Contacts of the helix formed by residues 103 - 116 (chain A) in PDB entry 1ISA
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 PHE 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A GLY 4.1 6.7 - - - -
87A GLU* 3.7 43.7 - - + +
88A PRO* 3.5 35.9 - - + -
96A ILE* 4.0 13.6 - - + +
97A ALA* 5.2 1.8 - - - +
102A SER* 1.3 71.8 - - - +
104A ALA* 1.3 60.0 + - - +
106A PHE* 3.1 21.3 + + - +
107A LYS* 2.9 58.9 + - + +
178A TRP* 4.5 7.9 - + + -
183A TRP* 3.7 26.0 - + - -
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Residues in contact with ALA 104 (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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87A GLU* 5.6 1.3 + - - +
102A SER* 3.2 8.4 + - - +
103A PHE* 1.3 83.0 - - + +
105A ASP* 1.3 64.3 + - - +
107A LYS* 3.5 8.4 + - - +
108A ALA* 3.1 25.1 + - - +
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Residues in contact with ASP 105 (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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100A PHE* 3.4 24.8 - - - +
101A GLY* 4.4 2.4 - - - -
102A SER* 2.9 20.3 + - - +
104A ALA* 1.3 79.6 - - - +
106A PHE* 1.3 62.6 + - - +
108A ALA* 3.4 5.3 + - - +
109A GLN* 3.0 40.0 + - - +
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Residues in contact with PHE 106 (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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96A ILE* 3.7 29.8 - - + -
100A PHE* 3.7 38.9 - + + +
102A SER 3.0 6.8 + - - +
103A PHE* 3.1 27.6 + + - +
105A ASP* 1.3 75.6 - - - +
107A LYS* 1.3 58.9 + - - +
109A GLN* 3.2 2.8 + - - +
110A PHE* 2.9 58.1 + + + +
125A LEU* 3.8 32.5 - - + -
135A ILE* 4.1 6.1 - - + -
153A LEU* 4.5 5.8 - - + -
178A TRP* 3.7 28.0 - + - -
183A TRP* 4.3 3.6 - + - -
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Residues in contact with LYS 107 (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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103A PHE* 2.9 48.0 + - + +
104A ALA* 3.9 7.4 - - - +
106A PHE* 1.3 73.9 - - - +
108A ALA* 1.3 57.9 + - - +
111A THR* 2.9 36.2 + - - +
178A TRP* 3.7 53.4 - - + +
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Residues in contact with ALA 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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104A ALA 3.1 17.7 + - - +
105A ASP* 3.8 5.6 - - - +
107A LYS* 1.3 78.0 - - - +
109A GLN* 1.3 58.0 + - + +
111A THR* 3.9 5.5 - - - -
112A ASP* 3.0 29.3 + - - +
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Residues in contact with GLN 109 (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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100A PHE* 3.7 28.5 + - - +
105A ASP* 3.0 37.0 + - - +
106A PHE* 3.8 1.1 - - - +
108A ALA* 1.3 76.5 - - + +
110A PHE* 1.3 56.2 + - - +
112A ASP* 3.4 6.2 + - - +
113A ALA* 3.0 30.0 + - - +
135A ILE* 3.7 15.9 - - + +
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Residues in contact with PHE 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 PHE* 2.9 34.5 + + + +
107A LYS 3.9 3.4 - - - +
109A GLN* 1.3 72.4 - - - +
111A THR* 1.3 64.7 + - - +
113A ALA* 3.3 2.6 + - - +
114A ALA* 3.0 24.8 + - - +
123A THR* 3.6 23.8 - - + +
124A TRP 3.8 6.7 - - - -
125A LEU* 3.7 27.4 - - + -
135A ILE* 3.5 20.3 - - + +
153A LEU* 4.3 15.3 - - + -
154A THR 4.5 1.8 - - - -
155A VAL* 3.7 27.4 - - + -
174A LEU* 4.6 5.4 - - + -
177A PHE* 3.9 17.3 - + - -
178A TRP* 3.6 24.5 - + + -
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Residues in contact with THR 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 LYS* 2.9 21.0 + - - +
108A ALA* 3.9 5.6 - - - -
110A PHE* 1.3 73.5 - - - +
112A ASP* 1.3 63.5 + - - +
114A ALA* 3.3 6.2 + - - +
115A ILE* 3.0 43.9 + - + +
171A PRO 5.6 1.6 - - - +
174A LEU* 4.2 19.2 - - + +
175A GLU 5.7 0.4 - - - +
178A TRP* 3.1 23.4 + - - +
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Residues in contact with ASP 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 ALA 3.0 20.1 + - - +
109A GLN* 3.7 7.4 - - - +
110A PHE 3.3 0.4 - - - -
111A THR* 1.3 75.1 - - - +
113A ALA* 1.3 62.8 + - - +
115A ILE* 3.4 5.3 + - - +
116A LYS* 3.0 65.4 + - - +
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Residues in contact with ALA 113 (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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109A GLN 3.0 16.8 + - - +
110A PHE 3.8 2.2 - - - +
112A ASP* 1.3 76.2 + - - +
114A ALA* 1.3 57.1 + - - +
116A LYS* 3.6 5.0 + - - +
117A ASN* 3.1 28.9 + - - +
123A THR* 3.8 7.6 - - + -
135A ILE* 3.8 25.6 - - + -
137A SER* 3.8 10.1 + - - +
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Residues in contact with ALA 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 PHE 3.0 17.3 + - - +
111A THR 3.3 4.2 + - - +
113A ALA* 1.3 76.3 - - - +
115A ILE* 1.3 59.6 + - - +
117A ASN* 3.4 7.3 + - - +
123A THR* 3.4 17.2 + - + +
155A VAL* 4.0 13.0 - - + -
157A VAL* 3.8 6.2 - - + +
170A ARG* 2.9 25.1 + - - -
174A LEU* 3.8 29.4 - - + -
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Residues in contact with ILE 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 THR* 3.0 36.0 + - + +
112A ASP* 3.9 5.8 - - - +
114A ALA* 1.3 77.6 - - - +
116A LYS* 1.3 63.4 + - + +
117A ASN 4.4 0.2 - - - +
170A ARG* 3.3 23.7 + - + +
171A PRO* 3.7 49.1 - - + -
174A LEU* 4.5 9.2 - - + -
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Residues in contact with LYS 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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112A ASP* 3.0 51.3 + - - +
113A ALA* 3.8 5.2 - - - +
115A ILE* 1.3 78.8 - - + +
117A ASN* 1.3 59.6 + - - +
118A PHE* 2.9 14.9 + - - +
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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