Contacts of the helix formed by residues 224 - 231 (chain C) in PDB entry 2DB3
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 HIS 224 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258B ASP* 2.9 40.6 + - - -
262B LYS* 4.9 2.5 - - - -
223C ILE* 1.3 90.1 + - + +
225C PHE* 1.3 64.7 + - - +
226C SER* 3.2 2.9 - - - -
227C LYS* 2.8 62.0 + - + +
228C TYR* 4.0 2.3 + - - -
464C ASP* 3.1 28.4 - - - +
584C GLY* 2.9 22.5 + - - +
586C ASN* 3.4 17.2 + - - -
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Residues in contact with PHE 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C SER* 3.6 24.5 - - - +
222C GLY 3.0 16.2 + - - +
223C ILE 3.5 0.8 - - - -
224C HIS* 1.3 75.9 - - - +
226C SER* 1.3 67.0 + - - +
228C TYR* 3.0 54.8 + + + +
267C ILE* 3.7 40.8 - - + -
268C PRO 5.2 0.9 - - - -
269C THR* 4.2 14.4 - - - -
583C VAL* 3.8 13.5 - - + +
584C GLY* 3.7 5.8 - - - -
2903C ANP 3.7 32.3 - + - -
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Residues in contact with SER 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C ILE 5.0 4.6 + - - -
224C HIS 3.2 1.3 + - - -
225C PHE* 1.3 83.0 - - - +
227C LYS* 1.3 68.9 + - - +
228C TYR 3.0 1.9 + - - -
229C ASN* 3.1 31.9 + - - +
230C ASN* 4.6 1.6 + - - -
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Residues in contact with LYS 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B LYS* 3.9 19.4 - - - +
344B GLU* 5.2 8.6 + - - -
223C ILE 5.9 0.2 - - - -
224C HIS* 2.8 55.6 + - + +
226C SER* 1.3 81.4 + - - +
228C TYR* 1.3 63.2 + - - +
229C ASN 3.0 2.5 - - - -
230C ASN* 3.0 35.2 + - - +
231C ILE* 4.0 7.7 - - - +
464C ASP* 5.9 0.2 - - - +
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Residues in contact with TYR 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C HIS 4.0 1.5 + - - -
225C PHE* 3.0 60.7 + + + +
226C SER 3.0 0.4 - - - -
227C LYS* 1.3 78.7 - - - +
229C ASN* 1.3 63.5 + - - +
230C ASN 3.2 0.9 + - - -
231C ILE* 3.3 36.6 + - + +
233C VAL* 6.1 0.2 - - - +
269C THR* 4.1 9.4 - - - -
270C PRO* 3.5 35.8 - - + +
290C GLN* 3.5 24.5 + - - -
292C GLY 3.1 24.4 + - - -
293C SER* 3.5 20.2 - - - -
455C ILE* 6.1 0.2 - - + -
464C ASP* 5.5 2.4 + - - -
583C VAL* 3.4 11.7 + - + +
584C GLY* 3.7 9.9 + - - -
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Residues in contact with ASN 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C SER* 3.1 24.6 - - - +
227C LYS 3.0 0.4 - - - -
228C TYR* 1.3 82.1 - - - +
230C ASN* 1.3 65.2 + - - +
231C ILE 3.3 4.3 + - - +
267C ILE* 6.1 2.2 - - - +
270C PRO* 5.2 4.0 - - - +
273C LYS* 3.9 22.6 - - - +
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Residues in contact with ASN 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C SER 4.6 0.8 + - - -
227C LYS* 3.0 35.8 + - - +
229C ASN* 1.3 86.8 - - - +
231C ILE* 1.3 62.9 + - - +
232C PRO* 3.4 8.8 - - - +
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Residues in contact with ILE 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C LYS 4.0 8.1 - - - +
228C TYR* 3.3 44.6 + - + +
229C ASN 3.3 3.7 - - - +
230C ASN* 1.3 77.5 - - - +
232C PRO* 1.3 74.4 - - + +
233C VAL* 3.3 14.0 + - - +
290C GLN* 4.0 23.1 - - - +
455C ILE* 3.9 17.9 - - + +
456C GLY* 3.4 33.4 - - - +
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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