Contacts of the helix formed by residues 146 - 152 (chain J) in PDB entry 3E1O
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 LEU 146 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82J ASP* 6.4 2.7 - - + -
83J VAL* 4.9 10.8 - - + -
84J GLU* 5.7 5.4 - - + +
141J ILE* 3.7 24.1 + - + +
145J GLY* 1.3 70.4 - - - -
147J GLN* 1.3 60.0 + - + +
149J TYR* 3.0 11.1 + - + +
150J LEU* 2.8 59.3 + - + +
250J SO4 3.1 17.3 + - - +
143K LYS 5.6 2.0 - - - +
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Residues in contact with GLN 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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145J GLY 3.5 0.2 - - - -
146J LEU* 1.3 74.6 - - + +
148J ASN* 1.3 64.1 + - - +
150J LEU* 3.3 4.1 + - - +
151J GLN* 3.1 19.6 + - - +
250J SO4 3.0 31.6 + - - +
142K GLN 4.6 3.4 + - - -
143K LYS 3.4 20.2 + - - +
144K MET* 3.5 41.2 + - - +
145K GLY* 3.6 10.0 - - - +
148K ASN* 3.7 8.8 - - - +
250K SO4 4.7 9.0 + - - -
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Residues in contact with ASN 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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147B GLN* 3.8 13.9 - - - +
148B ASN* 2.7 26.2 + - - +
151B GLN* 3.4 25.6 + - + +
144J MET* 3.4 31.4 + - + +
145J GLY 3.6 2.0 + - - -
146J LEU 3.4 0.6 - - - -
147J GLN* 1.3 78.4 - - - +
149J TYR* 1.3 62.7 + - - +
151J GLN* 3.3 2.0 + - - -
152J ALA* 3.1 21.8 + - - +
250J SO4 4.5 0.8 + - - -
148K ASN* 2.7 39.9 + - - +
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Residues in contact with TYR 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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154B ILE* 5.4 1.1 - - + -
40J LEU* 3.5 21.8 - - + +
83J VAL* 4.1 6.1 - - + -
87J LEU* 3.9 4.9 - - - +
137J GLU* 2.5 46.7 + - + +
140J LEU* 4.2 14.8 - - + -
141J ILE* 3.5 47.6 - - + -
144J MET* 3.7 15.1 - - + -
145J GLY 3.1 14.0 + - - +
146J LEU* 3.0 12.0 + - + +
148J ASN* 1.3 77.9 - - - +
150J LEU* 1.3 75.1 + - + +
152J ALA* 3.0 11.2 + - - +
153J GLN* 3.1 44.7 + - + +
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Residues in contact with LEU 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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37J LEU* 4.0 24.0 - - + +
83J VAL* 3.8 29.6 - - + -
146J LEU* 2.8 47.0 + - + +
147J GLN* 3.3 6.5 + - - +
149J TYR* 1.3 82.3 - - + +
151J GLN* 1.3 63.1 + - - +
153J GLN* 3.0 19.1 + - + +
154J ILE* 3.8 4.9 + - - +
140K LEU* 6.0 0.4 - - + -
143K LYS* 4.0 37.7 - - + +
144K MET* 4.0 17.2 - - + +
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Residues in contact with GLN 151 (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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151B GLN* 3.3 23.3 + - - +
147J GLN 3.1 11.5 + - - +
148J ASN* 3.7 6.0 + - - +
149J TYR 3.3 0.2 - - - -
150J LEU* 1.3 75.2 - - - +
152J ALA* 1.3 59.9 + - - +
153J GLN 3.0 5.8 + - - -
154J ILE* 3.2 18.6 + - - +
155J ARG* 4.8 0.5 + - - +
144K MET* 3.6 22.4 - - - +
148K ASN* 3.3 39.7 + - + +
151K GLN* 3.2 35.1 + - - +
152K ALA* 3.8 23.5 - - + +
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Residues in contact with ALA 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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151B GLN* 4.0 22.0 - - + +
154B ILE* 4.1 18.6 - - + +
155B ARG* 3.3 28.1 + - - +
39J ARG* 4.5 3.3 + - - -
148J ASN 3.1 12.3 + - - +
149J TYR* 3.0 13.8 + - - +
151J GLN* 1.3 77.7 - - - +
153J GLN* 1.3 67.5 + - - +
154J ILE 3.5 0.4 - - - -
155J ARG 5.2 0.4 - - - -
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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