Contacts of the helix formed by residues 231 - 236 (chain A) in PDB entry 1S5E
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 231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ASP 3.2 3.0 + - - -
230A ILE* 1.3 72.4 - - - +
232A THR* 1.3 66.9 + - - +
233A HIS* 3.4 11.3 + - - +
234A ASN* 3.3 38.2 + - + +
235A ARG* 3.1 23.7 - - - +
63F LYS 5.2 0.5 - - - +
67F ARG* 3.4 37.0 + - - +
70F ASP* 3.4 9.6 - - - +
66G GLU* 4.7 9.7 - - - +
70G ASP* 3.3 25.4 - - - +
73G ARG* 5.4 0.2 + - - -
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Residues in contact with THR 232 (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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230A ILE* 4.0 5.7 - - - +
231A ASP* 1.3 72.4 - - - +
233A HIS* 1.3 65.2 + - - +
235A ARG* 3.0 18.2 + - - +
236A ILE* 2.9 20.0 + - - +
63E LYS* 4.7 9.0 - - + +
66E GLU* 5.5 3.6 - - + -
67E ARG* 3.4 50.8 + - + +
70E ASP* 4.5 6.2 + - - +
66F GLU* 4.3 6.1 - - - +
70F ASP* 2.6 26.8 + - - -
73F ARG* 4.1 7.1 + - - -
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Residues in contact with HIS 233 (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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231A ASP* 3.4 12.1 + - - +
232A THR* 1.3 79.9 - - - +
234A ASN* 1.3 65.8 + - - +
236A ILE* 3.1 23.5 + - - +
62F LYS* 4.6 6.4 - - + +
63F LYS* 3.8 43.7 + - + +
66F GLU* 3.9 30.3 - - + +
66G GLU* 6.2 2.2 - - - +
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Residues in contact with ASN 234 (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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231A ASP* 3.3 27.8 + - + +
232A THR 3.2 0.6 - - - -
233A HIS* 1.3 82.1 + - - +
235A ARG* 1.3 63.1 + - - +
236A ILE 5.3 0.2 - - - -
63G LYS* 4.3 26.7 + - - +
66G GLU* 5.9 7.1 - - + +
63H LYS* 6.0 2.3 - - - -
66H GLU* 5.5 8.9 + - - +
70H ASP* 5.7 0.7 - - - +
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Residues in contact with ARG 235 (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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230A ILE* 3.9 22.1 - - - +
231A ASP 3.1 28.5 + - - +
232A THR* 3.0 12.1 + - - +
234A ASN* 1.3 85.4 - - - +
236A ILE* 1.3 63.7 + - - +
63D LYS* 5.9 2.9 - - - +
66D GLU* 5.9 7.2 - - + -
67D ARG* 4.5 8.7 - - - +
70D ASP* 3.0 30.6 + - - +
66E GLU* 5.8 2.8 - - - +
70E ASP* 3.2 35.4 + - - -
73E ARG* 4.2 5.3 - - - +
63H LYS* 6.5 0.9 - - - +
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Residues in contact with ILE 236 (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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232A THR* 2.9 15.6 + - - -
233A HIS* 3.1 18.8 + - - +
234A ASN 5.2 0.2 - - - -
235A ARG* 1.3 81.4 - - - +
63E LYS* 5.5 15.3 - - - +
66E GLU* 6.0 7.9 - - - -
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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