Contacts of the helix formed by residues 146 - 159 (chain B) in PDB entry 2JJ7
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 SER 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A GLU* 5.8 0.9 - - - -
144B PHE* 3.4 5.3 - - - -
145B PHE* 1.3 91.9 - - - +
147B ILE* 1.3 60.1 + - - +
148B ASN* 3.4 6.4 + - - +
149B HIS* 2.8 42.7 + - - +
150B THR* 2.8 32.1 + - - -
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Residues in contact with ILE 147 (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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130B LYS* 3.9 29.2 - - + +
133B LEU* 3.5 38.4 - - + -
134B GLN* 4.0 17.0 - - + +
137B GLU* 5.4 2.0 - - - +
144B PHE* 3.8 21.3 - - + -
146B SER* 1.3 72.7 + - - +
148B ASN* 1.3 69.9 + - - +
150B THR* 3.4 3.2 + - - -
151B ILE* 2.9 41.8 + - + +
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Residues in contact with ASN 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ILE* 5.1 3.0 - - + +
130B LYS* 5.0 7.8 + - - +
146B SER* 3.4 6.9 + - - +
147B ILE* 1.3 86.3 - - - +
149B HIS* 1.3 63.8 + - + +
151B ILE* 3.5 16.4 + - - +
152B HIS* 2.9 28.4 + - - +
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Residues in contact with HIS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A TYR* 3.7 12.7 + - + -
106A GLU* 2.9 50.8 + - - +
109A ILE* 3.5 29.6 - - + +
110A LYS* 3.8 19.8 - - + +
160A PHE* 4.6 1.1 - - - -
145B PHE* 3.5 26.3 - + + -
146B SER* 2.8 35.6 + - - +
148B ASN* 1.3 80.9 - - + +
150B THR* 1.3 52.7 + - - +
152B HIS* 3.4 4.3 + - - -
153B TRP* 2.8 33.9 + - - +
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Residues in contact with THR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A PHE* 4.1 10.2 - - + -
133B LEU* 3.9 18.6 - - + -
144B PHE* 3.2 24.0 - - + +
145B PHE* 4.9 0.9 + - - -
146B SER 2.8 22.7 + - - -
147B ILE* 3.6 4.5 - - - -
149B HIS* 1.3 74.0 - - - +
151B ILE* 1.3 65.0 + - - +
153B TRP* 3.3 15.4 + - + +
154B ILE* 3.0 28.2 + - + +
180B LEU* 3.6 30.1 - - + -
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Residues in contact with ILE 151 (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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108B ILE* 6.5 0.9 - - + -
129B LEU* 4.1 19.0 - - + +
130B LYS* 3.7 32.8 - - + +
133B LEU* 3.9 16.2 - - + -
147B ILE* 2.9 34.4 + - + +
148B ASN* 3.7 16.6 - - - +
150B THR* 1.3 76.5 - - - +
152B HIS* 1.3 62.6 + - - +
154B ILE* 3.3 1.6 + - - +
155B THR* 2.8 37.8 + - - +
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Residues in contact with HIS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A TYR* 3.2 23.8 - - - -
109A ILE* 3.3 30.2 - - + +
152A HIS* 3.3 28.5 + + - +
105B TYR* 3.3 27.8 + + - -
109B ILE* 4.0 18.3 - - + +
148B ASN 2.9 19.3 + - - +
149B HIS 3.8 3.1 - - - +
151B ILE* 1.3 78.2 - - - +
153B TRP* 1.3 62.3 + - - +
155B THR* 3.7 7.0 - - - +
156B SER* 3.0 23.5 + - - -
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Residues in contact with TRP 153 (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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105A TYR* 3.2 14.7 + - - +
156A SER* 3.5 27.5 + - - -
157A ILE* 5.5 0.2 - - - +
