Contacts of the helix formed by residues 242 - 254 (chain A) in PDB entry 5NO6
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 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A ASN* 6.0 2.9 - - - +
240A PHE 5.4 1.1 - - - +
241A ILE* 1.3 85.8 - - - +
243A LYS* 1.3 74.6 + - - +
244A ASP* 3.1 27.5 + - - +
245A LYS* 2.8 33.9 + - + +
246A ARG* 2.9 11.8 + - - +
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Residues in contact with LYS 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A THR* 1.3 79.6 - - - +
244A ASP* 1.3 72.6 + - - +
246A ARG* 2.8 18.8 + - - +
247A ARG* 2.8 32.6 + - - +
257A GLU* 5.5 1.7 - - - +
33C C 5.2 1.3 + - - -
34C C 3.7 23.2 + - - +
7F A 5.6 0.4 - - - +
8F T 4.1 19.2 + - - +
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Residues in contact with ASP 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A THR* 3.1 29.9 + - - +
243A LYS* 1.3 83.9 + - - +
245A LYS* 1.3 64.1 + - - +
247A ARG* 3.6 8.3 + - - +
248A LYS* 3.2 31.6 + - - +
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Residues in contact with LYS 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A GLU* 3.3 32.5 - - + +
237A ALA* 6.2 1.1 - - - -
238A ASN* 4.2 27.5 - - + +
240A PHE 5.1 3.8 - - - +
241A ILE* 3.8 19.3 - - + -
242A THR* 2.8 35.6 + - + +
244A ASP* 1.3 76.0 + - - +
246A ARG* 1.3 66.7 + - - +
247A ARG 3.1 0.2 + - - -
248A LYS* 3.4 9.3 + - + +
249A ILE* 2.8 32.3 + - + +
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Residues in contact with ARG 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A ILE* 3.3 41.8 + - + +
242A THR* 2.9 10.0 + - - +
243A LYS* 2.8 19.1 + - - +
245A LYS* 1.3 69.5 - - - +
247A ARG* 1.3 55.8 + - - +
249A ILE* 3.8 1.5 - - - +
250A SER* 2.8 38.4 + - - -
257A GLU* 3.7 33.4 - - + +
260A ILE* 4.1 15.5 - - + +
261A THR* 2.5 49.3 + - - +
8F T 2.9 62.3 + - - -
9F G 4.2 0.6 + - - -
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Residues in contact with ARG 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A LYS* 2.8 24.1 + - - +
244A ASP* 3.8 7.0 - - - +
246A ARG* 1.3 73.9 - - - +
248A LYS* 1.3 70.7 + - - +
250A SER* 3.0 12.1 + - - -
251A ALA* 3.1 11.8 + - - +
257A GLU* 3.8 21.8 - - - +
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Residues in contact with LYS 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A GLU* 5.9 4.0 - - - +
244A ASP* 3.2 21.2 + - - +
245A LYS* 3.9 8.6 - - + +
247A ARG* 1.3 79.6 - - - +
249A ILE* 1.3 70.6 + - + +
251A ALA* 3.2 18.1 + - - +
252A ALA* 3.3 7.1 + - + +
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Residues in contact with ILE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLU* 3.9 15.9 - - - +
231A LEU* 4.2 16.8 - - + -
234A GLU* 3.6 32.8 - - + +
241A ILE* 3.3 31.6 - - + -
245A LYS* 2.8 32.8 + - + +
246A ARG* 3.8 3.4 - - - +
248A LYS* 1.3 76.0 - - + +
250A SER* 1.3 51.5 + - - +
252A ALA* 2.8 12.8 + - - +
253A THR* 2.8 56.4 + - + +
260A ILE* 4.2 9.4 - - + -
264A PHE* 4.9 2.9 - - + -
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Residues in contact with SER 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A ARG 2.8 23.1 + - - -
247A ARG* 3.0 6.5 + - - -
249A ILE* 1.3 72.2 - - - +
251A ALA* 1.3 54.6 + - - +
253A THR* 2.9 9.6 + - - -
254A SER* 2.8 33.1 + - - -
255A LEU 2.5 24.2 + - - +
256A SER* 4.4 1.1 - - - -
257A GLU* 4.0 22.0 + - - +
260A ILE* 4.4 4.6 - - - +
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Residues in contact with ALA 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ARG 3.1 8.0 + - - +
248A LYS* 3.3 12.8 - - - +
250A SER* 1.3 80.1 + - - +
252A ALA* 1.3 61.1 + - - +
254A SER* 3.6 7.4 + - - -
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Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLN* 5.2 1.0 + - - -
230A GLU* 4.0 27.9 - - + +
248A LYS* 3.3 6.9 + - + +
249A ILE* 2.8 11.9 + - - +
251A ALA* 1.3 77.8 - - - +
253A THR* 1.3 61.8 + - - +
254A SER* 4.8 1.4 - - - -
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Residues in contact with THR 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLN* 2.7 46.1 + - - +
230A GLU* 4.2 20.0 - - + -
231A LEU* 4.9 3.1 - - + -
249A ILE* 2.8 42.6 + - + +
250A SER* 2.9 15.8 + - - -
252A ALA* 1.3 77.8 - - - +
254A SER* 1.3 62.0 + - - +
255A LEU* 3.0 29.1 + - + +
260A ILE* 3.8 2.8 - - + +
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Residues in contact with SER 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLN* 4.4 7.6 - - - -
250A SER 2.8 11.5 + - - -
251A ALA 3.6 6.0 + - - -
252A ALA 3.3 4.4 - - - -
253A THR* 1.3 80.3 - - - +
255A LEU* 1.3 59.0 + - - +
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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