Contacts of the helix formed by residues 407 - 418 (chain N) 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 TRP 407 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402N ASN* 5.9 0.4 - - - +
405N ARG 3.9 0.4 - - - -
406N LEU* 1.3 76.8 - - - +
408N LYS* 1.3 60.6 + - - +
409N ALA 3.3 3.1 - - - +
410N ALA* 3.4 7.4 + - - +
411N VAL* 2.9 23.7 + - - -
437N TRP* 6.4 1.8 - - - -
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Residues in contact with LYS 408 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407N TRP* 1.3 69.6 - - - +
409N ALA* 1.3 55.0 + - - +
411N VAL* 2.9 5.3 + - - +
412N GLU* 2.4 38.5 + - - +
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Residues in contact with ALA 409 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407N TRP* 3.3 1.6 - - - +
408N LYS* 1.3 74.1 - - - +
410N ALA* 1.3 59.6 + - - +
412N GLU* 4.5 1.4 - - - +
413N LEU* 3.6 11.1 + - - -
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Residues in contact with ALA 410 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407N TRP* 3.4 11.2 + - - +
408N LYS 3.0 0.6 - - - -
409N ALA* 1.3 73.1 - - - +
411N VAL* 1.3 53.9 - - - +
412N GLU 3.1 1.1 - - - -
413N LEU* 2.3 33.7 + - - +
414N GLU 2.9 4.3 + - - -
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Residues in contact with VAL 411 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407N TRP 2.9 13.4 + - - -
408N LYS* 2.9 7.8 + - - +
410N ALA* 1.3 70.3 - - - +
412N GLU* 1.3 57.2 + - - +
414N GLU* 2.8 20.9 + - - +
415N GLU* 3.2 7.8 + - - -
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Residues in contact with GLU 412 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408N LYS* 2.4 25.6 + - - +
409N ALA* 4.5 2.0 - - - +
411N VAL* 1.3 66.6 - - - +
413N LEU* 1.3 54.7 + - - +
415N GLU* 3.0 18.2 + - - +
416N PRO* 3.0 10.0 - - - +
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Residues in contact with LEU 413 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409N ALA 3.6 10.8 + - - -
410N ALA* 2.3 25.1 + - - +
412N GLU* 1.3 66.1 - - - +
414N GLU* 1.3 58.0 + - - +
416N PRO* 3.2 5.6 - - - +
417N GLU* 2.9 22.5 + - - -
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Residues in contact with GLU 414 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410N ALA 2.9 5.7 + - - -
411N VAL* 2.8 12.2 + - - +
413N LEU* 1.3 77.7 - - - +
415N GLU* 1.3 55.1 + - - +
417N GLU* 3.2 4.7 + - - +
418N ASP* 2.9 22.9 + - - -
426N ALA* 6.0 1.6 - - - -
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Residues in contact with GLU 415 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411N VAL 3.2 6.6 + - - -
412N GLU* 3.0 10.4 + - - +
414N GLU* 1.3 71.7 - - - +
416N PRO* 1.3 59.0 - - - +
418N ASP* 3.1 5.4 + - - +
419N ALA* 3.0 22.7 + - - -
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Residues in contact with PRO 416 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412N GLU 3.0 12.0 - - - +
413N LEU* 3.2 8.2 - - - +
415N GLU* 1.3 75.1 - - - +
417N GLU* 1.3 59.5 + - - +
419N ALA* 3.2 13.9 + - - +
420N ARG 4.0 1.6 + - - -
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Residues in contact with GLU 417 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391N ARG* 5.6 12.1 - - - +
413N LEU 2.9 13.4 + - - -
414N GLU* 3.2 7.7 + - - +
416N PRO* 1.3 75.5 - - - +
418N ASP* 1.3 51.7 + - - +
420N ARG* 2.9 28.2 + - - -
421N ILE 4.1 3.0 - - - +
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Residues in contact with ASP 418 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414N GLU 2.9 13.0 + - - -
415N GLU* 3.1 11.1 + - - +
417N GLU* 1.3 72.2 - - - +
419N ALA* 1.3 57.1 + - - +
420N ARG 2.4 21.9 - - - +
421N ILE 4.1 7.6 - - - +
422N MET 4.7 8.4 - - - +
423N LEU* 5.5 3.3 - - - +
426N ALA* 6.1 3.1 - - - +
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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