Contacts of the helix formed by residues 119 - 129 (chain E) in PDB entry 1S89
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 119 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109D ALA 3.3 18.8 + - - -
110D THR* 3.9 17.7 - - + +
113D ASN* 3.2 16.5 - - - +
114D ILE 2.9 26.6 + - - +
116D VAL* 4.1 5.3 - - - +
25E MET* 5.6 5.2 - - + -
89E PHE* 3.5 12.6 - - - -
117E ALA* 3.5 1.1 - - - +
118E THR* 1.3 83.4 + - - +
120E VAL* 1.3 58.4 + - - +
121E ALA 3.6 0.3 + - - -
122E THR* 2.7 42.4 + - - -
123E ALA* 3.0 23.0 + - - +
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Residues in contact with VAL 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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113D ASN* 3.3 12.4 + - - +
139D LEU* 6.3 4.9 - - + -
25E MET* 4.0 28.2 - - + +
29E TRP* 4.0 16.2 - - + -
32E ARG* 4.3 14.8 - - - +
89E PHE* 3.8 26.2 - - + -
119E ASN* 1.3 72.1 - - - +
121E ALA* 1.3 59.3 + - - +
123E ALA* 2.9 3.8 + - - +
124E ASP* 2.7 50.4 + - - +
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Residues in contact with ALA 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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113D ASN* 2.9 48.4 + - - +
114D ILE 4.2 7.9 - - - -
115D PRO* 4.2 6.3 - - + -
138D ILE* 4.1 15.5 - - + -
119E ASN* 4.0 0.4 - - - +
120E VAL* 1.3 74.8 - - - +
122E THR* 1.3 61.7 + - - +
124E ASP* 3.5 5.3 + - - +
125E PHE* 3.1 33.6 + - + -
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Residues in contact with THR 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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114D ILE 3.5 0.3 + - - -
115D PRO* 3.3 6.0 - - - +
116D VAL* 2.9 39.4 + - - +
122D THR* 4.5 0.2 - - + -
126D ILE* 4.4 8.1 - - + -
116E VAL 3.6 9.6 - - - +
117E ALA* 3.6 25.6 - - + -
118E THR* 4.5 1.4 + - - +
119E ASN* 2.7 32.2 + - - -
121E ALA* 1.3 71.3 - - - +
123E ALA* 1.3 66.3 + - - +
125E PHE* 3.3 4.3 + - - +
126E ILE* 3.0 30.6 + - + +
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Residues in contact with ALA 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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29E TRP* 3.6 29.4 - - + +
87E ILE* 4.6 4.9 - - + +
89E PHE* 4.2 10.1 - - + -
117E ALA* 3.6 16.1 - - + +
119E ASN 3.0 14.2 + - - +
120E VAL* 2.9 11.3 + - - +
122E THR* 1.3 77.4 - - - +
124E ASP* 1.3 62.5 + - - +
126E ILE* 3.3 4.9 + - - +
127E ILE* 3.0 28.2 + - - +
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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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29E TRP* 2.8 22.5 + - - -
32E ARG* 5.1 4.5 + - - -
33E HIS* 3.0 19.6 + - - -
120E VAL* 2.7 34.0 + - - +
121E ALA* 3.9 6.8 - - - +
123E ALA* 1.3 73.6 - - - +
125E PHE* 1.3 65.2 + - + +
127E ILE* 3.4 4.6 - - - +
128E GLN* 3.1 44.8 + - - +
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Residues in contact with PHE 125 (chain E).
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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8D LEU* 5.0 3.1 - - + -
12D LYS* 4.9 5.2 - - - -
85D VAL* 6.0 0.7 - - + -
115D PRO* 3.7 23.3 - - + -
125D PHE 4.0 1.9 - - - +
126D ILE* 3.7 28.9 - - + -
129D SER* 2.7 42.6 + - - -
131D HIS* 4.0 20.2 - - + -
132D PHE* 3.8 36.3 - + - -
136D VAL* 4.3 25.4 - - + -
138D ILE* 5.9 1.6 - - + -
121E ALA* 3.1 30.8 + - + +
122E THR* 3.7 6.1 - - - +
123E ALA 3.3 0.2 - - - -
124E ASP* 1.3 78.9 - - + +
126E ILE* 1.3 62.7 + - - +
128E GLN* 4.9 3.6 - - - -
129E SER* 3.3 9.5 + - - -
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Residues in contact with ILE 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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122D THR* 4.5 6.5 - - + -
125D PHE* 3.8 29.5 - - + -
126D ILE* 5.0 3.4 - - + -
85E VAL* 4.6 11.2 - - + -
87E ILE* 5.3 4.7 - - + -
115E PRO* 4.3 8.1 - - + -
116E VAL 3.8 35.0 - - - +
117E ALA* 3.8 13.5 - - + +
122E THR* 3.0 26.0 + - + +
123E ALA* 3.6 4.7 - - - +
124E ASP 3.2 0.2 - - - -
125E PHE* 1.3 74.7 - - - +
127E ILE* 1.3 67.5 + - + +
129E SER* 3.1 19.2 + - - -
132E PHE* 3.6 29.9 - - + +
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Residues in contact with ILE 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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29E TRP* 3.5 31.0 - - + -
33E HIS* 3.3 50.9 - - + +
36E LEU* 4.0 25.3 - - + +
37E LEU* 5.1 3.6 - - + -
87E ILE* 5.7 2.5 - - + -
123E ALA 3.0 12.0 + - - +
124E ASP* 3.4 9.4 - - - +
126E ILE* 1.3 76.7 - - + +
128E GLN* 1.3 66.0 + - + +
129E SER 4.2 0.3 - - - +
132E PHE* 3.8 41.5 - - + +
133E ASN* 4.8 4.2 + - - -
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Residues in contact with GLN 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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129D SER* 4.0 11.8 + - - +
130D PRO* 3.4 20.3 - - + +
131D HIS* 3.0 34.4 - - + +
33E HIS* 4.8 9.4 - - + -
124E ASP* 3.1 42.0 + - - +
125E PHE* 5.0 2.4 - - - -
127E ILE* 1.3 81.7 - - + +
129E SER* 1.3 64.8 - - - +
130E PRO* 3.6 1.0 - - - +
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Residues in contact with SER 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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125D PHE* 2.6 49.7 + - - -
128D GLN* 3.8 4.5 + - - +
129D SER* 3.8 7.3 + - - -
125E PHE 3.3 7.5 + - - -
126E ILE 3.1 14.7 + - - -
127E ILE 4.2 0.9 - - - +
128E GLN* 1.3 79.9 - - - +
130E PRO* 1.3 78.0 - - - +
131E HIS* 4.5 1.7 + - - +
132E PHE* 3.1 18.4 + - - +
133E ASN* 4.5 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