Contacts of the helix formed by residues 146 - 160 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A PHE* 3.7 2.0 - - - -
145A PHE* 1.3 81.2 - - - +
147A ILE* 1.3 60.3 + - - +
148A ASN* 3.5 3.5 + - - +
149A HIS* 3.1 24.0 + - - +
150A THR* 2.7 33.5 + - - -
102B THR* 4.4 15.9 - - - -
106B GLU* 2.7 29.0 + - - -
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Residues in contact with ILE 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LYS* 4.1 13.9 - - + +
133A LEU* 3.6 35.9 - - + -
134A GLN* 3.8 32.5 - - + +
137A GLU* 5.5 1.3 - - - +
144A PHE* 3.8 22.6 - - + -
145A PHE 4.3 0.2 - - - -
146A SER* 1.3 70.1 + - - +
148A ASN* 1.3 71.4 + - - +
150A THR* 3.2 3.1 + - - -
151A ILE* 2.8 46.8 + - + +
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Residues in contact with ASN 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LYS* 4.5 10.6 + - - +
146A SER* 3.2 6.3 + - - +
147A ILE* 1.3 86.6 - - - +
149A HIS* 1.3 65.9 + - - +
151A ILE* 3.3 14.9 + - - +
152A HIS* 2.9 38.3 + - + -
105B TYR* 4.7 0.9 - - - -
106B GLU* 4.5 9.8 + - - +
109B ILE* 4.9 12.1 - - + +
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Residues in contact with HIS 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A SER* 3.1 24.6 + - - +
148A ASN* 1.3 76.0 - - - +
150A THR* 1.3 53.5 + - - +
152A HIS* 3.2 1.6 + - - -
153A TRP* 2.8 31.0 + - + +
101B GLY 4.3 0.9 - - - -
102B THR* 4.3 9.3 + - - +
105B TYR* 3.5 58.1 - + + +
156B SER* 3.0 28.0 + - - -
159B LEU 3.3 29.6 - - - -
160B PHE* 3.4 19.6 + + + -
161B PRO* 4.1 8.4 - - + +
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Residues in contact with THR 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LEU* 3.9 17.0 - - + -
144A PHE* 3.4 24.9 - - + +
145A PHE 4.8 0.2 + - - -
146A SER 2.7 22.6 + - - -
147A ILE 3.5 4.9 - - - -
149A HIS* 1.3 75.1 - - - +
151A ILE* 1.3 64.4 + - - +
153A TRP* 3.7 0.5 - - - +
154A ILE* 3.1 30.4 + - + +
180A LEU* 3.6 30.5 - - + -
160B PHE* 3.7 22.0 - - + -
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Residues in contact with ILE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A PHE* 6.2 0.4 - - + -
129A LEU* 3.9 17.5 - - + +
130A LYS* 3.6 43.3 - - + +
133A LEU* 3.9 17.7 - - + -
147A ILE* 2.8 24.5 + - + +
148A ASN* 3.6 17.7 - - - +
150A THR* 1.3 74.6 - - - +
152A HIS* 1.3 68.3 + - + +
154A ILE* 3.9 1.7 - - - +
155A THR* 2.7 45.4 + - - +
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Residues in contact with HIS 152 (chain A).
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* 5.2 0.4 - - - -
108A ILE* 4.9 11.4 - - + -
109A ILE* 3.9 19.6 - - + +
148A ASN* 2.9 36.9 + - + +
149A HIS 3.2 2.7 + - - +
151A ILE* 1.3 85.0 - - + +
153A TRP* 1.3 60.5 + - - +
155A THR* 3.6 8.3 - - - +
156A SER* 2.8 35.3 + - - -
105B TYR* 3.2 26.9 - + + +
109B ILE* 5.9 2.2 - - + +
152B HIS* 3.3 22.7 + + - +
156B SER* 4.3 4.3 - - - -
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Residues in contact with TRP 153 (chain A).
