Contacts of the helix formed by residues 146 - 152 (chain C) in PDB entry 3E1J
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82C ASP* 6.4 2.0 - - + -
83C VAL* 5.0 10.5 - - + -
84C GLU* 5.8 3.4 - - + +
141C ILE* 3.8 24.6 + - + +
145C GLY* 1.3 71.4 - - - -
147C GLN* 1.3 64.5 + - + +
149C TYR* 3.1 10.3 + - + +
150C LEU* 2.9 53.0 + - + +
250C SO4 3.2 17.5 + - - +
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Residues in contact with GLN 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C GLY 3.5 0.4 - - - -
146C LEU* 1.3 74.2 - - + +
148C ASN* 1.3 68.6 + - - +
150C LEU* 3.3 10.3 + - + +
151C GLN* 3.1 22.1 + - - +
250C SO4 3.1 27.7 + - - +
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Residues in contact with ASN 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLN* 3.8 6.3 - - - +
148A ASN* 2.7 40.8 + - - +
151A GLN* 3.4 25.2 + - - +
144C MET* 3.4 33.7 - - + +
145C GLY 3.6 1.8 + - - -
146C LEU 3.4 0.4 - - - -
147C GLN* 1.3 78.1 - - - +
149C TYR* 1.3 65.9 + - - +
151C GLN* 3.4 11.3 + - - -
152C ALA* 3.2 19.1 + - - +
250C SO4 4.6 1.0 + - - -
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Residues in contact with TYR 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ILE* 5.3 1.6 - - + -
40C LEU* 3.5 14.5 - - + +
83C VAL* 4.0 14.6 - - + -
87C LEU* 3.9 4.7 - - - +
137C GLU* 2.5 45.9 + - + +
140C LEU* 4.2 13.7 - - + -
141C ILE* 3.6 47.1 - - + -
144C MET* 3.8 15.4 - - + +
145C GLY 3.0 18.5 + - - +
146C LEU* 3.1 8.7 + - + +
148C ASN* 1.3 78.2 - - - +
150C LEU* 1.3 75.8 + - + +
152C ALA* 3.2 7.0 + - - +
153C GLN* 2.9 50.1 + - + -
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Residues in contact with LEU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C LEU* 4.0 25.0 - - + +
83C VAL* 3.9 28.3 - - + -
146C LEU* 2.9 46.8 + - + +
147C GLN* 3.7 8.1 - - + +
149C TYR* 1.3 86.3 - - + +
151C GLN* 1.3 64.9 + - - +
153C GLN* 2.8 21.8 + - + +
154C ILE* 3.7 7.8 + - - +
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Residues in contact with GLN 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLN* 3.0 26.6 + - - +
147C GLN 3.1 15.7 + - - +
148C ASN* 3.9 12.4 + - - +
149C TYR 3.3 0.4 - - - -
150C LEU* 1.3 75.8 - - - +
152C ALA* 1.3 60.8 + - - +
153C GLN 3.1 1.6 + - - -
154C ILE* 3.4 32.6 + - + +
155C ARG* 4.9 0.7 + - - +
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Residues in contact with ALA 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLN* 4.0 22.7 - - + +
154A ILE* 4.2 17.9 - - + -
155A ARG* 3.3 28.8 + - - +
39C ARG* 4.5 3.6 + - - -
148C ASN 3.2 12.6 + - - +
149C TYR* 3.2 11.6 + - - +
150C LEU 3.0 1.0 - - - -
151C GLN* 1.3 77.3 - - - +
153C GLN* 1.3 67.8 + - - +
154C ILE 3.5 0.7 - - - -
155C ARG 5.1 0.2 - - - -
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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