Contacts of the helix formed by residues 147 - 152 (chain L) in PDB entry 1JJ2
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 147 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53L GLY* 4.1 19.3 - - - +
55L LYS* 4.2 9.4 - - + -
57L LYS* 5.4 1.1 - - + -
60L ILE* 3.9 31.0 - - + -
115L LEU* 4.3 24.7 - - + -
134L ILE* 4.8 10.1 - - + -
141L ILE* 4.3 17.3 - - + -
144L ASP* 3.2 26.2 + - + +
146L GLN* 1.3 88.3 - - + +
148L SER* 1.3 65.4 + - - +
149L TRP* 2.8 11.0 + - + +
150L ILE* 2.8 27.9 + - + +
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Residues in contact with SER 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141L ILE 3.5 9.5 + - - -
142L LYS* 3.6 23.3 - - - -
144L ASP 2.8 21.5 + - - -
145L ASP* 4.1 10.9 + - - -
147L LEU* 1.3 76.6 - - - +
149L TRP* 1.3 64.7 + - - +
150L ILE 3.0 0.4 - - - -
151L SER* 2.8 25.4 + - - -
152L ARG* 4.0 12.6 + - - -
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Residues in contact with TRP 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4320 G 3.4 29.2 + - - -
4330 C 3.4 46.8 - - - +
115L LEU* 3.5 25.8 - - + -
145L ASP 5.7 0.4 - - - -
146L GLN 3.1 30.0 + - - -
147L LEU* 2.8 8.9 + - + +
148L SER* 1.3 80.7 + - - +
150L ILE* 1.3 97.6 + - + +
152L ARG* 2.8 43.8 + - + +
155L HIS* 3.6 32.0 - + - -
158L ARG* 3.7 20.9 - - - -
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Residues in contact with ILE 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113L ARG* 2.7 43.4 + - + +
114L VAL 3.9 11.4 - - - +
115L LEU* 4.1 15.3 - - + -
134L ILE* 3.8 33.9 - - + +
136L PRO* 4.1 4.9 - - + +
141L ILE* 4.7 1.6 - - + -
147L LEU* 2.8 21.8 + - + +
149L TRP* 1.3 112.3 - - + +
151L SER* 1.3 57.1 + - - +
152L ARG 3.3 0.7 - - - -
155L HIS* 3.8 4.4 - - + +
158L ARG* 3.8 25.4 - - - -
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Residues in contact with SER 151 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113L ARG* 3.4 10.5 + - - +
136L PRO* 3.4 34.5 + - - +
141L ILE* 4.1 14.4 - - - +
142L LYS* 4.2 13.4 - - - -
148L SER* 2.8 19.1 + - - -
150L ILE* 1.3 77.3 - - - +
152L ARG* 1.3 65.3 + - - +
153L THR* 3.5 1.7 + - - -
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Residues in contact with ARG 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4330 C 5.9 0.4 + - - -
4340 U 5.3 4.9 - - - +
113L ARG* 2.9 18.2 + - - -
148L SER* 4.3 10.0 + - - -
149L TRP* 2.8 41.7 + - + +
150L ILE 3.3 0.2 - - - -
151L SER* 1.3 78.0 - - - +
153L THR* 1.3 64.6 + - - +
154L ARG* 4.2 14.1 - - + +
155L HIS* 2.9 18.5 + - + +
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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