - +
111A GLU* 3.4 20.1 + - - +
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Residues in contact with VAL 108 (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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64A TYR* 3.8 28.0 - - + +
65A THR* 4.5 0.2 - - - +
105A ALA* 3.2 21.9 + - + +
107A ASP* 1.3 93.7 + - - +
109A GLN* 1.3 64.8 + - - +
111A GLU* 3.3 8.1 + - + +
112A CYS* 3.0 34.1 + - - -
121A LEU* 3.8 16.4 - - + -
122A ALA* 3.7 24.0 - - + +
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Residues in contact with GLN 109 (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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104A THR* 3.9 2.4 - - + +
105A ALA 3.1 9.5 + - - +
106A ARG* 3.0 44.1 + - - +
108A VAL* 1.3 74.1 - - - +
110A ASP* 1.3 67.9 + - - +
112A CYS* 2.9 15.6 + - - +
113A LYS* 3.0 35.2 + - - +
119A TRP* 3.2 47.3 - - + +
122A ALA* 3.6 19.7 - - + +
123A LYS* 3.7 17.9 - - - +
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Residues in contact with ASP 110 (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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106A ARG* 3.1 28.2 + - - +
107A ASP* 3.7 12.2 - - - +
109A GLN* 1.3 79.8 - - - +
111A GLU* 1.3 59.9 + - - +
113A LYS* 3.6 18.7 + - - +
114A LYS* 3.2 27.7 + - + +
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Residues in contact with GLU 111 (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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107A ASP 3.4 9.2 + - - +
108A VAL* 3.3 12.0 + - + +
109A GLN 3.2 0.6 - - - -
110A ASP* 1.3 77.0 - - - +
112A CYS* 1.3 60.6 + - - +
114A LYS* 3.3 8.1 + - - +
115A LYS* 3.1 34.2 + - + +
117A LEU* 5.7 2.2 - - + -
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Residues in contact with CYS 112 (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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108A VAL* 3.0 39.2 + - - -
109A GLN* 2.9 9.3 + - - +
111A GLU* 1.3 73.8 - - - +
113A LYS* 1.3 65.2 + - - +
116A GLY* 3.0 5.7 + - - -
117A LEU* 3.0 55.2 + - - +
118A PRO 3.5 19.5 - - - -
119A TRP* 3.8 20.4 - - + -
121A LEU* 5.8 1.6 - - - -
122A ALA* 4.7 1.6 - - - -
116B GLY* 4.5 0.9 - - - -
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Residues in contact with LYS 113 (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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106A ARG* 5.8 0.4 - - - +
109A GLN* 3.0 37.6 + - + +
110A ASP* 3.7 20.0 + - - +
112A CYS* 1.3 75.7 - - - +
114A LYS* 1.3 61.4 + - + +
115A LYS 3.4 0.9 + - - -
116A GLY 3.7 1.9 + - - -
119A TRP* 3.8 26.7 - - + +
113B LYS 4.8 0.7 - - - +
114B LYS 5.5 0.9 - - - +
115B LYS 4.8 1.4 - - - +
116B GLY* 3.3 41.0 + - - +
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Residues in contact with LYS 114 (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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110A ASP 3.2 15.8 + - - +
111A GLU* 3.5 12.3 - - - +
112A CYS 3.2 0.6 - - - -
113A LYS* 1.3 81.6 - - + +
115A LYS* 1.3 63.1 + - + +
116A GLY 3.5 0.2 - - - -
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Residues in contact with LYS 115 (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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111A GLU* 3.1 19.8 + - + +
113A LYS 3.3 0.2 - - - -
114A LYS* 1.3 82.1 - - + +
116A GLY* 1.3 62.3 + - - +
117A LEU* 3.8 27.9 - - + +
113B LYS* 5.6 0.3 - - - +
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Residues in contact with GLY 116 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A CYS 3.0 6.5 + - - -
113A LYS 3.7 4.0 + - - -
114A LYS 3.5 2.4 - - - -
115A LYS* 1.3 79.1 - - - +
117A LEU* 1.3 62.3 + - - +
113B LYS* 3.3 42.4 + - - +
116B GLY* 4.6 4.0 - - - -
117B LEU 5.8 0.7 - - - -
119B TRP* 3.1 27.0 + - - -
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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