Contacts of the helix formed by residues 1143 - 1146 (chain A) in PDB entry 2JA5
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 LEU1143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1142A THR* 1.3 71.1 - - - +
1144A LYS* 1.3 54.8 + - - +
1146A VAL* 2.9 33.9 + - + +
1147A THR* 2.6 32.8 + - - +
1195A LEU* 4.2 16.4 - - + -
1197A LEU* 3.9 10.8 - - + -
1212A VAL* 3.9 22.7 - - + -
1216A ILE* 3.9 25.6 - - + -
1238A ILE* 5.0 1.1 - - + -
1267A MET* 3.6 32.5 - - + +
1268A LEU* 4.9 2.9 - - + -
1271A ILE* 3.8 16.3 + - + -
1273A LEU* 3.0 16.6 - - + +
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Residues in contact with LYS1144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1142A THR* 2.8 8.9 + - - +
1143A LEU* 1.3 78.8 - - - +
1145A SER* 1.3 57.2 + - - +
1146A VAL 3.5 0.5 + - - -
1147A THR* 3.9 17.3 + - - +
1268A LEU* 3.0 45.2 + - + +
1269A GLU* 3.4 34.1 + - + -
262B GLU* 3.8 35.7 + - - +
263B GLY* 4.9 0.8 - - - -
48I LEU* 4.1 21.9 - - + +
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Residues in contact with SER1145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1141A THR* 3.6 13.2 - - - +
1142A THR* 2.4 48.6 + - - -
1144A LYS* 1.3 73.6 - - - +
1146A VAL* 1.3 60.0 + - - +
1147A THR 5.2 0.7 - - - -
1201A ALA* 4.0 11.1 - - - +
1205A LYS* 3.7 18.9 + - - -
49I ILE* 6.0 2.1 - - - +
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Residues in contact with VAL1146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1141A THR* 5.1 2.5 - - + -
1142A THR 3.8 2.9 - - - +
1143A LEU* 2.9 39.3 - - + +
1145A SER* 1.3 85.4 - - - +
1147A THR* 1.3 60.8 + - - +
1197A LEU* 3.3 7.2 - - + +
1198A ASP* 2.9 31.3 + - - -
1201A ALA* 3.5 31.6 - - + +
1202A MET* 3.7 14.6 - - - -
1205A LYS* 5.6 2.7 - - + -
1207A LEU* 3.7 22.0 - - + -
1212A VAL* 5.9 0.4 - - + -
1273A LEU* 4.2 11.9 - - + -
49I ILE* 6.2 0.7 - - - -
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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