Contacts of the helix formed by residues 145 - 159 (chain A) in PDB entry 2J16
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 145 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ASP* 5.7 0.9 - - - -
140A CSD 3.5 1.2 + - - -
143A GLY 2.9 16.1 + - - -
144A LEU* 1.3 74.1 - - - +
146A ARG* 1.3 63.3 + - - +
147A SER 3.4 0.2 - - - -
148A ALA* 3.5 3.4 + - - +
149A THR* 2.5 38.0 + - - -
178A ASN* 2.9 22.0 + - - -
179A PRO* 3.8 8.4 - - - +
180A SER* 4.3 3.4 + - - -
183A LEU* 3.6 18.5 - - - +
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Residues in contact with ARG 146 (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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88A VAL* 4.2 18.7 + - + -
90A GLU* 4.0 13.3 + - - +
109A TRP* 2.6 67.4 + - + +
110A GLU 3.5 18.0 + - - -
111A HIS 3.9 3.0 - - - -
112A ASP* 2.8 28.7 + - - +
115A ILE* 3.9 22.3 - - + +
140A CSD 3.7 12.8 + - - +
145A SER* 1.3 79.8 - - - +
147A SER* 1.3 61.3 + - - +
149A THR* 3.4 8.8 - - - -
150A LEU* 2.9 28.6 + - - +
183A LEU* 4.4 7.6 - - + -
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Residues in contact with SER 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 3.5 19.3 - - - +
88A VAL* 4.0 8.9 - - - +
138A ILE* 3.7 28.4 - - - +
140A CSD 2.9 32.8 + - - -
144A LEU* 3.9 5.7 - - - -
146A ARG* 1.3 76.6 - - - +
148A ALA* 1.3 60.2 + - - +
150A LEU* 3.4 3.9 + - - +
151A ILE* 3.0 35.3 + - - +
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Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 4.8 3.3 - - + +
144A LEU 3.6 21.1 - - - +
145A SER 3.5 4.2 + - - +
146A ARG 3.3 0.4 - - - -
147A SER* 1.3 78.0 + - - +
149A THR* 1.3 59.7 + - - +
151A ILE* 3.2 3.1 + - - -
152A ILE* 2.9 38.0 + - + +
170A LEU* 3.6 22.1 - - + +
177A ILE* 4.0 23.1 - - + -
179A PRO* 4.6 4.7 - - + -
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Residues in contact with THR 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ILE* 4.5 16.6 - - + -
119A LEU* 5.3 2.5 - - + -
145A SER 2.5 23.9 + - - -
146A ARG* 3.4 9.2 - - - -
148A ALA* 1.3 75.4 - - - +
150A LEU* 1.3 57.5 + - - +
152A ILE* 3.4 1.6 + - - +
153A ALA* 2.8 28.8 + - - +
179A PRO* 3.5 6.2 - - - +
183A LEU* 3.4 37.1 - - + +
186A GLN* 5.3 2.2 - - + -
187A LEU* 3.5 34.4 - - + +
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Residues in contact with LEU 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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86A ILE* 4.1 4.7 - - + -
88A VAL* 4.0 22.2 - - + -
109A TRP* 4.9 2.0 - - + -
115A ILE* 6.2 1.3 - - + -
119A LEU* 4.8 7.0 - - + -
122A LEU* 3.4 48.9 - - + -
123A THR* 4.5 5.2 - - + +
126A ILE* 3.6 24.0 - - + -
138A ILE* 3.8 24.2 - - + -
146A ARG 2.9 17.1 + - - +
147A SER* 3.5 4.9 - - - +
149A THR* 1.3 77.1 - - - +
151A ILE* 1.3 62.6 + - - +
153A ALA* 3.3 6.1 + - - +
154A TYR* 3.0 20.6 + - - +
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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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63A VAL* 4.2 11.0 - - + -
64A LEU* 3.7 28.0 - - + -
68A ILE* 4.4 6.7 - - + -
69A TYR 4.8 0.2 - - - +
70A LEU* 4.1 37.5 - - + -
126A ILE* 5.0 1.3 - - - -
138A ILE* 3.8 29.6 - - + -
147A SER 3.0 22.1 + - - +
148A ALA 3.7 3.8 - - - +
150A LEU* 1.3 75.1 - - - +
152A ILE* 1.3 62.9 + - - +
154A TYR* 3.2 10.2 + - + +
155A ILE* 3.0 25.1 + - + +
170A LEU* 4.0 21.8 - - + -
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Residues in contact with ILE 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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148A ALA* 2.9 28.2 + - + +
149A THR* 3.7 6.5 - - - +
151A ILE* 1.3 73.9 - - - +
153A ALA* 1.3 65.5 + - - +
155A ILE* 3.1 9.6 + - + +
