Contacts of the helix formed by residues 242 - 250 (chain B) in PDB entry 1NYR
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 242 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238B ARG 3.0 8.2 + - - +
239B LYS* 3.3 16.7 + - - +
241B ARG* 1.3 75.5 - - - +
243B HIS* 1.3 71.6 + - - +
244B ARG* 2.6 72.6 + - - +
245B LYS* 3.0 21.7 + - + +
246B ILE* 3.3 13.6 + - - +
376B GLN* 5.3 2.3 + - - -
479B ALA* 4.6 9.7 - - - +
480B MET* 6.1 0.5 - - - +
533B GLU* 4.0 10.4 - - - +
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Residues in contact with HIS 243 (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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241B ARG 3.0 4.9 + - - -
242B ASP* 1.3 73.2 + - - +
244B ARG* 1.3 80.7 + - + +
246B ILE* 3.5 0.6 - - - +
247B GLY* 2.6 36.2 + - - -
253B PHE* 3.8 23.6 - + + -
373B SER* 5.3 0.9 - - - -
374B GLY* 3.9 0.8 - - - -
375B LEU* 3.2 25.4 + - + -
376B GLN* 3.3 40.4 + - + +
529B ALA* 3.8 18.1 - - + +
532B THR* 3.6 30.7 - - + +
533B GLU* 3.0 28.3 + - + -
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Residues in contact with ARG 244 (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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242B ASP* 2.6 52.0 + - - +
243B HIS* 1.3 102.1 - - - +
245B LYS* 1.3 89.8 + - - +
246B ILE 3.5 0.2 + - - -
247B GLY* 4.2 0.3 - - - -
248B LYS* 3.5 22.0 + - - +
253B PHE* 4.1 9.1 - - + -
373B SER* 3.5 25.8 + - - -
374B GLY* 3.9 15.7 - - - +
376B GLN* 5.8 1.2 - - - +
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Residues in contact with LYS 245 (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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239B LYS* 4.5 11.4 - - + +
242B ASP* 3.0 19.7 + - + +
244B ARG* 1.3 112.2 + - - +
246B ILE* 1.3 62.6 + - + +
248B LYS* 4.4 5.9 - - + +
249B GLU* 2.9 31.9 + - - +
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Residues in contact with ILE 246 (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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239B LYS 5.8 0.4 - - - +
240B GLU 4.5 5.8 - - - +
241B ARG* 4.1 20.6 - - - +
242B ASP 3.3 14.8 - - - +
243B HIS 3.1 5.1 + - - +
245B LYS* 1.3 82.0 - - + +
247B GLY* 1.3 56.9 + - - +
248B LYS 3.2 0.2 - - - -
249B GLU* 3.8 18.4 - - - +
250B LEU* 2.7 59.3 + - + +
252B LEU* 4.9 2.5 - - + -
532B THR* 4.1 17.9 - - + +
536B LYS* 4.0 26.9 - - + +
537B GLY* 3.9 12.6 - - - -
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Residues in contact with GLY 247 (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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243B HIS 2.6 21.6 + - - -
244B ARG 4.2 0.2 - - - -
246B ILE* 1.3 74.2 - - - +
248B LYS* 1.3 50.8 + - - +
251B GLU* 2.7 13.0 + - - -
252B LEU* 2.7 42.3 + - - +
253B PHE* 3.6 28.2 + - - +
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Residues in contact with LYS 248 (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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244B ARG 3.5 15.8 + - - +
245B LYS* 4.4 7.0 - - + +
246B ILE 3.2 0.4 - - - -
247B GLY* 1.3 72.8 - - - +
249B GLU* 1.3 68.6 + - - +
251B GLU* 3.0 19.7 + - - +
253B PHE* 4.5 7.0 + - - +
254B THR* 5.7 3.6 - - + -
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Residues in contact with GLU 249 (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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245B LYS* 2.9 27.4 + - - +
246B ILE* 3.4 21.7 - - - +
248B LYS* 1.3 82.8 - - - +
250B LEU* 1.3 74.9 + - + +
251B GLU* 3.7 3.3 + - - +
594B MET 5.2 3.8 - - - +
595B GLN* 3.0 16.3 + - - -
596B LYS* 4.1 13.3 + - - -
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Residues in contact with LEU 250 (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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246B ILE* 2.7 40.0 + - + +
249B GLU* 1.3 99.2 - - + +
251B GLU* 1.3 71.7 + - - +
252B LEU* 3.4 16.4 + - + +
269B ASN* 3.1 18.4 + - - -
537B GLY* 3.8 25.4 - - - +
539B PHE* 4.9 6.3 - - + -
545B PRO* 6.4 0.2 - - + -
594B MET 4.2 13.9 - - - +
595B GLN* 3.5 29.9 + - + +
596B LYS* 4.4 9.2 - - + -
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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