Contacts of the helix formed by residues 151 - 162 (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 HIS 151 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147J TRP 3.2 5.9 + - - -
148J GLU* 3.3 12.4 + - - +
149J ALA* 3.1 28.7 + - - -
150J ALA* 1.3 81.0 - - - +
152J VAL* 1.3 63.1 + - - +
154J GLU* 3.1 37.0 + - + +
155J GLN* 3.5 19.3 + - + +
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Residues in contact with VAL 152 (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* 5.6 0.4 - - - +
133J TRP* 4.0 7.9 - - + -
147J TRP* 3.0 46.0 + - + +
150J ALA* 4.0 9.9 - - + +
151J HIS* 1.3 74.8 - - - +
153J ALA* 1.3 66.4 + - - +
155J GLN* 3.2 11.7 + - - +
156J LEU* 3.0 44.2 + - + +
2L TYR* 5.6 2.9 - - + +
7L THR* 3.4 33.9 - - - +
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Residues in contact with ALA 153 (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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126J LEU* 4.0 9.3 - - + +
130J LEU 3.8 17.7 - - - +
131J ARG 4.1 9.4 - - - +
133J TRP* 3.8 31.1 - - + +
147J TRP 4.5 0.2 + - - -
151J HIS* 3.4 0.6 - - - +
152J VAL* 1.3 77.7 - - - +
154J GLU* 1.3 71.0 + - - +
156J LEU* 3.4 5.8 + - - +
157J ARG* 2.9 31.5 + - - +
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Residues in contact with GLU 154 (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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130J LEU 5.1 0.4 - - - +
131J ARG* 4.6 16.7 + - - +
148J GLU 5.2 0.2 - - - +
151J HIS* 3.1 46.8 + - + +
152J VAL 3.2 0.2 - - - -
153J ALA* 1.3 88.6 + - - +
155J GLN* 1.3 63.4 + - + +
157J ARG* 3.6 7.9 + - - +
158J ALA* 3.3 20.3 + - - +
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Residues in contact with GLN 155 (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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150J ALA 3.5 19.9 - - - +
151J HIS* 3.5 12.4 - - + +
152J VAL* 3.2 9.7 + - - +
154J GLU* 1.3 77.9 - - + +
156J LEU* 1.3 64.4 + - - +
158J ALA* 3.3 16.7 + - - +
159J TYR 3.3 8.8 + - - -
2L TYR* 3.2 19.7 + - - +
4L ASN* 3.1 40.3 + - - +
7L THR* 5.8 2.4 + - - -
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Residues in contact with LEU 156 (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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99J TYR* 5.8 1.8 - - + -
114J HIS* 3.5 46.9 - - + +
126J LEU* 4.4 10.3 - - + -
133J TRP* 3.5 27.1 - - + -
152J VAL* 3.0 30.2 + - + +
153J ALA 3.7 3.8 - - - +
155J GLN* 1.3 76.6 - - - +
157J ARG* 1.3 58.1 + - - +
159J TYR* 3.2 7.2 + - + +
160J LEU* 2.9 38.8 + - + +
2L TYR* 3.7 37.7 - - + +
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Residues in contact with ARG 157 (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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218G GLN* 5.5 0.4 - - - +
262G GLN* 4.5 15.0 - - - +
269G PRO* 6.3 1.5 - - + +
126J LEU* 5.3 0.4 - - - +
129J ASP 3.2 17.9 + - - -
130J LEU* 3.9 25.7 - - + +
131J ARG* 2.8 51.2 - - - +
153J ALA 2.9 18.1 + - - +
154J GLU* 3.7 9.0 - - - +
155J GLN 3.2 0.2 - - - -
156J LEU* 1.3 75.1 - - - +
158J ALA* 1.3 65.9 + - - +
160J LEU* 4.5 8.5 - - - +
161J GLU* 2.9 62.1 + - - +
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Residues in contact with ALA 158 (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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268G LYS* 6.5 0.4 - - + -
269G PRO* 5.8 9.6 - - + -
154J GLU 3.3 9.8 + - - +
155J GLN* 3.3 12.7 + - - +
156J LEU 3.3 0.4 - - - -
157J ARG* 1.3 80.0 - - - +
159J TYR* 1.3 57.4 + - - +
161J GLU* 5.2 1.6 - - - -
162J GLY* 2.9 28.4 + - - -
163J THR* 3.8 2.1 + - - -
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Residues in contact with TYR 159 (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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5J MET* 4.3 3.5 - - - +
7J TYR* 4.0 6.2 - - - -
99J TYR* 3.4 35.9 - + - -
155J GLN 3.3 1.6 + - - +
156J LEU* 3.2 9.9 + - + +
158J ALA* 1.3 80.0 - - - +
160J LEU* 1.3 78.2 + - + +
163J THR* 3.2 26.2 + - + -
164J CYS* 2.7 50.4 + - + +
0L ARG 2.7 28.7 + - - -
1L LEU 3.8 2.7 - - - -
2L TYR* 3.5 44.6 - + + -
3L GLN* 3.4 22.7 - - - +
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Residues in contact with LEU 160 (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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99J TYR* 4.7 2.5 - - + -
100J GLY 3.4 29.2 - - - +
101J CYS* 3.7 6.8 - - + +
109J PHE* 3.5 10.4 - - + -
112J GLY* 4.5 9.0 - - - -
113J TYR 3.5 23.3 - - - +
114J HIS* 4.9 1.1 - - + -
126J LEU* 4.1 12.3 - - + -
130J LEU* 3.7 31.2 - - + -
156J LEU* 2.9 27.5 + - + +
157J ARG* 3.9 3.1 - - - +
159J TYR* 1.3 98.4 - - + +
161J GLU* 1.3 60.3 + - - +
164J CYS* 3.7 5.1 - - + +
165J VAL* 3.4 18.4 - - - +
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Residues in contact with GLU 161 (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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262G GLN* 4.0 18.4 + - - +
269G PRO* 5.4 6.9 - - - +
109J PHE* 3.8 42.0 - - + +
130J LEU* 4.2 7.3 - - + +
157J ARG* 2.9 56.7 + - - +
158J ALA* 4.5 2.1 - - - +
160J LEU* 1.3 76.9 - - - +
162J GLY* 1.3 59.3 + - - +
165J VAL* 3.8 14.2 - - - +
166J GLU* 5.7 0.2 - - - +
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Residues in contact with GLY 162 (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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158J ALA 2.9 14.5 + - - -
160J LEU 3.4 0.2 - - - -
161J GLU* 1.3 76.7 - - - +
163J THR* 1.3 65.3 + - - +
164J CYS 3.3 1.3 - - - -
165J VAL* 3.0 5.4 + - - +
166J GLU* 2.8 40.8 + - - +
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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