Contacts of the helix formed by residues 412 - 417 (chain B) in PDB entry 3W3K
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 LYS 412 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384B GLU* 2.2 41.2 + - - +
410B ASP* 3.1 17.2 + - + +
411B PHE* 1.3 77.0 - - - +
413B LEU* 1.3 64.2 + - + +
414B PHE 3.3 0.4 - - - -
415B GLN* 3.5 21.1 - - - +
416B ASN* 4.1 2.8 + - - +
503B ASN* 3.5 43.1 - - + +
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Residues in contact with LEU 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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382B LEU* 3.8 23.1 - - + +
383B ARG 3.4 29.4 - - - +
384B GLU* 4.0 19.5 - - + +
387B PHE* 4.2 12.6 - - + -
391B MET* 3.7 15.6 - - + +
409B ILE* 4.4 1.8 - - + -
410B ASP 3.1 19.5 + - - +
411B PHE 3.0 1.4 + - - -
412B LYS* 1.3 79.4 - - - +
414B PHE* 1.3 89.6 + - + +
416B ASN* 2.9 28.4 + - - +
417B PHE* 3.7 23.9 - - + -
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Residues in contact with PHE 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B LEU* 4.3 16.6 - - + -
387B PHE* 5.0 6.3 - + - -
399B ILE* 4.4 11.7 - - + -
401B LEU* 5.2 0.9 - - + -
409B ILE* 4.0 19.1 - - + -
411B PHE* 3.2 37.5 + + + +
413B LEU* 1.3 96.5 - - + +
415B GLN* 1.3 62.7 + - - +
417B PHE* 3.4 21.7 + + - +
420B LEU* 3.7 23.4 - - + +
423B ILE* 3.7 46.4 - - + -
425B LEU* 4.3 14.1 - - + -
486B LEU* 5.6 0.9 - - + -
504B LEU* 4.9 3.1 - - + -
505B PRO* 4.2 13.9 - - + +
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Residues in contact with GLN 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 PHE 4.4 0.8 + - - -
412B LYS* 3.5 15.4 + - - +
414B PHE* 1.3 80.6 - - - +
416B ASN* 1.3 61.5 + - - +
417B PHE 3.2 9.4 + - - +
503B ASN* 3.1 47.2 + - - +
504B LEU 3.6 17.6 + - - -
505B PRO* 4.1 10.4 - - + +
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Residues in contact with ASN 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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384B GLU* 4.5 13.6 + - - +
388B GLN* 5.1 3.6 - - - +
391B MET* 3.4 39.7 - - + +
392B GLN* 4.0 12.5 + - - -
412B LYS 4.1 2.0 + - - +
413B LEU* 2.9 15.6 + - - +
415B GLN* 1.3 74.6 - - - +
417B PHE* 1.3 67.6 + - - +
418B SER* 3.6 1.4 + - - -
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Residues in contact with PHE 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B PHE* 3.9 22.7 - + + -
390B LEU* 3.6 42.6 - - + -
391B MET* 3.7 19.7 - - + +
393B LEU 6.1 0.2 - - - -
396B LEU* 3.9 17.3 - - + -
399B ILE* 5.5 4.5 - - + -
413B LEU* 3.7 34.5 - - + -
414B PHE* 3.5 13.6 - + - +
415B GLN 3.1 10.0 - - - +
416B ASN* 1.3 82.4 - - - +
418B SER* 1.3 70.1 + - - +
419B ASN* 4.5 0.4 - - - +
420B LEU* 3.4 44.3 + - + +
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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