Contacts of the helix formed by residues 137 - 150 (chain J) in PDB entry 3MGO
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 ASP 137 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85J TYR* 2.6 37.1 + - - -
123J TYR* 4.5 0.7 - - - -
136J ALA* 1.3 79.4 + - + +
138J MET* 1.3 62.2 + - + +
139J ALA 4.0 4.0 - - - -
140J ALA* 3.0 24.3 + - - +
141J GLN* 2.9 33.4 + - - +
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Residues in contact with MET 138 (chain J).
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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137J ASP* 1.3 75.5 - - + +
139J ALA* 1.3 68.8 + - - +
141J GLN* 2.8 31.9 + - + +
142J THR* 3.0 17.3 + - - -
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Residues in contact with ALA 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84J TYR* 3.9 26.7 - - + +
85J TYR* 3.4 42.8 - - + +
123J TYR* 3.0 14.0 + - + +
137J ASP* 3.4 2.3 + - - +
138J MET* 1.3 79.9 - - - +
140J ALA* 1.3 63.7 + - - +
142J THR* 3.2 16.1 + - - -
143J THR* 3.3 6.6 + - - -
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Residues in contact with ALA 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J TYR* 3.1 44.8 + - + +
124J ILE* 4.3 3.4 - - + +
135J ALA* 3.5 20.5 - - + +
136J ALA 4.1 1.3 - - - +
137J ASP* 3.0 19.1 + - - +
139J ALA* 1.3 76.6 - - - +
141J GLN* 1.3 60.4 + - - +
143J THR* 3.2 4.0 + - - -
144J LYS* 2.8 29.6 + - - +
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Residues in contact with GLN 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J ALA* 3.8 22.3 + - + +
136J ALA 5.7 0.4 - - - -
137J ASP 2.9 30.4 + - - +
138J MET* 2.8 31.9 + - + +
140J ALA* 1.3 76.0 - - - +
142J THR* 1.3 59.9 + - - +
144J LYS* 3.0 17.8 + - - +
145J HIS* 2.9 43.4 + - + +
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Residues in contact with THR 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84J TYR* 3.6 30.5 - - + +
138J MET 3.0 12.9 + - - -
139J ALA* 3.4 9.8 - - - -
141J GLN* 1.3 76.0 - - - +
143J THR* 1.3 64.2 + - - +
145J HIS* 3.2 14.4 + - + +
146J LYS* 3.1 26.7 + - - +
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Residues in contact with THR 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84J TYR* 3.7 1.7 - - - -
123J TYR* 2.7 30.5 + - + -
124J ILE* 4.0 9.9 - - + -
139J ALA 3.3 1.1 + - - -
140J ALA 3.2 8.2 + - - -
142J THR* 1.3 77.9 - - - +
144J LYS* 1.3 58.5 + - - +
146J LYS* 3.2 6.5 + - - +
147J TRP* 2.9 57.8 + - + +
9L ILE* 3.0 41.7 + - + +
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Residues in contact with LYS 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J ILE* 4.0 13.9 - - + +
132J SER* 6.3 0.2 - - - -
133J TRP* 3.8 41.5 - - + +
135J ALA* 4.1 17.7 - - + +
140J ALA 2.8 13.4 + - - +
141J GLN* 3.2 20.2 + - - +
143J THR* 1.3 76.0 - - - +
145J HIS* 1.3 65.4 + - - +
147J TRP* 3.3 4.3 + - - +
148J GLU* 2.8 65.8 + - + +
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Residues in contact with HIS 145 (chain J).
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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141J GLN* 2.9 44.9 + - + +
142J THR* 3.6 10.3 - - + +
144J LYS* 1.3 83.9 - - + +
146J LYS* 1.3 64.2 + - - +
148J GLU* 3.0 21.3 + - - +
149J ALA* 3.0 23.8 + - - +
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Residues in contact with LYS 146 (chain J).
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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80J THR* 4.9 2.0 - - - +
84J TYR* 2.9 18.7 + - - -
142J THR* 3.1 13.2 + - - +
143J THR* 3.3 8.3 - - - +
145J HIS* 1.3 80.2 - - - +
147J TRP* 1.3 67.0 + - + +
149J ALA* 3.3 5.3 + - - +
150J ALA* 3.1 23.9 + - + +
7L THR* 4.6 9.2 - - + -
8L TYR* 3.5 23.0 - - + +
9L ILE 2.8 28.8 + - - +
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Residues in contact with TRP 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J HIS* 4.2 8.3 - - - -
116J TYR* 3.5 32.5 - + - -
124J ILE* 3.8 22.7 - - + -
133J TRP* 3.5 49.0 + + + +
143J THR* 2.9 25.9 + - + +
144J LYS* 3.9 4.7 - - - +
146J LYS* 1.3 77.9 - - + +
148J GLU* 1.3 64.2 + - - +
151J HIS* 3.2 2.3 + - - -
152J VAL* 3.0 49.0 + - + +
153J ALA 4.5 1.4 + - - -
6L THR* 5.8 0.2 - - - -
7L THR* 3.9 32.8 + - + +
8L TYR 2.9 25.0 + - - -
9L ILE* 3.7 23.6 - - + -
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Residues in contact with GLU 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J TRP* 4.3 13.5 - - + +
144J LYS* 2.8 54.8 + - + +
145J HIS* 3.0 29.0 + - - +
147J TRP* 1.3 77.2 - - - +
149J ALA* 1.3 62.1 + - - +
151J HIS* 3.3 21.9 + - - +
154J GLU* 5.2 0.2 - - - +
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Residues in contact with ALA 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J HIS 3.0 14.8 + - - +
146J LYS* 3.8 5.8 - - - +
148J GLU* 1.3 73.8 - - - +
150J ALA* 1.3 56.8 + - - +
151J HIS* 3.1 24.2 + - - -
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Residues in contact with ALA 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146J LYS* 3.1 16.7 + - + +
147J TRP 3.7 0.2 + - - -
148J GLU 3.3 0.2 - - - -
149J ALA* 1.3 75.5 - - - +
151J HIS* 1.3 72.8 + - - +
152J VAL* 3.2 17.1 + - + +
155J GLN* 3.5 13.0 - - - +
7L THR* 4.5 14.1 - - + +
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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