Contacts of the helix formed by residues 232 - 240 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B TYR* 4.5 0.4 - - - -
155B LEU 4.0 8.3 - - - +
156B CYS* 3.2 20.4 - - - +
157B GLY 3.7 4.3 - - - +
158B PHE* 3.1 16.8 - - - -
159B ASN* 3.3 2.5 + - + +
223B ARG* 2.8 30.9 + - - -
230B SER* 3.2 9.0 - - - -
231B ASP* 1.3 79.6 - - - +
233B LEU* 1.3 64.2 + - - +
234B LEU* 3.7 4.8 - - - +
235B THR* 2.9 34.1 + - - -
236B HIS* 3.4 20.4 + - - -
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 4.1 7.2 - - + -
106B SER* 3.3 28.9 - - - +
107B PHE* 3.7 36.8 - - + -
115B TYR* 3.4 22.2 - - + +
153B ILE* 6.1 1.3 - - + -
156B CYS* 3.0 24.7 + - + +
157B GLY* 3.7 16.6 - - - +
232B ASP* 1.3 71.8 - - - +
234B LEU* 1.4 58.3 + - - +
236B HIS* 3.3 7.4 + - - +
237B MET* 2.9 36.0 + - + +
261B PHE* 4.0 20.9 - - + -
405B PHE* 5.2 4.7 - - + -
500B HEM 5.7 1.6 - - + -
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B GLY 2.9 17.4 + - - +
158B PHE* 4.0 16.2 - - + -
219B ILE* 4.2 14.4 - - + +
220B ILE* 3.9 17.0 - - + -
223B ARG* 3.7 38.8 - - + +
232B ASP* 3.2 8.2 - - - +
233B LEU* 1.4 72.7 - - - +
235B THR* 1.3 55.1 + - - +
237B MET* 3.2 6.8 + - - +
238B LEU* 2.8 53.6 + - + +
254B ILE* 3.6 28.7 - - + -
258B ILE* 4.3 3.1 - - + -
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Residues in contact with THR 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ARG* 3.0 12.3 + - - +
228B GLU 4.2 1.7 + - - +
229B GLN* 3.4 32.5 - - + +
230B SER 2.9 39.7 + - - +
232B ASP* 2.9 22.6 + - - -
234B LEU* 1.3 75.4 - - - +
236B HIS* 1.3 68.9 + - + +
238B LEU* 3.3 5.5 + - - +
239B ASN* 3.1 28.4 + - - +
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Residues in contact with HIS 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ILE* 4.8 5.4 - - + +
103B LEU* 5.6 1.3 - - + -
106B SER* 3.6 24.5 - - - +
111B ALA* 6.1 0.8 - - - +
115B TYR* 3.4 27.6 + - - -
230B SER 4.7 7.0 - - - -
231B ASP* 4.3 13.0 + - - -
232B ASP 3.4 19.4 + - - -
233B LEU* 3.3 9.6 + - - +
235B THR* 1.3 78.3 - - + +
237B MET* 1.3 59.1 + - + +
239B ASN* 3.3 4.0 + - - +
240B GLY* 2.8 31.4 + - - -
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Residues in contact with MET 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ILE* 4.9 7.9 - - + +
103B LEU* 3.6 24.5 - - + -
233B LEU* 2.9 28.2 + - + +
234B LEU* 3.7 4.5 - - - +
236B HIS* 1.3 75.0 - - - +
238B LEU* 1.3 65.6 + - - +
239B ASN 3.3 0.2 + - - -
240B GLY* 3.7 9.4 + - - +
248B PRO* 5.3 1.2 - - - +
249B LEU* 3.9 31.4 + - + +
254B ILE* 4.0 41.7 - - + +
257B GLN* 3.7 22.4 - - + -
258B ILE* 4.0 15.3 - - + -
261B PHE* 3.9 23.1 - - + -
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B ILE* 4.5 3.8 - - + +
223B ARG* 3.4 36.1 - - + -
224B LYS* 4.0 37.5 - - + +
234B LEU* 2.8 39.3 + - + +
235B THR* 3.8 5.6 - - - +
237B MET* 1.3 73.9 - - - +
239B ASN* 1.3 66.7 + - - +
240B GLY 3.9 1.2 + - - +
248B PRO* 5.4 5.0 - - - +
251B ASP* 4.2 3.8 - - - +
254B ILE* 3.9 19.5 - - + -
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Residues in contact with ASN 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B GLN* 2.7 38.3 + - - +
235B THR* 3.1 24.4 + - - +
236B HIS* 4.0 3.6 - - - +
238B LEU* 1.3 84.3 - - - +
240B GLY* 1.3 66.4 + - - +
241B LYS* 3.9 8.5 + - - +
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Residues in contact with GLY 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ILE* 4.4 16.5 - - - +
236B HIS 2.8 16.2 + - - -
237B MET 3.7 4.0 + - - +
238B LEU 3.5 1.2 - - - -
239B ASN* 1.3 81.7 - - - +
241B LYS* 1.3 66.2 + - - +
248B PRO* 3.4 20.1 - - - +
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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