Contacts of the helix formed by residues 145 - 154 (chain U) in PDB entry 3J0S
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 145 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68U TYR* 3.6 17.1 + - - -
141U GLU* 3.0 28.5 + - - +
142U GLU* 3.9 9.9 - - - +
143U VAL 3.4 1.0 - - - -
144U LYS* 1.3 85.1 - - - +
146U ARG* 1.3 66.0 + - - +
147U CYS* 3.4 11.2 + - + +
148U THR* 3.5 15.4 + - - +
149U LEU 4.1 0.3 + - - -
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Residues in contact with ARG 146 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66U ASP* 5.0 13.9 + - - +
68U TYR* 3.6 34.2 + - - +
69U ALA* 5.5 0.8 - - - +
144U LYS 3.5 12.8 + - - -
145U ASP* 1.3 70.8 - - - +
147U CYS* 1.3 63.7 + - - +
149U LEU 3.3 2.6 + - - -
150U ALA* 3.1 9.3 + - - +
161U LEU* 3.1 52.9 - - + +
162U GLU* 5.5 3.2 - - - +
165U PRO* 3.1 43.3 - - + +
166U LEU* 4.0 16.8 - - + -
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Residues in contact with CYS 147 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326H LYS* 6.3 0.4 - - - -
145U ASP* 3.2 7.4 - - + +
146U ARG* 1.3 80.1 - - - +
148U THR* 1.3 57.8 + - - +
150U ALA* 3.1 9.8 + - - +
151U GLU* 2.8 33.2 + - - +
166U LEU* 5.1 7.1 - - + +
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Residues in contact with THR 148 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68U TYR* 5.0 3.1 - - - +
135U LEU* 3.3 33.9 - - + +
136U GLN 5.6 6.1 - - - +
137U ALA* 6.0 2.2 - - + -
142U GLU* 3.2 37.1 + - + +
145U ASP* 3.5 9.8 + - - +
146U ARG 3.3 0.8 - - - -
147U CYS* 1.3 79.4 - - - +
149U LEU* 1.3 63.6 + - - +
151U GLU* 3.4 25.2 + - - +
152U LYS 3.9 0.5 + - - -
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Residues in contact with LEU 149 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68U TYR* 3.7 43.0 + - + +
85U TYR* 4.1 17.3 - - + -
87U ALA* 4.6 20.0 - - + +
89U TYR* 5.4 2.2 - - + -
100U VAL* 6.0 0.9 - - + -
135U LEU* 3.9 16.8 - - + +
145U ASP 4.1 0.8 + - - -
146U ARG 3.3 3.2 + - - +
147U CYS 3.3 0.2 - - - -
148U THR* 1.3 76.9 - - - +
150U ALA* 1.3 61.5 + - - +
152U LYS* 3.3 38.2 - - + +
153U LEU* 3.7 10.8 - - + +
161U LEU* 3.4 31.0 - - + -
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Residues in contact with ALA 150 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146U ARG 3.1 12.3 + - - +
147U CYS* 3.1 13.6 + - - +
149U LEU* 1.3 76.6 - - - +
151U GLU* 1.3 63.0 + - - +
153U LEU* 3.0 34.8 + - + +
154U GLY 3.2 4.5 + - - -
155U GLY* 3.4 16.4 + - - -
158U VAL* 5.4 2.2 - - + -
161U LEU* 4.0 1.5 - - + +
166U LEU* 3.8 23.6 - - + -
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Residues in contact with GLU 151 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291H LYS* 3.4 30.6 - - + +
292H ASP* 3.4 22.7 - - - +
326H LYS* 5.8 1.4 + - - -
135U LEU* 5.6 2.3 - - - +
147U CYS* 2.8 20.4 + - - +
148U THR* 3.4 22.3 - - - +
149U LEU 3.3 0.6 - - - -
150U ALA* 1.3 73.2 - - - +
152U LYS* 1.3 63.1 + - - +
154U GLY* 3.3 17.8 + - - +
155U GLY* 5.5 0.7 - - - -
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Residues in contact with LYS 152 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87U ALA* 4.9 2.2 - - + -
98U ASP* 4.1 21.5 - - + +
100U VAL* 3.1 35.4 - - + -
133U HIS* 4.1 31.2 + - + +
134U GLU 5.7 0.2 - - - +
135U LEU* 3.2 39.2 - - + +
148U THR 3.9 2.9 + - - +
149U LEU* 3.3 26.0 + - + +
151U GLU* 1.3 79.3 - - - +
153U LEU* 1.3 69.5 + - + +
154U GLY 3.5 0.3 + - - -
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Residues in contact with LEU 153 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89U TYR* 3.2 55.6 - - + +
98U ASP* 4.3 1.6 - - - +
149U LEU* 3.7 13.0 - - + +
150U ALA* 3.0 26.7 - - + +
152U LYS* 1.3 95.9 - - + +
154U GLY* 1.3 56.6 + - - +
155U GLY 3.7 0.9 - - - -
158U VAL* 3.5 40.6 - - + +
161U LEU* 5.3 5.2 - - + -
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Residues in contact with GLY 154 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150U ALA 3.2 4.2 + - - -
151U GLU* 3.3 11.7 + - - +
152U LYS 3.3 3.4 - - - -
153U LEU* 1.3 78.5 - - - +
155U GLY* 1.3 59.8 + - - +
156U SER* 3.4 6.5 + - - -
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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