Contacts of the helix formed by residues 415 - 420 (chain B) in PDB entry 6TXC
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 415 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401B GLY* 3.3 5.7 - - - -
402B ALA* 2.8 44.1 + - - +
407B TYR* 3.2 39.9 - - + +
411B THR 4.1 0.4 + - - -
412B ALA 2.9 20.0 + - - +
413B ILE 3.3 0.2 - - - -
414B ASP* 1.3 80.5 - - - +
416B MET* 1.3 62.6 + - - +
417B GLU* 3.7 6.0 + - - +
418B ALA* 3.1 7.3 + - - +
419B TYR 3.0 14.2 + - - -
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Residues in contact with MET 416 (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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231B TRP* 4.7 6.1 - - + -
236B GLY 4.4 2.0 - - - +
239B MET* 3.9 42.1 - - + +
240B MET* 3.7 39.6 - - + +
243B HIS* 3.7 25.6 - - + +
413B ILE* 3.2 31.0 - - - +
415B ASP* 1.3 71.5 + - - +
417B GLU* 1.3 53.4 + - - +
419B TYR* 3.7 21.3 - - + -
420B THR* 2.6 38.0 + - - -
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Residues in contact with GLU 417 (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* 3.7 26.1 + - + +
400B THR 4.3 2.9 - - - +
401B GLY* 3.6 14.0 - - - +
402B ALA* 3.5 34.2 - - + +
403B GLY 4.8 1.2 + - - -
415B ASP* 3.2 6.6 + - - +
416B MET* 1.3 77.7 - - - +
418B ALA* 1.3 62.3 + - - +
420B THR* 3.6 14.5 - - - -
421B LYS* 4.0 12.1 - - - +
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Residues in contact with ALA 418 (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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399B ILE* 3.6 11.8 - - + +
400B THR 3.8 12.3 - - - +
401B GLY* 3.8 4.4 - - - -
407B TYR* 3.8 38.6 - - + -
412B ALA* 4.3 8.7 - - + -
415B ASP* 3.1 13.7 + - - +
417B GLU* 1.3 77.2 - - - +
419B TYR* 1.3 59.4 + - - +
421B LYS* 2.9 26.3 + - - +
422B LEU* 3.6 4.2 + - - +
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Residues in contact with TYR 419 (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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143B ARG* 3.1 34.0 + - - -
209B GLY* 2.9 35.4 + - - -
211B GLY* 3.1 20.4 + - - -
217B PHE* 3.9 7.8 - + - -
231B TRP* 3.7 20.0 - + - -
236B GLY* 5.3 0.2 - - - -
240B MET* 3.5 20.2 - - + -
412B ALA* 3.4 27.3 + - - +
413B ILE* 3.9 12.8 - - + -
415B ASP 3.0 10.4 + - - +
416B MET* 3.9 22.9 - - + +
418B ALA* 1.3 76.2 - - - +
420B THR* 1.3 61.9 + - - +
422B LEU* 3.0 40.4 + - + +
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Residues in contact with THR 420 (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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432A TYR* 4.4 4.7 + - - -
139B PRO* 3.9 37.2 - - + +
140B GLN* 4.0 9.7 - - - +
143B ARG* 3.3 27.6 + - - +
240B MET* 3.8 12.8 - - - +
243B HIS* 3.9 9.4 + - - -
416B MET 2.6 23.3 + - - -
417B GLU* 3.6 10.8 - - - -
418B ALA 3.1 0.4 - - - -
419B TYR* 1.3 77.2 - - - +
421B LYS* 1.3 62.6 + - + +
422B LEU 3.6 0.5 + - - -
423B THR* 4.2 4.0 - - - +
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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