Contacts of the helix formed by residues 408 - 417 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148E GLU* 3.6 14.1 - - - +
150E GLY* 4.4 23.6 - - - +
152E GLY 6.1 0.7 - - - +
160E ARG* 3.3 6.2 + - - +
406E THR* 3.3 23.7 + - - +
407E LYS* 1.3 85.2 - - + +
409E ASN* 1.3 65.2 + - - +
410E ASP* 3.5 8.1 + - - +
411E ASP* 3.2 27.6 + - - +
412E PHE 3.5 3.3 + - - -
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Residues in contact with ASN 409 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E GLU* 2.9 26.7 + - - +
160E ARG* 2.6 63.9 + - - +
163E ASP* 5.1 2.0 - - - +
164E LEU* 4.0 28.1 - - + +
403E LEU* 3.7 11.1 - - - +
408E THR* 1.3 72.4 - - - +
410E ASP* 1.3 64.2 + - - +
411E ASP 3.4 0.2 - - - -
412E PHE* 3.4 6.3 + - - +
413E PHE* 3.1 32.7 + - + -
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Residues in contact with ASP 410 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379E LYS* 4.8 10.4 + - - -
408E THR* 3.3 9.5 + - - +
409E ASN* 1.3 76.7 - - - +
411E ASP* 1.3 70.3 + - - +
413E PHE* 3.4 6.0 + - - +
414E GLU* 3.1 26.8 + - - +
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Residues in contact with ASP 411 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406E THR* 3.3 25.3 + - - +
407E LYS* 5.2 1.2 + - - +
408E THR* 3.2 18.7 + - - +
409E ASN 3.4 0.2 - - - -
410E ASP* 1.3 81.8 - - - +
412E PHE* 1.3 61.6 + - - +
414E GLU* 3.4 6.7 + - - +
415E MET* 3.2 30.9 + - + +
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Residues in contact with PHE 412 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E LEU* 5.1 4.7 - - + -
383E LEU* 4.4 23.8 - - + -
398E PHE* 5.6 1.8 - + - -
399E LEU* 5.7 4.0 - - + -
402E LYS* 3.5 45.5 - - + -
403E LEU* 4.7 17.9 - - + -
406E THR* 3.8 19.4 - - + +
408E THR 3.5 5.3 + - - +
409E ASN* 3.4 10.7 + - - +
410E ASP 3.2 0.4 - - - -
411E ASP* 1.3 79.2 - - - +
413E PHE* 1.3 93.6 + + - +
415E MET* 3.3 6.5 + - + +
416E MET* 3.2 56.8 + - + +
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Residues in contact with PHE 413 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E LEU* 3.6 37.7 - - + -
376E GLU* 5.3 9.2 - - + -
379E LYS* 3.6 58.4 - - + +
380E MET* 5.0 7.4 - - + -
383E LEU* 4.4 14.1 - - + -
409E ASN* 3.1 20.6 + - + +
410E ASP* 4.0 5.4 - - - +
412E PHE* 1.3 108.7 - + - +
414E GLU* 1.3 61.3 + - - +
415E MET 3.6 0.2 + - - -
416E MET* 3.6 10.9 + - + +
417E LYS* 3.6 25.3 + - - +
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Residues in contact with GLU 414 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379E LYS* 4.7 5.2 + - - +
410E ASP* 3.1 21.7 + - - +
411E ASP* 3.8 9.0 - - - +
412E PHE 3.2 0.2 - - - -
413E PHE* 1.3 79.8 - - - +
415E MET* 1.3 66.6 + - + +
417E LYS* 3.8 33.6 + - - +
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Residues in contact with MET 415 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411E ASP* 3.2 19.5 + - + +
412E PHE* 3.3 5.8 + - + +
414E GLU* 1.3 82.0 - - + +
416E MET* 1.3 67.6 + - + +
417E LYS 3.3 4.4 - - - +
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Residues in contact with MET 416 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382E ILE* 6.6 0.2 - - + -
383E LEU* 6.2 2.5 - - + -
386E ILE* 4.6 20.4 - - + -
398E PHE* 5.0 12.8 - - + -
402E LYS* 4.5 15.5 - - - -
412E PHE* 3.2 51.5 + - + +
413E PHE* 4.0 9.6 - - + +
414E GLU 3.4 0.4 - - - -
415E MET* 1.3 80.2 - - - +
417E LYS* 1.3 65.5 + - + +
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Residues in contact with LYS 417 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379E LYS* 3.7 36.4 - - + +
382E ILE* 5.8 8.3 - - + -
413E PHE 3.6 19.4 + - - +
414E GLU* 3.8 31.4 + - - +
415E MET 3.3 5.9 - - - +
416E MET* 1.3 84.2 - - + +
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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