Contacts of the helix formed by residues 141 - 146 (chain J) in PDB entry 5M32
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 SER 141 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138J LEU 4.2 3.1 + - - -
139J THR 3.3 0.8 - - - -
140J LEU* 1.3 76.9 - - - +
142J ILE* 1.3 59.7 + - - +
144J ASP* 2.9 15.5 + - - +
145J ARG* 2.8 29.6 + - - +
134Y TYR* 3.3 46.9 + - - +
138Y VAL* 3.8 18.9 - - - +
162Y GLN* 4.0 14.9 + - - +
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Residues in contact with ILE 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139J THR* 3.3 13.2 + - - +
140J LEU 3.3 0.6 - - - -
141J SER* 1.3 76.8 - - - +
143J LEU* 1.3 62.1 + - - +
145J ARG* 4.4 1.8 - - - +
146J TYR* 3.3 47.2 + - + +
159J LEU* 4.0 8.7 - - + +
162J LYS* 4.4 6.1 - - + +
163J CYS* 3.8 20.4 - - - -
166J GLU* 3.6 37.5 - - + -
137Y GLY* 3.7 24.7 - - - +
138Y VAL* 4.3 2.2 - - - +
141Y ARG* 4.0 25.4 - - + -
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Residues in contact with LEU 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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5J ILE* 3.7 32.8 - - + -
7J ILE* 3.9 28.7 - - + -
129J PHE* 3.2 43.7 - - + -
139J THR 3.7 4.6 + - - +
140J LEU* 3.4 11.5 + - + +
141J SER 3.2 0.4 - - - -
142J ILE* 1.3 75.7 - - - +
144J ASP* 1.3 57.8 + - - +
147J TYR* 3.2 23.4 - - + +
159J LEU* 3.7 27.8 - - + -
163J CYS* 3.7 23.6 - - - -
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Residues in contact with ASP 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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129J PHE* 3.1 13.4 - - - -
140J LEU 3.1 14.2 + - - +
141J SER* 2.9 22.3 + - - +
143J LEU* 1.3 79.1 - - - +
145J ARG* 1.3 62.9 + - - +
146J TYR 3.5 0.4 - - - -
147J TYR 4.5 6.3 + - - +
162Y GLN* 3.3 30.6 + - - +
165Y TYR* 4.9 6.1 - - + -
166Y ARG* 2.7 46.6 + - - +
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Residues in contact with ARG 145 (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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141J SER 2.8 14.5 + - - +
142J ILE* 3.4 0.8 + - - -
144J ASP* 1.3 80.7 - - - +
146J TYR* 1.3 92.7 + - + +
147J TYR 5.4 0.6 - - - +
138Y VAL* 4.2 18.6 - - + -
158Y ARG* 3.7 45.6 - - - +
162Y GLN* 4.7 10.3 - - + +
199Y TYR* 5.6 4.6 - - - -
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Residues in contact with TYR 146 (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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142J ILE* 3.3 26.1 + - + +
145J ARG* 1.3 104.7 - - + +
147J TYR* 1.3 60.5 + - - +
148J THR* 3.1 16.3 + - - +
151J ILE* 4.8 4.2 - - - +
155J ARG* 3.6 29.4 + - - +
159J LEU* 3.6 25.5 - - + +
162J LYS* 4.7 11.7 - - + -
138Y VAL* 6.0 1.1 - - + -
141Y ARG* 3.5 42.6 + - + +
142Y GLY* 4.8 4.5 + - - -
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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