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 2.8 16.2 + - - +
150A THR* 3.7 4.7 - - + +
151A ILE 3.3 0.2 - - - -
152A HIS* 1.3 77.6 - - - +
154A ILE* 1.3 89.3 + - + +
156A SER* 3.2 4.9 + - - -
157A ILE* 3.1 51.1 + - + +
176A ILE* 4.3 14.4 - - + -
179A ALA* 3.8 27.1 - - + -
180A LEU* 5.0 4.5 - - + -
156B SER* 3.9 16.1 - - - +
157B ILE* 3.9 18.3 + - + +
160B PHE* 3.5 61.9 - + + +
163B PHE* 4.6 6.8 - - - +
166B PHE* 3.5 30.6 - + + -
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Residues in contact with ILE 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 5.1 2.7 - - + -
86A TYR* 5.1 1.8 - - + -
87A LEU* 4.1 15.7 - - + -
126A PHE* 5.4 1.1 - - + -
129A LEU* 3.7 22.0 - - + -
133A LEU* 4.1 30.7 - - + -
150A THR* 3.1 23.6 + - + +
151A ILE 3.9 2.5 - - - +
153A TRP* 1.3 92.9 - - + +
155A THR* 1.3 58.0 + - - +
157A ILE* 3.2 5.7 + - - +
158A VAL* 2.9 45.4 + - + +
176A ILE* 4.0 14.8 - - + -
180A LEU* 4.2 12.1 - - + -
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Residues in contact with THR 155 (chain A).
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* 3.8 16.9 - - + -
108A ILE* 4.4 16.8 - - + -
126A PHE* 3.5 26.0 - - + -
129A LEU* 4.3 1.6 - - - +
151A ILE* 2.7 31.8 + - - +
152A HIS* 3.6 13.2 + - + +
154A ILE* 1.3 75.6 - - - +
156A SER* 1.3 56.8 + - - +
159A LEU* 3.0 58.7 + - + +
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Residues in contact with SER 156 (chain A).
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* 3.0 26.8 + - - -
152A HIS 2.8 15.0 + - - -
153A TRP 3.5 4.9 - - - -
155A THR* 1.3 76.5 - - - +
157A ILE* 1.3 60.9 + - - +
160A PHE* 3.2 28.1 + - - +
163A PHE* 5.7 0.9 - - - -
153B TRP* 3.5 20.4 + - - -
156B SER* 2.6 29.7 + - - -
157B ILE* 3.8 7.4 - - - -
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Residues in contact with ILE 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A TRP* 3.1 65.4 + - + +
154A ILE* 3.8 6.7 - - - +
156A SER* 1.3 76.2 - - - +
158A VAL* 1.3 62.5 + - - +
160A PHE 4.6 5.7 - - - +
163A PHE* 4.9 25.1 - - + -
172A LEU* 4.2 16.5 - - + +
176A ILE* 3.9 23.1 - - + -
153B TRP* 5.5 0.2 - - - +
157B ILE* 4.6 9.0 - - + -
166B PHE* 3.9 28.9 - - + -
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A TYR* 5.9 0.2 - - + -
87A LEU* 4.0 16.8 - - + -
90A PHE* 4.4 11.7 - - + -
91A THR* 4.2 24.8 - - + +
94A ILE* 3.8 22.2 - - + +
126A PHE* 4.1 16.6 - - + -
154A ILE* 2.9 37.0 + - + +
155A THR 4.2 1.3 - - - +
157A ILE* 1.3 79.4 - - + +
159A LEU* 1.3 74.6 + - + +
160A PHE 5.0 0.3 - - - +
172A LEU* 5.0 1.8 - - + -
176A ILE* 4.2 12.8 - - + -
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ILE* 3.9 14.9 - - + +
98A PRO 4.6 2.1 - - - +
101A GLY* 3.4 33.7 - - - +
102A THR 3.7 1.0 + - - -
104A ALA* 4.2 3.4 - - + -
105A TYR* 3.8 22.7 - - + +
108A ILE* 3.8 21.3 - - + -
122A PHE* 3.6 30.3 - - + -
126A PHE* 3.8 20.0 - - + -
155A THR* 3.0 35.2 + - + +
158A VAL* 1.3 83.5 - - + +
160A PHE* 1.3 67.3 + - - +
161A PRO* 3.3 3.6 - - - +
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Residues in contact with PHE 160 (chain A).
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* 3.9 20.6 - + + -
155A THR 4.1 0.4 + - - -
156A SER* 3.2 23.0 + - - +
157A ILE 4.6 4.5 - - - +
158A VAL 5.0 0.3 - - - +
159A LEU* 1.3 78.4 - - - +
161A PRO* 1.4 96.5 - - + +
162A LYS 3.9 0.5 + - - -
163A PHE* 4.0 11.4 + - - +
144B PHE* 5.2 6.1 - - + -
145B PHE* 4.3 16.8 - + - -
149B HIS 4.3 2.9 - - - -
150B THR* 4.1 22.7 - - + -
153B TRP* 3.4 74.5 - + + +
179B ALA* 5.0 4.3 - - + -
180B LEU* 5.3 3.8 - - + -
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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