Contacts of the helix formed by residues 408 - 417 (chain B) in PDB entry 6XAV
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 408 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B GLU* 3.8 13.7 - - - +
150B GLY* 5.5 9.6 - - - +
160B ARG* 3.2 11.7 + - - -
406B THR* 3.3 16.4 + - - +
407B LYS* 1.3 84.0 - - + +
409B ASN* 1.3 62.8 + - - +
410B ASP* 3.4 9.2 + - - +
411B ASP* 3.0 31.4 + - - -
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Residues in contact with ASN 409 (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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148B GLU* 4.1 14.5 + - - +
160B ARG* 2.4 73.9 + - - +
163B ASP* 5.0 4.0 + - - +
164B LEU* 3.4 33.0 - - + +
403B LEU* 4.6 2.7 - - + +
408B THR* 1.3 71.7 - - - +
410B ASP* 1.3 63.7 + - - +
411B ASP 3.3 0.2 - - - -
412B PHE* 3.3 8.8 + - + +
413B PHE* 3.2 30.1 + - + -
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Residues in contact with ASP 410 (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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379B LYS* 3.7 20.1 + - - +
408B THR* 3.2 9.5 + - - +
409B ASN* 1.3 79.1 - - - +
411B ASP* 1.3 65.3 - - - +
413B PHE* 3.4 7.3 + - - +
414B GLU* 3.1 24.5 + - - +
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Residues in contact with ASP 411 (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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406B THR* 3.1 27.8 + - - +
407B LYS* 5.8 0.2 - - - +
408B THR* 3.0 19.2 + - - +
409B ASN 3.3 0.4 - - - -
410B ASP* 1.3 81.9 - - - +
412B PHE* 1.3 61.8 + - - +
414B GLU* 3.4 7.0 + - - +
415B MET* 3.2 30.4 + - + +
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Residues in contact with PHE 412 (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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164B LEU* 4.8 2.7 - - + -
383B LEU* 3.7 29.2 - - + -
398B PHE* 4.9 4.7 - + - -
399B LEU* 4.7 9.9 - - + -
402B LYS* 3.5 40.6 - - + -
403B LEU* 4.0 26.5 - - + -
406B THR* 4.1 13.1 - - + +
408B THR 3.8 1.8 + - - -
409B ASN 3.3 10.8 + - - +
410B ASP 3.2 0.6 - - - -
411B ASP* 1.3 79.5 - - - +
413B PHE* 1.3 95.7 + + - +
415B MET* 3.3 7.3 + - + +
416B MET* 3.2 48.1 + - + +
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Residues in contact with PHE 413 (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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164B LEU* 3.6 33.0 - - + -
376B GLU* 5.0 6.5 - - + -
379B LYS* 3.6 60.9 - - + +
380B MET* 4.3 12.6 - - + -
383B LEU* 3.6 18.2 - - + -
409B ASN* 3.2 17.9 + - + +
410B ASP* 3.4 7.2 + - - +
412B PHE* 1.3 104.3 - + - +
414B GLU* 1.3 62.4 + - - +
416B MET* 3.4 15.9 + - + +
417B LYS* 3.6 21.0 + - - +
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Residues in contact with GLU 414 (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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379B LYS* 4.5 8.7 + - - +
410B ASP* 3.1 18.4 + - - +
411B ASP* 3.7 9.2 - - - +
412B PHE 3.2 0.2 - - - -
413B PHE* 1.3 79.2 - - - +
415B MET* 1.3 65.0 + - + +
416B MET 3.6 0.2 + - - -
417B LYS* 3.6 37.4 + - - +
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Residues in contact with MET 415 (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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411B ASP* 3.2 18.8 + - + +
412B PHE* 3.9 6.7 - - + +
413B PHE 3.3 0.4 - - - -
414B GLU* 1.3 80.6 - - + +
416B MET* 1.3 66.7 + - + +
417B LYS 3.5 3.7 + - - -
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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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382B ILE* 6.3 2.9 - - + -
383B LEU* 5.4 4.7 - - + -
386B ILE* 3.9 30.1 - - + -
398B PHE* 4.4 23.6 - - + -
402B LYS* 5.4 5.8 - - - -
412B PHE* 3.2 49.9 + - + +
413B PHE* 3.8 11.9 - - + +
414B GLU 3.4 0.4 - - - -
415B MET* 1.3 82.1 - - - +
417B LYS* 1.3 63.1 + - + +
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Residues in contact with LYS 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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379B LYS* 4.2 25.9 - - + +
382B ILE* 5.8 8.5 - - + -
413B PHE 3.6 16.0 + - - +
414B GLU* 3.6 38.7 + - - +
415B MET 3.3 6.5 - - - -
416B MET* 1.3 82.2 - - + +
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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