160A PHE* 3.4 61.8 - + + +
163A PHE* 3.6 35.0 - + + +
149B HIS 2.8 20.4 + - - +
150B THR* 3.6 6.7 - - + +
151B ILE 3.3 0.2 - - - -
152B HIS* 1.3 72.7 - - - +
154B ILE* 1.3 89.2 + - + +
156B SER* 2.8 19.8 + - - -
157B ILE* 3.2 25.7 + - + +
176B ILE* 4.0 25.1 - - + -
179B ALA* 3.7 21.3 - - + -
180B LEU* 4.4 9.9 - - + -
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Residues in contact with ILE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 5.0 2.9 - - + -
86B TYR* 4.9 3.1 - - + -
87B LEU* 4.0 13.2 - - + -
126B PHE* 5.1 1.8 - - + -
129B LEU* 3.8 36.8 - - + -
133B LEU* 4.4 1.6 - - + -
150B THR* 3.0 27.7 + - + +
153B TRP* 1.3 90.4 - - + +
155B THR* 1.3 61.5 + - - +
157B ILE* 3.3 6.6 + - - -
158B VAL* 2.8 54.4 + - + +
176B ILE* 3.9 22.2 - - + -
180B LEU* 4.2 16.6 - - + -
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Residues in contact with THR 155 (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 TYR* 4.0 15.7 - - + -
108B ILE* 3.9 27.2 - - + +
109B ILE* 5.6 0.7 - - + -
126B PHE* 3.4 22.3 - - + -
129B LEU* 4.6 1.6 - - - +
151B ILE* 2.8 32.1 + - - +
152B HIS* 3.7 10.1 - - - +
154B ILE* 1.3 77.2 - - - +
156B SER* 1.3 61.9 + - - +
159B LEU* 3.2 48.6 + - + +
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Residues in contact with SER 156 (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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149A HIS* 3.0 22.5 + - - -
152A HIS 3.9 16.6 + - - -
153A TRP* 3.9 3.6 - - - -
156A SER* 2.6 31.6 + - - -
105B TYR* 3.8 21.8 - - - -
152B HIS* 3.0 20.1 + - - -
153B TRP 2.8 13.7 + - - -
155B THR* 1.3 77.0 - - - +
157B ILE* 1.3 62.1 + - - +
160B PHE* 3.5 7.6 + - - +
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Residues in contact with ILE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A TRP* 3.9 18.4 - - + +
156A SER* 3.8 23.1 - - - -
157A ILE* 4.6 10.3 - - + -
163A PHE* 4.7 5.6 - - + -
153B TRP* 3.2 41.5 + - + +
154B ILE* 3.4 9.4 - - - +
156B SER* 1.3 81.5 + - - +
158B VAL* 1.3 67.3 + - - +
159B LEU 3.5 0.2 + - - -
160B PHE* 3.6 12.1 + - - +
163B PHE* 3.8 15.6 - - - +
172B LEU* 4.2 16.1 - - + +
176B ILE* 3.6 35.2 - - + -
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B TYR* 5.9 0.2 - - + -
87B LEU* 4.0 10.8 - - + -
90B PHE* 4.1 19.1 - - + -
91B THR* 4.1 19.5 - - + +
94B ILE* 3.7 7.1 - - - +
126B PHE* 4.0 24.2 - - + -
154B ILE* 2.8 34.9 + - + +
157B ILE* 1.3 72.2 - - - +
159B LEU* 1.3 62.5 + - + +
163B PHE* 3.5 19.9 - - - -
172B LEU* 4.7 5.8 - - + -
176B ILE* 3.7 28.0 - - + -
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Residues in contact with LEU 159 (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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149A HIS* 3.3 13.1 - - + -
94B ILE* 3.9 15.5 - - + +
101B GLY* 3.2 29.6 - - - +
104B ALA* 4.3 2.9 - - + -
105B TYR* 3.8 21.3 - - - +
108B ILE* 3.7 30.1 - - + -
122B PHE* 3.6 32.1 - - + -
126B PHE* 3.8 19.5 - - + -
155B THR* 3.2 25.0 + - + +
158B VAL* 1.3 77.8 - - + +
160B PHE* 1.3 64.5 + - - +
161B PRO 3.2 3.6 - - - -
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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