156A MET* 2.9 37.3 + - - +
163A LEU* 3.9 7.6 - - + -
166A SER* 3.8 17.0 - - - +
167A TYR* 4.0 37.7 - - + +
170A LEU* 3.8 19.1 - - + -
177A ILE* 4.5 4.9 - - + -
179A PRO* 4.8 4.9 - - + -
187A LEU* 3.8 24.2 - - + -
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Residues in contact with ALA 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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119A LEU* 3.6 26.7 - - + -
123A THR* 3.7 6.4 - - + +
149A THR 2.8 18.4 + - - +
150A LEU 3.6 5.4 - - - +
152A ILE* 1.3 76.2 - - - +
154A TYR* 1.3 61.1 + - - +
156A MET* 3.6 0.8 + - - -
157A LYS* 3.2 14.9 + - - +
187A LEU* 3.8 13.4 - - + +
190A TRP* 3.0 35.1 + - + +
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Residues in contact with TYR 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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64A LEU* 4.4 2.9 - - + -
66A GLU* 2.7 30.5 + - - -
68A ILE* 3.5 23.1 - - + -
123A THR* 3.5 13.6 - - + +
126A ILE* 3.6 31.2 - - + -
127A HIS* 3.7 26.4 + - + -
130A THR* 3.5 19.4 + - + +
150A LEU 3.0 12.9 + - - +
151A ILE* 3.3 11.4 - - - +
152A ILE 3.2 0.2 - - - -
153A ALA* 1.3 74.1 - - - +
155A ILE* 1.3 67.4 + - + +
157A LYS 3.4 0.3 + - - -
158A TYR* 2.9 55.2 + + + +
159A HIS* 4.1 10.2 + + - -
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Residues in contact with ILE 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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64A LEU* 3.8 40.4 - - + -
151A ILE* 3.0 23.5 + - + +
152A ILE* 3.1 7.4 + - - +
154A TYR* 1.3 78.2 - - + +
156A MET* 1.3 66.8 + - - +
159A HIS* 3.1 36.6 + - + +
161A LEU* 3.8 22.3 + - + -
166A SER* 3.3 36.3 - - - +
169A LEU* 4.8 6.5 - - + -
170A LEU* 4.9 6.5 - - + -
65B PRO* 4.6 4.9 - - + -
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Residues in contact with MET 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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152A ILE* 2.9 33.0 + - - +
153A ALA 3.7 4.3 - - - +
155A ILE* 1.3 79.2 - - - +
157A LYS* 1.3 61.2 + - - +
160A ASN* 3.3 6.1 - - - +
161A LEU 3.2 32.9 + - - +
162A SER 4.1 2.7 - - - +
163A LEU* 3.9 22.0 - - + -
166A SER* 3.3 19.0 + - - +
187A LEU* 3.3 30.5 - - - +
190A TRP* 3.8 17.5 - - + +
191A GLU* 3.6 27.4 - - + +
194A LEU* 3.9 12.1 - - + +
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Residues in contact with LYS 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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120A PRO* 5.4 4.9 - - - -
123A THR* 3.9 5.4 - - - +
153A ALA 3.2 15.0 + - - +
154A TYR* 5.0 0.2 - - - -
156A MET* 1.3 83.5 - - - +
158A TYR* 1.3 105.0 + - + +
160A ASN* 3.6 9.2 + - - +
190A TRP* 3.5 28.0 - - + -
194A LEU* 3.7 29.6 - - + +
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Residues in contact with TYR 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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123A THR* 3.2 29.6 - - - -
124A SER* 3.5 21.5 + - - -
127A HIS* 3.3 46.1 - + + +
154A TYR* 2.9 49.3 + + + +
157A LYS* 1.3 105.1 - - + +
159A HIS* 1.3 66.4 + - + +
160A ASN 3.5 0.7 - - - -
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Residues in contact with HIS 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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64A LEU* 6.1 0.2 - - + -
66A GLU* 2.7 34.0 + - - -
154A TYR* 4.1 15.9 + + - -
155A ILE* 3.1 22.0 + - + +
158A TYR* 1.3 84.6 + - - +
160A ASN* 1.3 71.6 + - - +
161A LEU* 3.1 15.5 + - + +
65B PRO* 3.7 45.7 + - + +
66B GLU* 4.0 15.7 + - + +
67B LYS* 3.9 8.8 - - - +
159B HIS* 6.2 1.8 - + - -
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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