Contacts of the helix formed by residues 115 - 126 (chain B) in PDB entry 1R2B
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 GLU 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B MET* 4.5 20.7 - - + +
113B GLN* 3.5 31.1 + - - +
114B MET* 1.3 73.1 + - - +
116B HIS* 1.3 69.5 + - + +
118B VAL* 3.2 8.7 + - - +
119B ASP* 2.8 30.5 + - - +
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Residues in contact with HIS 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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11A PHE* 5.2 0.9 - - + -
114B MET 3.4 0.8 - - - -
115B GLU* 1.3 83.4 + - + +
117B VAL* 1.3 57.9 + - - +
119B ASP* 3.3 7.9 + - - +
120B THR* 2.9 33.4 + - - +
1423D ARG* 3.2 51.2 - - + +
1424D SER* 3.6 12.1 - - - +
1425D ILE* 3.4 31.2 + - - -
1426D HIS* 3.9 8.3 + - - -
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 4.1 8.3 - - + -
86B LEU* 4.1 18.2 - - + -
89B PHE* 3.7 38.1 - - + -
95B LEU* 3.9 24.2 - - + -
105B VAL* 5.1 1.6 - - + -
109B ALA* 4.3 6.3 - - + -
114B MET* 3.3 20.3 + - + +
115B GLU 3.3 0.4 - - - -
116B HIS* 1.3 73.5 - - - +
118B VAL* 1.3 65.6 + - - +
120B THR* 3.3 7.9 + - - -
121B CYS* 3.0 28.4 + - - -
1424D SER 3.8 10.1 + - - +
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Residues in contact with VAL 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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106B MET* 3.2 52.0 - - + +
109B ALA* 3.7 10.3 - - + -
110B MET* 3.8 33.0 - - + +
114B MET 3.1 15.8 + - - +
115B GLU* 3.4 9.4 - - - +
117B VAL* 1.3 76.3 - - - +
119B ASP* 1.3 59.6 + - - +
121B CYS* 3.2 5.6 + - - -
122B ARG* 3.0 32.6 + - - +
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Residues in contact with ASP 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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115B GLU 2.8 17.2 + - - +
116B HIS* 3.6 7.9 - - - +
118B VAL* 1.3 80.0 - - - +
120B THR* 1.3 56.8 + - - +
122B ARG* 3.3 25.8 + - - +
123B LYS* 3.0 29.8 + - - +
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Residues in contact with THR 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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9A ILE* 3.9 33.7 - - + -
11A PHE* 3.5 23.3 - - + -
116B HIS* 2.9 23.8 + - - +
117B VAL 3.6 5.2 - - - -
118B VAL 3.3 0.2 - - - -
119B ASP* 1.3 73.4 - - - +
121B CYS* 1.3 60.5 + - - +
123B LYS* 3.2 13.3 + - - +
124B PHE* 2.9 26.3 + - - +
1420D GLU* 3.7 27.4 - - + +
1423D ARG 5.5 0.7 + - - -
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Residues in contact with CYS 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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9A ILE* 5.1 2.0 - - - -
95B LEU* 4.2 23.1 - - - -
97B LEU* 4.2 8.7 - - - -
102B ILE* 3.8 13.0 - - + -
105B VAL* 4.8 6.7 - - - -
106B MET* 3.5 32.1 - - + -
117B VAL* 3.0 21.6 + - - -
118B VAL* 3.2 8.9 + - - +
120B THR* 1.3 75.2 - - - +
122B ARG* 1.3 66.1 + - - +
124B PHE* 2.8 19.5 + - - +
125B ILE* 2.9 17.2 + - - +
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Residues in contact with ARG 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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106B MET* 3.2 13.7 - - + +
118B VAL* 3.0 22.6 + - - +
119B ASP* 3.3 26.7 + - - +
121B CYS* 1.3 76.5 - - - +
123B LYS* 1.3 64.9 + - - +
124B PHE 3.0 0.9 + - - -
125B ILE* 3.1 15.4 + - + +
126B LYS* 3.2 27.7 + - + +
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Residues in contact with LYS 123 (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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119B ASP* 3.0 15.9 + - - +
120B THR* 3.4 13.7 - - - +
122B ARG* 1.3 76.9 - - - +
124B PHE* 1.3 63.1 - - - +
126B LYS* 3.5 19.9 + - + +
127B ALA* 3.9 6.1 + - - +
1420D GLU* 3.2 34.8 + - - -
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Residues in contact with PHE 124 (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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7A SER* 4.0 31.6 - - - -
9A ILE* 4.3 17.7 - - + -
97B LEU* 4.6 17.5 - - + -
102B ILE* 4.7 11.0 - - + -
120B THR 2.9 12.9 + - - +
121B CYS* 2.8 16.5 + - - +
123B LYS* 1.3 75.4 - - - +
125B ILE* 1.3 68.4 + - + -
127B ALA* 3.0 9.6 + - + +
128B SER* 2.9 51.8 + - - -
1418D VAL* 4.7 17.0 - - + -
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Residues in contact with ILE 125 (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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102B ILE* 4.4 5.6 - - + -
103B MET* 3.1 38.1 - - + -
106B MET* 3.8 24.2 - - + -
121B CYS 2.9 10.2 + - - +
122B ARG* 3.6 7.4 - - + +
124B PHE* 1.3 85.0 - - + +
126B LYS* 1.3 62.3 + - + +
127B ALA 3.0 2.3 + - - -
128B SER 3.3 22.8 - - - -
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Residues in contact with LYS 126 (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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122B ARG* 3.2 25.2 + - + +
123B LYS* 3.7 12.8 - - - +
124B PHE 3.1 1.4 - - - -
125B ILE* 1.3 75.8 - - + +
127B ALA* 1.3 57.2 + - - +
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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