Contacts of the strand formed by residues 113 - 122 (chain C) in PDB entry 1SOT
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 VAL 113 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62C TYR* 6.0 0.7 - - + -
105C ILE* 3.4 26.9 - - + -
106C VAL 3.4 6.3 - - - +
107C ALA* 4.5 12.1 - - + -
111C GLY 3.4 16.6 - - - +
112C ARG* 1.3 74.5 - - - +
114C PHE* 1.3 72.7 + - - +
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Residues in contact with PHE 114 (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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105C ILE* 3.3 8.8 - - - +
106C VAL* 2.8 38.2 + - + +
108C LEU* 3.9 26.7 - - + -
112C ARG* 3.8 47.6 - - + -
113C VAL* 1.3 79.8 - - - +
115C GLU* 1.3 69.5 + - - +
132C ILE* 3.8 28.7 - - + -
133C ASN* 3.4 45.3 - - + +
136C GLY 6.4 0.2 - - - -
138C LEU* 4.1 3.8 - - + -
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Residues in contact with GLU 115 (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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103C GLN* 4.7 17.3 + - + +
104C ILE 3.7 9.9 - - - +
105C ILE* 4.1 12.8 - - + -
114C PHE* 1.3 78.6 - - - +
116C ALA* 1.3 69.3 + - - +
131C LYS 4.2 0.2 - - - +
132C ILE* 3.6 14.9 - - - +
133C ASN 4.9 1.2 + - - -
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Residues in contact with ALA 116 (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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104C ILE* 2.8 35.1 + - + +
106C VAL* 4.1 8.3 - - + -
115C GLU* 1.3 84.5 - - - +
117C LEU* 1.3 60.9 + - - +
118C LEU 3.9 1.2 + - - -
130C LEU* 4.1 27.8 - - + -
131C LYS 3.5 4.7 - - - +
132C ILE* 3.6 18.8 - - + -
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Residues in contact with LEU 117 (chain C).
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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116C ALA* 1.3 73.0 - - - +
118C LEU* 1.3 74.8 + - - +
119C VAL* 3.5 9.9 + - + +
130C LEU* 3.2 8.8 - - - -
131C LYS* 2.9 54.2 + - + +
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Residues in contact with LEU 118 (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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98C ILE* 4.3 25.6 - - + +
104C ILE* 4.3 18.3 - - + +
116C ALA 3.9 2.4 + - - -
117C LEU* 1.3 83.5 - - - +
119C VAL* 1.3 60.6 + - - +
120C GLY* 2.9 51.4 - - - +
121C SER* 4.8 6.1 - - - +
128C ALA* 5.2 0.4 - - + -
129C VAL 3.8 6.7 - - - +
130C LEU* 4.1 7.2 - - + +
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Residues in contact with VAL 119 (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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90C TYR* 4.0 13.5 - - + -
117C LEU* 3.9 12.6 - - + +
118C LEU* 1.3 74.9 - - - +
120C GLY* 1.3 58.2 + - - +
129C VAL* 2.9 38.9 + - + +
130C LEU 3.9 13.7 - - - -
131C LYS* 4.1 6.3 - - + -
248C LEU 3.6 30.7 - - - +
249C ILE* 4.1 11.7 - - + +
252C GLY* 3.8 11.1 - - - +
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Residues in contact with GLY 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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118C LEU* 2.9 16.5 - - - +
119C VAL* 1.3 82.3 - - - +
121C SER* 1.3 61.2 + - - -
128C ALA* 3.3 0.5 - - - -
129C VAL 2.9 24.6 + - - +
248C LEU* 3.7 20.4 - - - -
252C GLY 4.0 7.9 - - - -
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Residues in contact with SER 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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95C LYS* 3.5 31.3 - - - +
98C ILE* 4.4 10.4 - - - +
118C LEU* 4.8 4.3 - - - +
120C GLY* 1.3 75.4 - - - -
122C ASP* 1.3 64.0 + - - +
127C LEU 3.4 11.9 - - - -
128C ALA* 3.9 8.7 - - - +
248C LEU* 3.7 14.8 - - - +
252C GLY 4.8 1.2 + - - -
253C ARG* 4.8 6.4 - - - +
254C VAL 4.9 0.9 + - - -
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Residues in contact with ASP 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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95C LYS* 3.7 3.5 - - - +
121C SER* 1.3 78.3 - - - +
123C SER* 1.3 60.9 + - - +
124C LEU* 4.0 4.2 + - - +
125C THR* 2.8 25.1 + - - +
126C ASP* 2.9 24.3 + - - -
127C LEU 2.8 17.5 + - - +
244C ILE* 4.0 8.6 - - + +
248C LEU* 4.7 0.2 - - - +
254C VAL* 3.7 24.9 + - + +
256C ARG* 2.7 45.5 + - - -
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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