Contacts of the helix formed by residues 253 - 262 (chain B) in PDB entry 2R9R
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 ASN 253 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154B GLU* 5.5 4.9 + - - -
249B GLY 4.0 7.7 + - - +
250B PHE 3.0 2.1 + - - +
252B THR* 1.3 79.0 - - - +
254B ILE* 1.3 66.7 + - - +
255B MET* 2.9 41.5 + - - +
256B ASN* 3.0 34.5 + - - +
257B ILE* 3.2 13.8 + - - +
305B ARG* 5.7 0.8 - - - +
512B PGW 5.4 0.7 - - - +
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Residues in contact with ILE 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 THR 3.3 6.0 + - - +
253B ASN* 1.3 73.8 + - - +
255B MET* 1.3 59.3 + - - +
257B ILE* 3.2 14.7 + - + +
258B ILE* 3.0 38.0 + - + +
512B PGW 3.6 106.4 - - + +
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Residues in contact with MET 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 ASN* 2.9 22.5 + - - +
254B ILE* 1.3 78.2 - - - +
256B ASN* 1.3 61.2 + - - +
258B ILE* 3.4 9.3 + - - +
259B ASP* 2.9 27.6 + - - +
304B SER* 3.4 27.4 - - - +
305B ARG* 3.2 60.6 + - + +
311B GLN* 4.1 5.6 - - - +
512B PGW 3.8 42.8 - - + +
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Residues in contact with ASN 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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150B TRP* 6.0 2.0 - - - -
240B ARG* 4.4 8.1 - - - -
249B GLY 4.7 0.4 + - - -
250B PHE* 2.8 76.7 + - + +
251B PHE* 5.0 2.2 - - - -
253B ASN* 3.0 21.4 + - - +
255B MET* 1.3 73.8 - - - +
257B ILE* 1.3 67.2 + - - +
259B ASP* 3.0 10.4 + - - +
260B ILE* 3.0 29.4 + - + +
305B ARG* 3.9 12.6 + - - -
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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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251B PHE* 3.5 31.6 - - + +
252B THR 5.1 1.1 - - - -
253B ASN 3.3 14.8 - - - +
254B ILE* 3.3 17.3 - - + +
256B ASN* 1.3 78.3 - - - +
258B ILE* 1.3 64.1 + - + +
260B ILE* 3.1 9.4 + - + +
261B VAL* 2.9 39.4 + - + +
514B PGW 3.7 29.8 - - + -
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Residues in contact with ILE 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 ILE* 3.0 36.1 + - + +
255B MET* 3.5 13.9 - - - +
257B ILE* 1.3 77.9 - - + +
259B ASP* 1.3 57.7 + - - +
261B VAL* 3.3 8.3 + - - +
262B ALA* 2.9 28.8 + - - +
298B LEU 4.8 4.7 - - - +
301B PHE* 3.5 39.3 - - + +
302B LYS* 3.8 15.5 - - + +
304B SER* 3.6 22.7 - - - +
512B PGW 4.8 9.2 - - + -
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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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233B PHE 5.0 0.7 - - - +
236B GLU* 4.4 1.4 - - - +
237B PHE* 4.6 22.7 + - + +
240B ARG* 4.2 17.6 + - - -
255B MET 2.9 12.6 + - - +
256B ASN* 3.0 15.2 + - - +
258B ILE* 1.3 76.9 - - - +
260B ILE* 1.3 62.5 + - - +
262B ALA* 3.6 10.4 + - - +
263B ILE* 3.9 13.7 - - - +
302B LYS* 3.1 36.9 + - - +
305B ARG* 2.8 36.5 + - - -
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Residues in contact with ILE 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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237B PHE* 3.5 25.6 - - + -
250B PHE* 4.9 0.4 - - + -
251B PHE* 3.5 39.5 - - + -
256B ASN 3.0 19.7 + - - +
257B ILE* 3.1 9.8 + - - +
259B ASP* 1.3 73.4 - - - +
261B VAL* 1.3 60.6 + - + +
262B ALA 2.9 2.0 - - - -
263B ILE* 2.8 38.1 + - + +
264B ILE* 3.0 31.5 + - + +
514B PGW 4.2 16.8 - - + -
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Residues in contact with VAL 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* 2.9 34.9 + - + +
258B ILE* 3.7 7.9 - - - +
260B ILE* 1.3 75.6 - - + +
262B ALA* 1.3 61.7 + - - +
264B ILE* 4.0 15.7 - - + -
265B PRO* 3.1 21.8 - - - +
295B MET* 4.4 14.4 - - + +
296B ARG* 5.9 0.2 - - - -
298B LEU* 3.7 39.7 - - + +
514B PGW 5.1 10.1 - - + -
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Residues in contact with ALA 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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230B ILE* 4.6 7.3 - - - +
233B PHE* 4.1 17.4 - - + -
258B ILE* 2.9 16.9 + - + +
259B ASP 3.6 8.7 - - - +
260B ILE 2.9 1.4 - - - -
261B VAL* 1.3 77.9 - - - +
263B ILE* 1.3 60.9 + - + +
265B PRO* 4.2 3.7 - - - +
296B ARG* 6.0 1.4 - - - +
298B LEU* 5.7 0.4 - - - -
299B ARG* 4.4 26.7 + - - +
302B LYS* 3.8 28.7 - - + -
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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