Contacts of the helix formed by residues 109 - 120 (chain A) in PDB entry 2ISZ
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 SER 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A LYS* 4.0 1.6 - - - +
107A VAL 3.5 1.4 + - - -
108A MET* 1.3 77.6 - - - +
110A GLU* 1.3 59.9 + - - +
111A ASP* 3.5 19.1 - - - +
112A VAL* 3.2 18.2 + - - +
113A GLU* 3.1 24.8 + - - +
92B LEU* 5.1 0.3 - - - +
100B GLU* 2.7 32.6 + - - -
103B ARG* 3.6 9.4 - - - +
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Residues in contact with GLU 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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74A ALA* 4.6 7.3 - - - +
77A ARG* 2.7 24.6 + - - +
78A LYS* 3.7 6.9 - - - +
109A SER* 1.3 71.8 - - - +
111A ASP* 1.3 67.1 + - - +
113A GLU* 3.4 19.4 - - - +
114A ARG* 3.0 52.8 + - - +
137A GLU 5.3 3.7 - - - +
138A LEU* 4.4 6.2 - - + +
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Residues in contact with ASP 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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109A SER* 3.5 15.4 + - - +
110A GLU* 1.3 80.4 - - - +
112A VAL* 1.3 61.4 + - - +
114A ARG* 3.4 24.3 + - - +
115A ARG* 3.3 22.3 + - - +
92B LEU* 3.9 11.2 - - + -
96B GLU* 3.5 28.0 - - - +
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Residues in contact with VAL 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 MET* 4.1 18.2 - - + -
109A SER* 3.2 10.5 + - - +
110A GLU 3.2 0.2 - - - -
111A ASP* 1.3 77.1 - - - +
113A GLU* 1.3 61.3 + - - +
115A ARG* 3.3 6.4 + - - +
116A LEU* 2.9 37.3 + - + +
86B LEU* 3.5 30.5 - - + -
90B ILE* 4.4 7.3 - - + +
92B LEU* 3.8 16.4 - - + -
100B GLU* 3.5 21.1 - - - +
104B TRP* 3.9 19.7 - - + -
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Residues in contact with GLU 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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77A ARG* 2.5 54.7 + - - +
78A LYS* 2.3 47.2 + - + +
81A LEU* 3.6 16.7 - - + +
108A MET* 4.1 8.7 - - + -
109A SER 3.1 15.0 + - - +
110A GLU* 3.1 13.3 + - - +
112A VAL* 1.3 78.4 - - - +
114A ARG* 1.3 58.6 + - - +
116A LEU* 3.2 7.6 + - - +
117A VAL* 3.0 30.3 + - - +
138A LEU* 4.0 9.6 - - + -
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Residues in contact with ARG 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 GLU* 3.0 36.5 + - - +
111A ASP* 3.6 34.9 + - - +
113A GLU* 1.3 73.4 - - - +
115A ARG* 1.3 65.2 + - + +
117A VAL* 3.4 14.1 + - - +
118A LYS* 3.4 17.2 + - - +
138A LEU* 3.2 48.8 + - + +
139A GLY 5.4 4.3 - - - -
140A VAL* 5.4 6.4 - - + +
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Residues in contact with ARG 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 ASP 3.3 13.2 + - - +
112A VAL 3.3 8.8 + - - +
114A ARG* 1.3 78.1 - - + +
116A LEU* 1.3 57.2 + - - +
118A LYS* 3.1 20.6 + - - +
119A VAL* 2.8 45.5 + - - +
89B VAL 5.1 0.4 + - - -
90B ILE* 2.8 45.3 + - + +
91B GLY* 3.3 24.4 + - - +
92B LEU* 4.4 12.6 - - + +
93B PRO* 5.1 4.3 - - + -
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Residues in contact with LEU 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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81A LEU* 4.2 27.1 - - + +
82A ALA* 5.2 0.2 - - - -
85A LEU* 4.1 30.3 - - + -
108A MET* 3.8 28.5 - - + -
112A VAL* 2.9 23.4 + - + +
113A GLU* 3.2 9.6 + - - +
115A ARG* 1.3 73.4 - - - +
117A VAL* 1.3 60.9 + - - +
119A VAL* 4.3 6.1 - - + +
120A LEU* 2.9 50.2 + - + +
90B ILE* 3.9 27.4 - - + -
104B TRP* 5.7 0.9 - - + -
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Residues in contact with VAL 117 (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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81A LEU* 4.3 11.4 - - + -
113A GLU 3.0 16.5 + - - +
114A ARG 3.6 8.5 - - - +
115A ARG 3.3 0.6 - - - -
116A LEU* 1.3 76.6 - - - +
118A LYS* 1.3 64.0 + - - +
121A ASN 3.5 0.5 + - - -
122A ASN* 2.7 52.4 + - - +
123A PRO* 3.6 9.8 - - + +
135A LEU* 4.1 17.0 - - + -
138A LEU* 3.7 22.4 - - + -
140A VAL* 3.7 30.5 - - + -
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Residues in contact with LYS 118 (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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114A ARG 3.4 10.7 + - - +
115A ARG* 3.1 25.2 + - - +
117A VAL* 1.3 87.2 - - - +
119A VAL* 1.3 65.9 + - + +
121A ASN* 3.1 21.1 + - - -
122A ASN* 3.4 25.9 + - - +
140A VAL* 4.6 11.9 - - - +
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Residues in contact with VAL 119 (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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85A LEU* 6.4 1.1 - - + -
89A VAL* 5.6 4.3 - - + -
115A ARG* 2.8 37.1 + - - +
116A LEU* 4.1 10.1 - - + +
118A LYS* 1.3 72.6 - - - +
120A LEU* 1.3 65.5 + - + +
121A ASN* 3.2 11.3 + - - +
89B VAL* 3.7 30.5 - - + +
90B ILE* 3.5 26.9 - - + +
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Residues in contact with LEU 120 (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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81A LEU* 4.1 9.2 - - + +
84A ARG* 3.9 28.5 - - + +
85A LEU* 4.0 19.7 - - + +
88A ASP* 4.5 13.6 - - + +
89A VAL* 3.7 29.6 - - + -
116A LEU* 2.9 39.9 + - + +
119A VAL* 1.3 79.6 - - + +
121A ASN* 1.3 70.3 + - - +
122A ASN 3.5 2.2 + - - -
123A PRO* 3.8 25.3 - - + +
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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