Contacts of the helix formed by residues 279 - 286 (chain K) 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 CYS 279 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245K LEU* 6.1 1.1 - - - -
275K ILE* 3.4 22.0 + - - +
276K GLN* 3.4 2.1 + - - +
277K GLN 3.3 0.6 - - - -
278K LEU* 1.3 76.7 - - - +
280K GLU* 1.3 62.0 + - - +
281K ASP 3.2 1.3 - - - -
282K ILE* 3.2 26.4 + - - +
283K ILE* 3.3 9.4 + - - +
296K ILE* 6.1 0.9 - - - -
300K ALA* 4.5 9.6 - - - -
303K TYR* 3.3 31.8 - - + -
304K LEU* 3.7 35.0 - - + -
307K ALA* 4.8 0.7 - - - +
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Residues in contact with GLU 280 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257I PRO* 5.8 2.8 - - - +
276K GLN* 3.4 14.8 + - - +
277K GLN* 3.6 32.9 - - - +
278K LEU 3.2 1.4 - - - -
279K CYS* 1.3 78.0 - - - +
281K ASP* 1.3 64.4 + - - +
283K ILE* 3.4 4.8 + - - +
284K GLN* 3.3 31.6 + - - +
303K TYR* 3.4 24.1 + - + +
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Residues in contact with ASP 281 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257I PRO* 4.0 16.0 - - - +
258I GLU* 5.9 2.3 - - - +
261I ASP* 5.4 3.8 - - - +
243K SER 3.9 15.6 - - - +
244K SER* 3.3 24.0 + - - +
246K GLU* 3.9 19.8 - - - +
277K GLN 4.9 2.9 - - - +
278K LEU* 3.5 5.8 + - - +
279K CYS 3.2 0.2 - - - -
280K GLU* 1.3 77.2 - - - +
282K ILE* 1.3 58.2 + - - +
283K ILE 3.3 0.2 - - - -
284K GLN* 3.8 16.4 - - - +
285K LEU* 2.9 39.7 + - + +
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Residues in contact with ILE 282 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244K SER* 3.3 27.4 - - - +
245K LEU* 3.8 16.8 - - + -
278K LEU 4.4 0.4 - - - +
279K CYS* 3.2 29.1 + - - +
280K GLU 3.2 0.4 - - - -
281K ASP* 1.3 75.6 - - - +
283K ILE* 1.3 63.3 + - - +
286K LYS* 3.3 6.8 + - - +
287K PRO* 3.3 23.9 - - + +
290K VAL* 3.8 19.3 - - + -
304K LEU* 3.7 29.4 - - + -
307K ALA* 3.8 6.6 - - + +
309K ILE* 3.7 27.5 - - + +
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Residues in contact with ILE 283 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279K CYS 3.3 11.7 + - - +
280K GLU* 3.4 8.0 + - - +
282K ILE* 1.3 77.3 - - - +
284K GLN* 1.3 69.9 + - + +
286K LYS* 3.4 23.1 - - + +
303K TYR* 3.4 31.4 - - + +
306K ARG* 3.8 31.0 - - + +
307K ALA* 3.7 21.3 - - + +
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Residues in contact with GLN 284 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280K GLU* 3.3 20.7 + - - +
281K ASP* 3.4 14.8 + - - +
283K ILE* 1.3 83.9 - - + +
285K LEU* 1.3 72.8 + - + +
286K LYS* 4.5 4.0 - - - +
336K GLU* 4.7 2.6 - - - +
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Residues in contact with LEU 285 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261I ASP* 5.2 0.4 - - - +
243K SER 3.3 32.1 - - - +
244K SER* 3.9 8.7 - - - +
281K ASP* 2.9 24.6 + - + +
284K GLN* 1.3 86.3 - - + +
286K LYS* 1.3 71.1 + - - +
287K PRO* 3.9 1.1 - - - -
333K SER 5.0 0.7 - - - +
334K ARG* 3.4 50.0 - - + +
335K PRO* 3.3 18.2 - - + +
336K GLU* 3.4 23.4 - - - +
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Residues in contact with LYS 286 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237K ARG* 2.9 19.4 + - - +
282K ILE 3.3 5.9 + - - +
283K ILE* 3.4 20.4 - - + +
284K GLN 4.5 4.3 - - - +
285K LEU* 1.3 80.6 - - - +
287K PRO* 1.3 75.8 - - - +
307K ALA 4.4 17.0 - - - +
308K ASN* 5.8 4.0 - - - +
309K ILE* 5.0 3.1 - - - -
335K PRO* 3.2 8.0 - - + +
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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