Contacts of the helix formed by residues 119 - 129 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89C PHE* 3.4 13.1 - - - -
117C ALA* 3.6 1.3 - - - +
118C THR* 1.3 81.2 + - - +
120C VAL* 1.3 57.6 + - - +
121C ALA 4.2 0.2 - - - -
122C THR* 2.7 41.1 + - - -
123C ALA* 3.0 24.1 + - - +
109F ALA 3.2 20.2 + - - -
110F THR* 3.9 17.1 + - + +
113F ASN* 3.3 15.8 - - + +
114F ILE 3.1 27.0 + - - +
116F VAL* 4.2 3.6 - - - +
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Residues in contact with VAL 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C MET* 4.5 24.5 - - + +
29C TRP* 4.1 18.2 - - + -
32C ARG* 4.7 9.4 - - - +
89C PHE* 3.8 25.1 - - + -
119C ASN* 1.3 71.2 - - - +
121C ALA* 1.3 68.9 + - - +
123C ALA* 3.0 3.0 + - - +
124C ASP* 2.8 39.7 + - - +
113F ASN* 3.2 13.1 + - - +
139F LEU* 6.3 5.4 - - + -
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Residues in contact with ALA 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ASN* 4.0 1.1 - - - +
120C VAL* 1.3 75.7 - - - +
122C THR* 1.3 62.8 + - - +
124C ASP* 3.4 6.2 + - - +
125C PHE* 3.2 31.1 + - + -
113F ASN* 2.9 47.4 + - - +
115F PRO* 4.1 16.2 - - + -
138F ILE* 4.1 15.5 - - + -
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Residues in contact with THR 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C VAL 3.8 8.7 - - - +
117C ALA* 3.8 8.1 - - + -
118C THR* 4.6 2.4 + - - +
119C ASN* 2.7 28.9 + - - -
121C ALA* 1.3 70.2 - - - +
123C ALA* 1.3 66.0 + - - +
125C PHE* 3.3 4.5 + - - +
126C ILE* 3.0 44.0 + - + +
114F ILE 3.5 0.3 + - - -
115F PRO* 3.3 7.0 - - - +
116F VAL* 3.0 43.3 + - - +
122F THR* 4.6 0.2 - - + -
126F ILE* 4.3 8.7 - - + -
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Residues in contact with ALA 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C TRP* 3.5 38.0 - - + +
87C ILE* 4.5 5.5 - - + +
89C PHE* 3.9 14.8 - - + -
117C ALA* 3.6 16.1 - - + +
119C ASN 3.0 19.2 + - - +
120C VAL 3.0 5.1 + - - +
122C THR* 1.3 77.1 - - - +
124C ASP* 1.3 61.5 + - - +
126C ILE* 3.9 2.5 - - - +
127C ILE* 3.1 19.6 + - - +
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Residues in contact with ASP 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C TRP* 2.6 33.4 + - - -
32C ARG* 5.6 1.3 + - - -
33C HIS* 3.3 12.9 + - + -
120C VAL* 2.8 31.1 + - - +
121C ALA* 3.7 6.1 - - - +
123C ALA* 1.3 75.0 - - - +
125C PHE* 1.3 67.8 + - + +
127C ILE* 3.4 8.3 - - - +
128C GLN* 3.2 36.4 + - - +
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Residues in contact with PHE 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ALA* 3.2 25.4 + - + +
122C THR* 3.8 7.9 - - - +
124C ASP* 1.3 82.4 - - + +
126C ILE* 1.3 62.6 + - - +
128C GLN* 5.2 1.3 - - - -
129C SER* 3.3 9.9 + - - -
8F LEU* 4.9 2.2 - - + -
12F LYS* 4.7 7.2 - - - -
85F VAL* 6.3 0.2 - - + -
115F PRO* 3.7 26.5 - - + -
125F PHE 3.8 2.3 - - - +
126F ILE* 3.8 25.1 - - + -
129F SER* 2.8 43.3 + - - -
131F HIS* 3.9 16.8 - - + -
132F PHE* 3.7 36.3 - + - -
136F VAL* 4.1 30.3 - - + -
138F ILE* 6.1 0.2 - - + -
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Residues in contact with ILE 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C VAL* 4.8 7.2 - - + -
87C ILE* 5.4 4.5 - - + -
115C PRO* 4.4 12.6 - - + -
116C VAL 3.6 39.7 - - - +
117C ALA* 3.8 6.7 - - + +
122C THR* 3.0 31.4 + - + +
123C ALA* 3.9 4.0 - - - +
124C ASP 3.2 0.2 - - - -
125C PHE* 1.3 78.1 - - - +
127C ILE* 1.3 63.9 + - + +
129C SER* 3.3 20.4 + - - -
132C PHE* 3.5 28.0 - - + -
122F THR* 4.3 8.5 - - + -
125F PHE* 3.7 24.5 - - + -
126F ILE* 4.8 4.0 - - + -
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Residues in contact with ILE 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C TRP* 3.7 25.8 - - + -
33C HIS* 3.8 43.3 - - + +
36C LEU* 3.3 39.6 - - + +
37C LEU* 4.0 17.5 - - + -
123C ALA 3.1 15.0 + - - +
124C ASP* 3.4 11.0 - - - +
126C ILE* 1.3 80.3 - - + +
128C GLN* 1.3 68.6 + - + +
129C SER 4.2 0.2 - - - +
132C PHE* 3.8 27.8 - - + +
133C ASN* 5.6 0.5 + - - -
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Residues in contact with GLN 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C HIS* 5.6 4.7 - - + -
124C ASP* 3.2 25.4 + - - +
125C PHE* 5.2 0.7 - - - -
127C ILE* 1.3 87.1 - - + +
129C SER* 1.3 66.8 + - - +
130C PRO* 3.3 3.1 - - - +
129F SER* 4.1 9.1 + - - +
130F PRO* 3.5 19.7 - - + +
131F HIS* 3.4 36.8 + - - +
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Residues in contact with SER 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C PHE 3.3 8.7 + - - -
126C ILE 3.3 15.6 + - - -
128C GLN* 1.3 78.3 - - - +
130C PRO* 1.3 79.0 - - - +
131C HIS* 4.2 2.3 + - - +
132C PHE* 3.0 21.5 + - - +
133C ASN* 5.6 0.3 + - - -
125F PHE* 3.0 48.7 + - - -
128F GLN* 4.1 6.1 + - - +
129F SER* 3.7 4.7 + - - -
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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