Contacts of the helix formed by residues 246 - 256 (chain W) in PDB entry 6AH0
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 VAL 246 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242W ALA 3.1 8.6 + - - -
243W LEU* 3.1 11.3 + - - +
245W ASN* 1.3 71.6 - - - +
247W PRO* 1.4 63.3 - - - +
248W PRO 3.5 2.2 - - - -
249W LEU* 3.2 7.3 + - - -
250W ARG* 2.9 20.3 + - - -
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Residues in contact with PRO 247 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245W ASN 3.0 7.5 - - - +
246W VAL* 1.4 69.5 - - - +
248W PRO* 1.4 56.3 - - - +
250W ARG* 4.6 1.8 - - - +
251W ASN* 2.9 26.7 + - - -
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Residues in contact with PRO 248 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246W VAL 3.2 1.2 - - - -
247W PRO* 1.4 72.5 - - - +
249W LEU* 1.3 61.8 + - - +
251W ASN* 4.1 0.4 - - - -
252W TYR* 3.0 21.8 + - - -
343W THR 5.1 4.9 - - - +
344W ILE 5.4 4.0 - - - -
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Residues in contact with LEU 249 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243W LEU 4.9 4.5 - - - -
246W VAL 3.2 6.1 + - - -
248W PRO* 1.3 75.5 - - - +
250W ARG* 1.3 62.2 + - - +
252W TYR* 3.4 1.4 + - - -
253W PHE* 3.1 18.0 + - - -
343W THR 5.8 1.3 - - - -
344W ILE 5.2 7.9 + - - -
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Residues in contact with ARG 250 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243W LEU 4.3 5.5 + - - -
244W SER* 4.5 17.5 - - - +
246W VAL 2.9 15.4 + - - -
247W PRO* 4.0 1.8 - - - -
249W LEU* 1.3 75.2 - - - +
251W ASN* 1.3 56.5 + - - +
253W PHE* 3.1 3.1 + - - -
254W LEU* 3.0 25.3 + - - -
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Residues in contact with ASN 251 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247W PRO* 2.9 17.6 + - - +
248W PRO 4.1 0.2 - - - -
250W ARG* 1.3 70.6 - - - +
252W TYR* 1.3 67.2 + - - +
254W LEU* 3.4 1.7 + - - +
255W GLU* 3.1 19.9 + - - -
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Residues in contact with TYR 252 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248W PRO 3.0 14.8 + - - -
249W LEU* 3.7 4.0 - - - +
251W ASN* 1.3 76.8 - - - +
253W PHE* 1.3 62.9 + - - +
255W GLU 3.9 0.2 - - - -
256W GLU* 3.1 19.9 + - - -
343W THR 5.3 7.6 - - - -
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Residues in contact with PHE 253 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249W LEU 3.1 15.0 + - - -
250W ARG* 3.1 1.3 + - - +
252W TYR* 1.3 76.2 - - - +
254W LEU* 1.3 64.5 + - - +
255W GLU 3.0 1.7 + - - -
256W GLU* 3.1 12.4 + - - +
278W GLY* 5.5 16.3 - - - -
282W ARG* 6.0 0.9 - - - -
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Residues in contact with LEU 254 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195W PRO 5.1 2.6 - - - +
196W THR* 5.1 2.8 - - - -
197W PHE* 4.2 18.7 + - - -
250W ARG 3.0 15.4 + - - -
251W ASN* 3.4 2.0 + - - +
253W PHE* 1.3 73.8 - - - +
255W GLU* 1.3 55.9 + - - +
257W ASP* 6.0 0.3 - - - -
281W MET 6.1 0.8 - - - -
282W ARG* 5.3 13.8 - - - +
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Residues in contact with GLU 255 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197W PHE 4.4 14.1 - - - +
198W THR* 6.2 0.2 - - - +
251W ASN 3.1 13.4 + - - -
252W TYR 3.9 1.6 - - - -
254W LEU* 1.3 75.9 - - - +
256W GLU* 1.3 56.8 + - - +
257W ASP* 3.2 10.3 + - - +
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Residues in contact with GLU 256 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252W TYR 3.1 16.8 + - - -
253W PHE* 3.1 9.8 + - - +
255W GLU* 1.3 76.1 - - - +
257W ASP* 1.3 56.1 + - - +
258W ASN 2.9 12.3 + - - -
259W TYR* 3.6 9.9 + - - -
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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