Contacts of the helix formed by residues 121 - 135 (chain E) in PDB entry 3IZ0
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 121 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119E ALA 3.6 1.4 + - - -
120E PRO* 1.3 76.5 - - - +
122E VAL* 1.3 64.1 + - - +
123E LYS* 3.5 9.6 + - - +
124E ASP* 2.9 34.9 + - - +
125E PHE* 2.9 21.1 + - - +
172E VAL* 4.6 0.7 - - - -
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Residues in contact with VAL 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E PRO 4.0 0.4 + - - -
121E SER* 1.3 71.8 - - - +
123E LYS* 1.3 62.8 + - - +
125E PHE* 3.3 2.5 + - + +
126E LEU* 2.9 36.3 + - + +
147E PHE* 3.6 29.8 - - + -
169E MET 3.6 13.5 - - - +
170E TYR* 3.6 26.0 - - - +
171E THR* 4.9 0.4 - - - -
172E VAL* 3.8 19.9 - - + +
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Residues in contact with LYS 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E SER* 3.2 9.5 - - - +
122E VAL* 1.3 79.6 - - - +
124E ASP* 1.3 65.6 + - - +
126E LEU* 3.5 7.6 + - - +
127E LYS* 3.3 54.8 + - - +
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Residues in contact with ASP 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E TYR* 4.3 0.6 + - - -
116E SER* 5.1 4.5 - - - +
120E PRO* 4.1 11.4 - - + +
121E SER* 2.9 32.0 + - - +
123E LYS* 1.3 76.6 - - - +
125E PHE* 1.3 67.5 + - - +
127E LYS* 2.9 20.7 + - - +
128E ILE* 2.9 31.6 + - + +
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Residues in contact with PHE 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E PRO* 4.5 7.3 - - + +
121E SER 2.9 11.6 + - - +
122E VAL* 3.5 7.0 - - - +
124E ASP* 1.3 76.7 - - - +
126E LEU* 1.3 74.6 + - + +
128E ILE* 3.1 8.7 + - - -
129E PHE* 2.7 41.0 + + + +
147E PHE* 5.4 2.0 - + - -
151E VAL* 4.0 28.0 - - + -
155E PHE* 5.3 2.0 - + - -
169E MET* 4.4 9.4 - - + -
172E VAL* 3.7 34.1 - - + -
178E TRP* 4.6 4.5 - + - -
181E ILE* 3.4 32.1 - - + -
185E LEU* 3.7 32.8 - - + -
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Residues in contact with LEU 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E VAL* 2.9 36.3 + - + +
123E LYS* 3.9 7.4 - - - +
124E ASP 3.1 0.2 - - - -
125E PHE* 1.3 91.8 - - + +
127E LYS* 1.3 58.5 + - - +
129E PHE* 4.1 3.0 - - + +
130E THR* 2.7 37.4 + - - -
142E LEU* 3.7 28.3 - - + -
147E PHE* 3.6 41.3 - - + -
151E VAL* 4.1 6.5 - - + -
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Residues in contact with LYS 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E TYR* 3.1 18.8 - - + +
110E HIS* 3.5 38.0 + - + +
123E LYS* 3.3 49.2 + - + +
124E ASP* 2.9 17.5 + - - +
126E LEU* 1.3 76.0 - - - +
128E ILE* 1.3 57.0 + - - +
130E THR* 3.8 4.3 - - - -
131E PHE* 3.0 27.5 + - - +
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Residues in contact with ILE 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E LEU* 4.1 14.1 - - + -
103E LEU* 3.9 13.7 - - + -
108E TYR* 3.5 25.8 - - + +
112E VAL* 5.0 3.8 - - + -
117E LEU* 3.8 28.9 - - + -
120E PRO* 5.3 4.3 - - + -
124E ASP* 2.9 24.8 + - + +
125E PHE* 3.5 9.2 - - - +
127E LYS* 1.3 74.6 - - - +
129E PHE* 1.3 64.7 + - - +
131E PHE* 3.2 2.6 + - - +
132E LEU* 3.0 34.3 + - + +
178E TRP* 5.7 2.0 - - + -
185E LEU* 3.8 26.9 - - + -
