Contacts of the helix formed by residues 114 - 124 (chain E) in PDB entry 3VZC
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 ASN 114 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79E SER 3.4 20.4 - - - +
80E GLY* 3.9 1.3 - - - -
81E ASP* 3.7 3.1 - - - +
109E PRO* 3.6 24.5 - - + +
110E ALA 3.5 9.9 + - - -
111E GLY 2.9 25.6 + - - +
112E SER* 4.3 0.4 - - - +
113E GLY* 1.3 81.0 - - - +
115E ALA* 1.3 65.3 + - - +
116E LEU 3.3 3.4 + - - -
117E ALA* 3.3 3.9 + - + +
118E ALA* 2.9 24.8 + - - +
134E LEU* 4.5 9.5 - - + +
269E GLY* 5.1 1.2 - - - -
270E SER* 4.6 13.9 + - - +
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Residues in contact with ALA 115 (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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81E ASP* 2.9 6.1 + - - +
113E GLY* 5.8 0.4 - - - -
114E ASN* 1.3 76.4 - - - +
116E LEU* 1.3 57.2 + - - +
118E ALA* 3.3 1.9 + - - +
119E SER* 2.8 35.0 + - - -
167E LEU* 3.4 25.4 - - + -
267E HIS* 3.2 21.2 - - - +
268E LEU 3.6 7.4 - - - +
269E GLY* 3.6 25.1 - - - +
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Residues in contact with LEU 116 (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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81E ASP* 3.0 17.1 + - - +
84E MET* 3.7 31.4 - - + -
107E SER* 4.1 13.0 - - - +
115E ALA* 1.3 72.7 - - - +
117E ALA* 1.3 66.6 + - - +
119E SER* 3.1 5.1 + - - -
120E LEU* 3.0 31.5 + - + +
166E VAL* 4.6 12.8 - - + +
167E LEU* 3.9 12.9 - - + +
265E HIS* 3.5 38.8 - - + +
361E MET* 3.8 35.0 - - + -
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Residues in contact with ALA 117 (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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81E ASP* 4.6 0.2 + - - -
107E SER* 3.7 21.4 + - - +
109E PRO* 3.7 26.9 - - + -
114E ASN* 3.3 7.8 + - + +
116E LEU* 1.3 77.9 - - - +
118E ALA* 1.3 57.6 + - - +
120E LEU* 3.5 7.7 + - - +
121E ASN* 3.0 28.2 + - - +
134E LEU* 3.8 2.4 - - + +
138E CYS* 3.6 27.1 - - - -
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Residues in contact with ALA 118 (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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114E ASN 2.9 17.9 + - - +
115E ALA 3.6 3.6 - - - +
117E ALA* 1.3 75.2 - - - +
119E SER* 1.3 64.9 + - - +
121E ASN* 3.4 4.2 + - - +
122E HIS* 3.1 22.9 + - - +
128E GLN* 6.2 0.7 - - + -
129E VAL 5.7 0.9 - - - +
134E LEU* 4.0 13.4 - - + +
267E HIS* 4.1 10.8 + - + -
269E GLY 4.1 4.3 - - - +
270E SER* 3.4 35.0 - - - +
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Residues in contact with SER 119 (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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115E ALA 2.8 21.1 + - - -
116E LEU 3.5 4.9 - - - -
118E ALA* 1.3 73.4 - - - +
120E LEU* 1.3 56.4 + - - +
122E HIS* 3.2 2.4 + - - +
123E TYR* 2.9 51.8 + - - -
265E HIS* 3.3 14.7 - - - +
266E SER* 3.2 17.2 + - - -
267E HIS* 2.9 30.1 + - - -
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Residues in contact with LEU 120 (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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107E SER* 4.8 11.9 - - - +
116E LEU* 3.0 29.1 + - + +
117E ALA* 3.9 7.6 - - - +
119E SER* 1.3 72.9 - - - +
121E ASN* 1.3 64.8 + - - +
122E HIS 3.1 1.6 - - - -
123E TYR* 3.4 17.0 + - + +
124E ALA* 3.1 23.6 + - - +
138E CYS* 5.6 2.2 - - - -
141E LEU* 4.1 15.0 - - + +
150E MET* 4.0 24.7 - - - -
361E MET* 3.8 26.2 - - + -
362E VAL 3.9 13.0 - - - +
363E SER* 3.6 25.0 - - - -
364E GLY 5.1 2.3 + - - -
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Residues in contact with ASN 121 (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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117E ALA 3.0 19.1 + - - +
118E ALA 3.5 6.6 - - - +
120E LEU* 1.3 76.2 - - - +
122E HIS* 1.3 60.9 + - - +
124E ALA* 3.4 10.1 + - - +
126E TYR* 3.2 49.5 + - - +
127E GLU 2.8 26.5 - - - +
128E GLN* 4.6 1.7 - - - -
129E VAL* 3.7 5.0 + - - +
134E LEU* 3.5 18.9 - - + +
137E ASN* 3.2 24.9 - - - +
138E CYS* 4.8 3.1 - - - -
141E LEU* 4.6 5.8 - - - +
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Residues in contact with HIS 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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118E ALA 3.1 17.0 + - - +
119E SER 3.5 4.5 - - - +
120E LEU 3.1 0.2 - - - -
121E ASN* 1.3 76.3 - - - +
123E TYR* 1.3 67.8 + + - +
124E ALA 3.0 4.5 - - - -
125E GLY* 3.1 14.2 + - - -
126E TYR 4.4 13.2 - - - +
127E GLU 6.4 0.2 - - - -
128E GLN* 5.6 4.5 - - + -
266E SER* 3.8 14.1 + - - -
267E HIS* 3.5 21.1 - + + +
273E PHE* 3.3 37.6 - + - -
276E PRO 5.8 0.2 - - - -
277E MET 5.9 1.3 - - - -
278E GLY* 5.9 5.4 - - - -
279E ARG 6.0 0.4 - - - -
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Residues in contact with TYR 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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119E SER* 2.9 27.3 + - - -
120E LEU* 3.4 24.0 + - + +
122E HIS* 1.3 82.8 - + - +
124E ALA* 1.3 58.6 + - - +
125E GLY* 3.2 0.6 + - - -
150E MET* 4.8 0.4 - - + -
264E LEU 4.6 0.3 + - - -
265E HIS* 2.8 39.2 + + - +
266E SER* 3.2 34.3 + - - -
279E ARG* 3.4 67.6 - - + +
363E SER* 5.7 1.8 - - - -
364E GLY 3.5 16.8 - - - +
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Residues in contact with ALA 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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120E LEU 3.1 16.0 + - - +
121E ASN 3.5 8.5 - - - +
122E HIS 3.0 1.0 - - - -
123E TYR* 1.3 78.4 - - - +
125E GLY* 1.3 59.5 + - - +
126E TYR* 3.5 24.8 + - + -
141E LEU* 3.8 21.3 - - + -
364E GLY* 4.1 14.6 - - - -
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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