Contacts of the helix formed by residues 257 - 261 (chain B) in PDB entry 2R5N
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 THR 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187B ILE* 4.0 6.1 - - - +
192B HIS* 6.0 0.9 - - - -
247B ILE* 3.6 5.7 - - - +
253B ASN 4.1 10.5 - - - +
254B LYS* 2.7 22.2 + - - +
255B ALA 3.6 11.7 - - - +
256B GLY* 1.3 83.9 - - - +
258B HIS* 1.3 66.9 + - - +
259B ASP* 3.2 29.7 + - - +
260B SER* 3.0 19.2 + - - -
261B HIS 4.2 0.7 + - - -
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Residues in contact with HIS 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A PRO* 5.9 4.3 - - + -
187B ILE* 3.6 17.3 - - + +
188B SER 3.6 21.8 - - - +
189B ILE* 4.0 17.4 - - - +
190B ASP 5.3 1.1 - - - -
191B GLY* 4.1 16.1 - - - -
257B THR* 1.3 73.2 - - - +
259B ASP* 1.3 86.7 + - - +
260B SER 3.1 0.2 - - - -
261B HIS* 3.1 21.1 + - - +
262B GLY 4.5 0.7 + - - -
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Residues in contact with ASP 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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253B ASN 6.1 0.4 - - - -
254B LYS* 4.3 29.0 + - + +
257B THR* 3.0 21.9 + - - +
258B HIS* 1.3 107.2 + - - +
260B SER* 1.3 57.3 + - - +
261B HIS 3.5 0.7 + - - -
262B GLY 4.4 4.0 + - - -
263B ALA* 4.4 15.2 + - - +
264B PRO 5.4 0.3 - - - +
265B LEU* 5.4 0.2 - - - +
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Residues in contact with SER 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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27B PRO* 3.4 8.5 - - - +
28B GLY* 2.8 27.0 + - - -
247B ILE* 3.5 21.5 - - - +
248B GLY* 4.1 15.3 - - - -
254B LYS* 3.4 26.0 + - - +
257B THR* 3.0 15.5 + - - -
258B HIS 3.1 0.2 - - - -
259B ASP* 1.3 77.2 - - - +
261B HIS* 1.3 61.7 + - - +
262B GLY 3.5 0.7 - - - -
263B ALA 5.0 0.2 - - - -
265B LEU* 4.3 16.4 - - - -
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Residues in contact with HIS 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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670A R5P 2.6 31.6 + - - -
26B HIS* 3.2 30.0 - + - +
27B PRO* 4.2 0.4 - - - -
28B GLY* 4.1 2.5 + - - -
29B ALA 5.2 0.5 + - - -
66B HIS* 3.7 15.3 - + - -
187B ILE* 5.2 3.1 - - + -
188B SER* 5.5 1.3 - - - +
189B ILE* 3.5 28.4 - - + +
247B ILE* 4.0 13.5 - - + -
257B THR 4.2 0.2 + - - -
258B HIS* 3.1 18.9 + - + +
260B SER* 1.3 82.6 + - - +
262B GLY* 1.3 64.7 + - - +
263B ALA 3.9 0.2 - - - -
672B TPP 2.7 57.0 + - - +
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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