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Residues in contact with PHE 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E PHE* 2.7 33.7 + + + +
126E LEU* 4.1 4.3 - - - +
128E ILE* 1.3 75.3 - - - +
130E THR* 1.3 66.9 + - - +
132E LEU* 3.3 3.3 + - - +
133E TYR* 2.9 40.0 + + + +
140E TYR* 4.3 16.4 - + - -
142E LEU* 4.7 7.2 - - + -
151E VAL* 3.9 29.8 - - + -
154E ILE* 3.9 37.9 - - + -
155E PHE* 3.6 32.5 - + - -
158E LEU* 6.2 0.2 - - + -
185E LEU* 4.5 8.7 - - + +
188E LEU* 4.3 17.5 - - + -
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Residues in contact with THR 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E LEU 2.7 23.4 + - - -
127E LYS* 3.8 5.8 - - - -
129E PHE* 1.3 81.6 - - - +
131E PHE* 1.3 63.1 + - - +
133E TYR* 4.0 3.0 - - - +
134E GLY* 3.1 20.1 + - - -
140E TYR* 3.4 33.6 - - + +
141E GLU* 4.4 6.7 - - + -
142E LEU* 3.6 27.6 - - + +
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Residues in contact with PHE 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E PHE* 4.6 3.1 - + - -
103E LEU* 3.5 31.0 - - + -
106E ASN* 3.4 32.3 - - + -
107E GLY 4.6 2.5 - - - -
108E TYR* 3.4 37.7 - + + -
109E ALA 5.2 1.1 - - - -
127E LYS 3.0 18.3 + - - +
128E ILE 3.5 4.0 - - - +
129E PHE 3.2 0.2 - - - -
130E THR* 1.3 77.8 - - - +
132E LEU* 1.3 66.3 + - + +
134E GLY* 3.1 13.4 + - - -
135E PHE* 3.3 40.5 - + - -
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Residues in contact with LEU 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E LEU* 4.1 11.4 - - + -
102E PHE* 3.5 37.7 - - + -
103E LEU* 4.2 13.2 - - + -
128E ILE* 3.0 30.2 + - + +
129E PHE 3.8 1.1 - - - +
131E PHE* 1.3 78.4 - - + +
133E TYR* 1.3 63.1 + - - +
135E PHE* 3.1 24.5 + - - +
136E LEU* 4.2 0.9 + - - +
185E LEU* 4.0 39.9 - - + +
188E LEU* 3.7 16.2 - - + -
189E ILE* 4.0 10.5 - - + -
192E ILE* 3.4 13.8 - - + +
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Residues in contact with TYR 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E PHE* 2.9 31.5 + + + +
130E THR 4.2 2.5 - - - +
132E LEU* 1.3 77.9 - - - +
134E GLY* 1.3 53.0 + - - +
136E LEU* 2.8 39.9 + - + +
137E CYS* 2.8 25.9 + - - -
140E TYR* 3.5 43.7 - + + -
154E ILE* 3.4 45.9 - - + +
158E LEU* 4.2 14.1 - - + -
188E LEU* 4.3 8.3 - - + +
110F LEU* 3.2 34.1 - - + +
111F CYS* 5.9 0.7 - - - +
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Residues in contact with GLY 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E THR 3.1 14.7 + - - -
131E PHE 3.1 8.4 + - - -
133E TYR* 1.3 74.9 - - - +
135E PHE* 1.3 62.4 + - - +
136E LEU 3.1 1.1 + - - -
137E CYS 3.3 14.3 - - - +
138E PRO* 3.4 24.2 - - - +
139E SER 4.5 1.6 + - - -
140E TYR* 4.5 7.8 - - - +
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Residues in contact with PHE 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E PHE* 4.1 9.4 - + - -
106E ASN* 3.8 40.6 - - + -
131E PHE* 3.3 46.4 - + - -
132E LEU* 3.1 15.8 + - - +
133E TYR 3.1 0.6 - - - -
134E GLY* 1.3 76.9 - - - +
136E LEU* 1.3 63.1 + - - +
138E PRO* 5.1 2.8 - - - +
192E ILE* 3.9 34.3 - - + +
195E HIS* 4.9 5.4 - - - -
196E THR* 5.8 1.3 - - - -
199E LYS* 5.8 1.7 - - - -
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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