Contacts of the helix formed by residues 253 - 263 (chain B) 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 ARG 253 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251B ASP 4.0 1.0 + - - -
252B LEU* 1.3 75.2 - - - +
254B ASP* 1.3 66.9 + - - +
255B ILE* 3.4 9.0 - - + +
256B ILE* 3.2 13.4 + - + +
257B ILE* 3.1 16.8 + - - +
305B SER* 2.8 24.5 + - - +
308B LEU* 3.3 53.7 + - + +
309B GLU* 3.9 24.3 + - + +
311B PRO* 5.6 0.6 - - - +
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Residues in contact with ASP 254 (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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252B LEU 3.5 2.1 + - - -
253B ARG* 1.3 74.7 - - - +
255B ILE* 1.3 60.5 + - - +
257B ILE* 3.2 18.6 + - - +
258B ASP* 2.8 29.6 + - - +
223C ILE* 3.9 27.9 - - + +
586C ASN* 5.0 4.0 + - - -
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Residues in contact with ILE 255 (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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253B ARG* 4.6 11.2 - - + +
254B ASP* 1.3 73.6 - - - +
256B ILE* 1.3 62.5 + - + +
258B ASP* 3.3 3.0 + - - +
259B ASN* 2.9 39.3 + - - +
308B LEU* 3.2 41.5 - - + -
343B PHE 5.3 2.5 - - - +
344B GLU* 5.1 9.4 - - + +
345B SER* 3.9 19.5 - - - -
223C ILE* 3.9 20.2 - - + -
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Residues in contact with ILE 256 (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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252B LEU* 4.6 10.3 - - + -
253B ARG* 3.2 11.0 + - + +
254B ASP 3.2 0.4 - - - -
255B ILE* 1.3 77.3 - - + +
257B ILE* 1.3 66.3 + - - +
259B ASN* 3.0 3.7 + - - +
260B VAL* 2.9 21.5 + - + +
301B LEU* 4.0 39.7 - - + +
304B LEU* 3.9 21.8 - - + -
305B SER* 4.0 18.8 - - - -
308B LEU* 3.9 26.2 - - + -
341B PHE 3.2 24.7 - - - +
342B ALA* 4.7 4.3 - - - -
345B SER* 5.7 0.7 - - - -
347B LEU* 5.4 0.2 - - + -
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Residues in contact with ILE 257 (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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247B PHE* 4.1 28.3 - - + +
248B THR* 4.6 15.3 - - + +
252B LEU* 2.9 43.3 - - + +
253B ARG 3.1 10.4 + - - +
254B ASP* 3.2 20.8 + - - +
256B ILE* 1.3 76.2 - - - +
258B ASP* 1.3 62.4 + - - +
260B VAL* 3.1 12.4 + - + +
261B ASN* 3.1 18.5 + - - +
586C ASN* 6.0 2.5 - - - +
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Residues in contact with ASP 258 (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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254B ASP* 2.8 18.3 + - - +
255B ILE* 3.6 5.8 - - - +
257B ILE* 1.3 77.1 - - - +
259B ASN* 1.3 62.8 + - - +
261B ASN* 3.2 11.4 + - - +
262B LYS* 3.1 39.2 + - - +
223C ILE* 4.2 12.7 - - + +
224C HIS* 2.9 34.3 + - - -
586C ASN* 2.9 28.8 + - - +
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Residues in contact with ASN 259 (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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215B PHE* 3.5 9.6 - - + -
255B ILE* 2.9 23.9 + - - +
256B ILE* 3.0 3.5 + - - +
258B ASP* 1.3 75.0 - - - +
260B VAL* 1.3 63.9 + - - +
262B LYS* 3.4 10.9 + - - +
263B SER* 2.8 29.3 + - - -
340B LYS 3.6 15.7 - - - +
341B PHE* 2.7 34.5 + - - +
342B ALA* 3.7 1.2 - - - +
343B PHE* 3.0 44.1 + - - +
345B SER* 5.5 0.6 - - - -
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Residues in contact with VAL 260 (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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247B PHE* 3.8 29.6 - - + -
252B LEU* 5.2 2.2 - - + -
256B ILE* 2.9 21.7 + - + +
257B ILE* 3.1 11.4 + - + +
259B ASN* 1.3 74.2 - - - +
261B ASN* 1.3 67.7 + - - +
263B SER* 3.3 11.1 + - - -
265B TYR* 3.3 44.1 + - + +
301B LEU* 3.7 37.5 - - + -
341B PHE* 4.7 4.9 - - + -
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Residues in contact with ASN 261 (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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257B ILE 3.1 11.8 + - - +
258B ASP* 3.3 22.1 + - - +
260B VAL* 1.3 78.2 - - - +
262B LYS* 1.3 61.6 + - - +
264B GLY* 2.8 26.7 + - - -
265B TYR 4.8 5.4 - - - -
466C LYS* 3.5 41.9 + - - +
586C ASN* 4.5 18.0 + - + +
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Residues in contact with LYS 262 (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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215B PHE* 3.4 49.1 - - + +
258B ASP* 3.1 33.5 + - - +
259B ASN* 3.8 10.0 + - - +
260B VAL 3.4 0.2 - - - -
261B ASN* 1.3 84.1 - - - +
263B SER* 1.3 59.4 + - - +
264B GLY 3.1 1.0 + - - -
343B PHE* 4.0 21.8 - - + -
344B GLU* 4.6 6.3 + - - -
224C HIS* 4.9 1.8 - - - -
227C LYS* 3.9 21.7 - - - +
466C LYS* 5.5 1.1 + - - +
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Residues in contact with SER 263 (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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215B PHE* 3.6 12.7 - - - -
259B ASN 2.8 21.6 + - - -
260B VAL 3.6 7.0 - - - -
261B ASN 3.1 0.4 - - - -
262B LYS* 1.3 76.7 - - - +
264B GLY* 1.3 60.1 + - - +
265B TYR* 3.7 26.3 + - - -
340B LYS* 3.5 20.6 + - - +
341B PHE* 3.4 19.4 - - - -
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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