Contacts of the strand formed by residues 113 - 122 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B ILE* 3.1 37.2 - - + -
106B VAL 3.5 6.1 - - - +
107B ALA* 4.2 12.8 - - + -
111B GLY 3.1 18.4 - - - +
112B ARG* 1.3 74.7 - - - +
114B PHE* 1.3 71.7 + - - +
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Residues in contact with PHE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ILE* 3.3 7.2 - - - +
106B VAL* 2.8 42.2 + - + +
108B LEU* 4.1 19.5 - - + -
112B ARG* 3.9 37.0 - - + -
113B VAL* 1.3 81.2 - - - +
115B GLU* 1.3 68.7 + - - +
132B ILE* 3.7 33.4 - - + -
133B ASN 3.7 18.8 - - - -
134B ALA* 3.5 30.7 - - + -
138B LEU* 4.3 3.8 - - + -
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B GLN* 3.0 40.4 + - + +
104B ILE 3.7 10.8 - - - +
105B ILE* 4.4 4.5 - - + +
114B PHE* 1.3 77.1 - - - +
116B ALA* 1.3 66.3 + - - +
131B LYS 4.3 0.2 - - - +
132B ILE* 3.7 14.2 - - - +
133B ASN 5.1 1.4 + - - -
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ILE* 2.8 42.9 + - + +
106B VAL* 4.4 7.0 - - + -
115B GLU* 1.3 82.1 - - - +
117B LEU* 1.3 63.5 + - - +
118B LEU 4.0 1.2 + - - -
130B LEU* 4.1 21.1 - - + -
131B LYS 3.4 4.3 - - - +
132B ILE* 3.6 18.2 - - + -
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Residues in contact with LEU 117 (chain B).
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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116B ALA* 1.3 72.9 - - - +
118B LEU* 1.3 77.3 + - + +
119B VAL* 3.4 7.1 + - + +
130B LEU* 3.1 7.4 - - - -
131B LYS* 2.7 57.3 + - + +
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ILE* 4.3 26.9 - - + +
101B ALA* 6.2 0.7 - - + -
104B ILE* 3.8 24.5 - - + +
116B ALA 4.0 2.4 + - - -
117B LEU* 1.3 82.1 - - + +
119B VAL* 1.3 63.9 + - - +
120B GLY* 3.4 31.4 - - - +
121B SER* 5.9 1.6 - - - +
128B ALA* 4.5 1.6 - - + -
129B VAL 3.6 8.5 - - - +
130B LEU* 4.0 10.0 - - + +
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B TYR* 4.3 7.4 - - + -
117B LEU* 3.8 17.3 - - + +
118B LEU* 1.3 75.1 - - - +
120B GLY* 1.3 58.5 + - - +
129B VAL* 2.9 37.5 + - + +
131B LYS* 4.0 18.4 - - + -
248B LEU* 3.4 28.5 - - + +
249B ILE* 4.0 11.0 - - + +
252B GLY* 3.5 18.9 - - - +
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Residues in contact with GLY 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LEU* 3.3 15.9 - - - +
119B VAL* 1.3 84.2 - - - +
121B SER* 1.3 63.3 + - - -
128B ALA* 3.3 1.0 - - - -
129B VAL 3.0 24.1 + - - -
248B LEU* 3.9 11.0 - - - -
252B GLY 3.6 13.5 - - - -
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Residues in contact with SER 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LYS* 3.4 34.6 - - - -
98B ILE* 4.6 6.3 - - - +
118B LEU* 5.0 2.1 - - - +
120B GLY* 1.3 75.8 - - - -
122B ASP* 1.3 62.9 + - - +
127B LEU 3.3 11.9 - - - -
128B ALA* 3.8 8.5 - - - +
248B LEU* 3.6 15.6 - - - +
252B GLY 4.4 1.6 + - - -
253B ARG* 4.4 8.3 - - - +
254B VAL 4.7 1.4 + - - -
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Residues in contact with ASP 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LYS* 4.0 3.1 - - - -
121B SER* 1.3 77.2 - - - +
123B SER* 1.3 58.7 + - - +
124B LEU 4.1 2.9 + - - -
125B THR* 2.6 35.3 + - - +
126B ASP* 2.9 24.8 + - - -
127B LEU 2.7 17.1 + - - +
244B ILE* 3.9 9.0 - - + +
248B LEU* 4.9 0.4 - - + -
254B VAL* 3.7 22.8 - - + +
256B ARG* 3.0 39.5 + - - -
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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