Contacts of the helix formed by residues 270 - 274 (chain J) in PDB entry 6NR8
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 ALA 270 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255J ARG* 3.8 13.9 + - - +
257J ARG* 5.1 5.6 - - - -
266J GLU 3.4 10.7 + - - +
267J ILE* 4.0 18.8 - - + +
268J GLU 3.3 1.4 - - - -
269J HIS* 1.3 76.4 - - - +
271J GLU* 1.3 63.8 + - - +
272J LYS 3.2 2.9 - - - -
273J GLU* 3.3 11.2 + - - +
274J LYS* 3.4 21.7 + - - +
261L ASP* 3.3 26.5 - - - +
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Residues in contact with GLU 271 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246J THR* 2.9 32.1 + - + +
247J ASP* 2.9 22.9 - - - +
267J ILE* 4.2 13.9 - - - +
268J GLU* 4.0 15.9 - - - +
269J HIS 3.2 1.4 - - - -
270J ALA* 1.3 76.9 - - - +
272J LYS* 1.3 64.6 + - + +
273J GLU 3.3 0.2 - - - -
274J LYS* 2.6 38.7 + - - +
275J MET* 3.5 25.6 - - + +
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Residues in contact with LYS 272 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268J GLU 5.4 0.2 - - - +
269J HIS 4.2 3.4 - - - +
270J ALA 3.2 0.8 - - - -
271J GLU* 1.3 84.4 - - - +
273J GLU* 1.3 60.9 + - + +
274J LYS 3.5 0.3 + - - -
275J MET* 3.5 22.6 + - + +
276J LYS* 4.4 10.9 - - - +
299J TYR* 3.5 58.5 + - + -
303J LEU* 4.4 3.8 - - - +
252L CYS* 5.4 1.8 + - - +
254L SER* 5.7 2.0 - - - +
259L ASP* 2.8 66.1 + - + +
305L LEU* 3.9 21.7 - - + +
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Residues in contact with GLU 273 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255J ARG* 3.5 17.1 + - - +
270J ALA 3.3 8.7 + - - +
271J GLU 3.3 0.2 - - - -
272J LYS* 1.3 76.3 - - + +
274J LYS* 1.3 64.3 + - - +
275J MET 3.2 2.0 + - - -
276J LYS* 3.7 31.0 + - + +
277J GLU* 4.6 9.0 + - - +
259L ASP 4.5 2.9 - - - +
260L MET* 3.4 23.3 - - + +
261L ASP* 2.9 47.6 + - - +
263L GLN* 5.4 4.9 + - - -
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Residues in contact with LYS 274 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244J MET* 5.0 1.3 - - - +
246J THR 3.8 13.0 - - - +
247J ASP* 4.0 8.8 + - - +
248J LYS* 3.3 54.6 - - - +
249J ILE* 5.0 13.9 - - - +
255J ARG* 3.4 21.1 - - - +
267J ILE* 6.1 3.7 - - - +
270J ALA* 3.4 16.8 + - - +
271J GLU* 2.6 43.7 + - - +
272J LYS 3.3 0.8 - - - -
273J GLU* 1.3 78.0 - - - +
275J MET* 1.3 62.1 + - - +
276J LYS 3.2 1.4 + - - -
277J GLU* 3.8 9.0 + - - +
278J LYS 4.5 0.5 + - - -
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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