Contacts of the helix formed by residues 232 - 240 (chain A) in PDB entry 4DTZ
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 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A TYR* 4.4 0.4 - - - -
155A LEU 3.9 7.9 - - - +
156A CYS* 3.2 20.2 - - - +
157A GLY 3.8 5.4 - - - +
158A PHE* 3.1 15.2 - - - -
159A ASN* 3.3 2.9 + - + +
223A ARG* 2.8 34.6 + - - -
230A SER* 3.3 7.2 - - - -
231A ASP* 1.3 80.5 - - - +
233A LEU* 1.3 67.3 + - - +
234A LEU* 3.6 6.9 - - - +
235A THR* 2.8 38.1 + - - -
236A HIS* 3.3 19.5 + - - -
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Residues in contact with LEU 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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103A LEU* 4.1 6.1 - - + -
106A SER* 3.4 26.0 - - - +
107A PHE* 3.6 38.8 - - + -
115A TYR* 3.2 29.2 - - + +
153A ILE* 6.4 0.9 - - + -
156A CYS 2.9 17.8 + - - +
157A GLY* 3.5 11.6 + - - +
232A ASP* 1.3 74.2 - - - +
234A LEU* 1.3 60.5 + - - +
236A HIS* 3.1 7.1 + - - +
237A MET* 2.8 35.1 + - + +
261A PHE* 3.8 25.6 - - + -
405A PHE* 5.1 8.3 - - + -
500A HEM 5.6 1.3 - - + -
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Residues in contact with LEU 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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157A GLY 2.8 17.9 + - - +
158A PHE* 4.0 18.8 - - + -
219A ILE* 4.0 14.8 - - + -
220A ILE* 4.0 18.4 - - + -
223A ARG* 4.0 29.4 - - + +
232A ASP* 3.2 10.7 - - - +
233A LEU* 1.3 75.9 - - - +
235A THR* 1.3 52.8 + - - +
237A MET* 3.0 7.9 + - - +
238A LEU* 2.8 54.6 + - + +
254A ILE* 3.6 28.7 - - + -
258A ILE* 4.3 2.9 - - + -
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Residues in contact with THR 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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223A ARG* 3.3 8.3 + - - +
228A GLU 4.5 0.7 + - - +
229A GLN* 3.7 15.9 - - + +
230A SER 2.8 40.2 + - - +
232A ASP* 2.8 25.3 + - - -
234A LEU* 1.3 75.5 - - - +
236A HIS* 1.3 71.1 + - + +
238A LEU* 3.4 6.0 + - - +
239A ASN* 3.1 40.3 + - - +
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Residues in contact with HIS 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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102A ILE* 4.7 6.0 - - + +
103A LEU* 5.6 1.1 - - + -
106A SER* 3.8 23.3 - - - +
115A TYR* 3.4 27.7 + - - -
230A SER 5.0 8.7 - - - -
231A ASP* 4.4 9.0 + - - -
232A ASP 3.3 21.7 + - - -
233A LEU* 3.1 8.7 + - - +
235A THR* 1.3 82.5 - - + +
237A MET* 1.3 60.1 + - + +
239A ASN* 3.7 4.5 + - - +
240A GLY* 2.9 29.8 + - - -
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Residues in contact with MET 237 (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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102A ILE* 5.0 6.5 - - + +
103A LEU* 3.6 27.1 - - + -
233A LEU* 2.8 30.0 + - + +
234A LEU* 3.0 7.6 + - - +
236A HIS* 1.3 76.2 - - - +
238A LEU* 1.3 64.7 + - - +
240A GLY* 3.7 9.8 + - - +
248A PRO* 5.3 1.4 - - - +
249A LEU* 4.2 22.4 + - + +
254A ILE* 4.1 32.6 - - + +
257A GLN* 3.8 28.7 - - + -
258A ILE* 3.9 27.1 - - + -
261A PHE* 4.0 14.8 - - + -
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Residues in contact with LEU 238 (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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220A ILE* 4.3 6.3 - - + +
223A ARG* 3.6 35.0 - - + -
224A LYS* 3.9 37.2 - - + +
234A LEU* 2.8 32.1 + - + +
235A THR* 4.0 5.6 - - - +
237A MET* 1.3 79.1 - - - +
239A ASN* 1.3 63.2 + - - +
240A GLY 3.5 1.8 - - - +
248A PRO* 5.4 4.9 - - - +
251A ASP* 4.1 5.4 - - - +
254A ILE* 3.9 21.1 - - + -
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Residues in contact with ASN 239 (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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229A GLN* 3.0 30.8 + - - +
235A THR* 3.1 26.7 + - - +
236A HIS* 4.1 4.1 + - - +
238A LEU* 1.3 82.2 - - - +
240A GLY* 1.3 64.3 + - - +
241A LYS* 3.9 9.2 + - - +
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Residues in contact with GLY 240 (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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102A ILE* 4.2 18.6 - - - +
236A HIS 2.9 16.3 + - - -
237A MET 3.7 4.4 + - - +
238A LEU 3.5 1.5 - - - +
239A ASN* 1.3 80.8 - - - +
241A LYS* 1.3 62.4 + - - +
248A PRO* 3.4 25.6 - - - +
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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