Contacts of the helix formed by residues 114 - 129 (chain A) in PDB entry 1ZP2
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 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A CYS* 4.0 8.7 - - - -
112A LYS* 4.7 1.6 - - - -
113A LEU* 1.3 74.6 - - - +
115A ARG* 1.3 68.2 + - - +
116A SER* 3.4 9.4 + - - -
117A ASN* 2.6 47.5 + - - +
118A ILE* 3.1 9.5 + - - +
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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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95A HIS* 3.5 13.5 + - - -
96A ILE* 3.2 47.4 - - + +
97A ARG* 3.0 40.3 - - - +
100A CYS* 4.3 4.9 - - - -
114A SER* 1.3 73.7 - - - +
116A SER* 1.3 63.5 + - - +
118A ILE* 3.4 8.6 - - - +
119A SER* 3.0 25.6 + - - -
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Residues in contact with SER 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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114A SER* 3.3 9.9 + - - -
115A ARG* 1.3 79.4 - - - +
117A ASN* 1.3 72.4 + - - +
119A SER* 3.6 6.0 - - - -
120A GLU* 2.9 38.4 + - - +
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Residues in contact with ASN 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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73A PHE* 4.9 0.7 - - - -
111A VAL* 4.3 14.2 - - - +
112A LYS 2.9 18.9 + - - +
113A LEU* 3.9 15.7 - - + +
114A SER* 2.6 48.3 + - - +
116A SER* 1.3 87.5 + - - +
118A ILE* 1.3 62.4 + - - +
120A GLU* 3.3 14.9 + - - +
121A ILE* 3.2 21.4 + - + +
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Residues in contact with ILE 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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80A ALA* 5.1 5.4 - - + -
81A THR* 3.4 21.0 - - + +
84A TYR* 3.8 30.1 - - + -
96A ILE* 3.2 38.6 - - + +
99A ILE* 5.4 7.4 - - + -
100A CYS* 4.3 11.9 - - - -
113A LEU* 4.5 23.8 - - + -
114A SER 3.1 9.4 + - - +
115A ARG 3.4 10.5 - - - +
117A ASN* 1.3 79.4 - - - +
119A SER* 1.3 57.4 + - - +
121A ILE* 3.3 9.8 + - - -
122A GLU* 2.7 36.1 + - - +
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Residues in contact with SER 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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96A ILE* 6.5 0.2 - - - -
115A ARG 3.0 20.4 + - - -
116A SER* 3.6 8.3 - - - -
117A ASN 3.2 0.2 - - - -
118A ILE* 1.3 77.7 - - - +
120A GLU* 1.3 65.5 + - - +
122A GLU* 3.4 17.4 + - - +
123A PHE* 3.1 22.5 + - - +
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Residues in contact with GLU 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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73A PHE* 4.9 14.4 - - + -
116A SER* 2.9 37.4 + - - +
117A ASN* 3.3 10.0 + - - +
119A SER* 1.3 76.8 - - - +
121A ILE* 1.3 53.5 + - + +
123A PHE* 3.3 6.8 + - - +
124A GLU* 2.8 33.1 + - - +
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Residues in contact with ILE 121 (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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73A PHE* 3.1 28.9 - - + -
77A ALA* 3.7 27.6 - - + +
78A LEU* 3.6 26.9 - - + -
81A THR* 3.2 31.9 - - + +
113A LEU* 4.7 5.2 - - + -
117A ASN* 3.2 19.1 - - + +
118A ILE* 3.4 10.5 - - - +
120A GLU* 1.3 73.3 - - - +
122A GLU* 1.3 55.4 + - - +
124A GLU* 2.9 11.2 + - + +
125A ILE* 2.7 41.8 + - + +
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Residues in contact with GLU 122 (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 THR* 3.4 14.3 - - + +
84A TYR* 3.5 18.9 + - + -
85A LEU* 3.3 32.6 - - + +
88A LYS* 3.0 27.9 + - - -
118A ILE 2.7 21.8 + - - +
119A SER* 3.5 18.0 + - - +
121A ILE* 1.3 73.4 - - - +
123A PHE* 1.3 63.4 + - - +
125A ILE* 3.2 3.9 + - - +
126A ILE* 2.9 38.7 + - + +
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Residues in contact with PHE 123 (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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119A SER 3.1 10.2 + - - +
120A GLU* 3.6 9.2 - - - +
122A GLU* 1.3 79.0 - - - +
124A GLU* 1.3 55.0 + - - +
126A ILE* 4.4 12.1 - - + -
127A SER* 2.6 67.6 + - - -
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Residues in contact with GLU 124 (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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63A TYR* 2.7 32.0 + - + +
67A LYS* 5.4 1.2 - - - +
71A LYS* 4.0 25.0 - - - +
73A PHE* 4.1 18.2 - - + -
120A GLU 2.8 15.2 + - - +
121A ILE* 3.0 17.5 - - + +
123A PHE* 1.3 78.7 - - - +
125A ILE* 1.3 55.9 + - + +
127A SER* 3.9 4.0 - - - -
128A VAL* 3.0 56.8 + - - +
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Residues in contact with ILE 125 (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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59A LEU* 4.8 6.3 - - + +
63A TYR* 3.9 27.6 - - + -
78A LEU* 4.8 5.8 - - + -
81A THR* 3.8 19.5 - - + -
82A CYS* 4.2 22.2 - - - +
85A LEU* 4.2 19.7 - - + -
121A ILE* 2.7 39.9 + - + +
122A GLU 3.6 4.0 - - - +
124A GLU* 1.3 71.0 - - + +
126A ILE* 1.3 57.9 + - - +
128A VAL* 3.1 1.9 + - - -
129A LEU* 2.6 61.5 + - + +
133A LEU* 5.3 0.7 - - + -
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Residues in contact with ILE 126 (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* 4.0 21.1 - - + -
122A GLU* 2.9 46.7 + - + +
123A PHE* 3.9 11.2 - - + +
125A ILE* 1.3 72.3 - - - +
127A SER* 1.3 66.7 + - - +
130A ASP 2.9 19.6 + - - -
131A ALA* 2.9 29.6 + - + +
133A LEU* 4.1 24.2 - - + -
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Residues in contact with SER 127 (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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123A PHE* 2.6 54.3 + - - -
124A GLU* 3.9 4.9 - - - -
126A ILE* 1.3 77.6 - - - +
128A VAL* 1.3 63.9 + - - +
130A ASP* 3.1 16.8 + - - +
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Residues in contact with VAL 128 (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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63A TYR* 4.0 13.9 - - + -
66A LYS* 3.5 40.5 - - + +
67A LYS* 4.0 13.2 - - - +
71A LYS* 6.2 0.2 - - - -
124A GLU* 3.0 45.1 + - - +
125A ILE 3.7 2.0 - - - +
127A SER* 1.3 77.7 - - - +
129A LEU* 1.3 62.2 + - + +
130A ASP* 3.1 9.9 + - - +
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Residues in contact with LEU 129 (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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59A LEU* 3.5 44.9 - - + +
62A ARG* 3.8 31.6 - - + +
63A TYR* 3.8 14.8 - - + +
66A LYS* 4.2 15.9 - - + +
125A ILE* 2.6 35.3 + - + +
126A ILE 4.1 1.8 - - - +
128A VAL* 1.3 72.8 - - + +
130A ASP* 1.3 69.3 + - - +
131A ALA 3.2 0.9 - - - -
132A PHE* 2.7 39.6 + - + +
133A LEU* 4.5 4.5 - - + -
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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