Contacts of the helix formed by residues 403 - 410 (chain B) in PDB entry 3HN8
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 ASN 403 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375B LEU 5.0 2.2 - - - -
376B ALA* 5.0 12.8 - - + +
378B ARG 4.6 7.5 + - - -
379B LYS* 5.4 0.2 - - - +
402B ASP* 1.3 93.6 + - - +
404B LEU* 1.3 64.4 + - - +
405B LEU* 3.3 6.0 + - + +
406B GLU* 3.5 38.5 + - - +
407B LEU* 3.1 19.4 - - - +
452B LYS* 6.1 0.9 - - - +
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Residues in contact with LEU 404 (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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305B LEU* 4.5 9.5 - - + +
314B LEU* 3.5 27.6 - - + -
341B LEU* 4.3 4.9 - - + -
375B LEU* 3.9 27.2 + - + +
378B ARG* 4.0 25.4 - - + +
379B LYS 4.2 1.3 - - - -
380B LEU* 3.7 39.9 - - + +
401B LEU* 3.7 25.8 - - + +
402B ASP 2.8 5.7 + - - +
403B ASN* 1.3 70.1 - - - +
405B LEU* 1.3 69.2 + - - +
407B LEU* 3.1 15.1 + - + +
408B ALA* 3.2 14.1 + - - +
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Residues in contact with LEU 405 (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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307B TYR* 5.0 4.5 - - + -
309B TYR* 4.6 12.3 - - + +
372B LEU* 3.8 20.2 - - + -
375B LEU* 3.8 38.9 + - + +
376B ALA* 5.4 4.0 - - + +
403B ASN* 3.3 3.7 - - + -
404B LEU* 1.3 78.1 - - - +
406B GLU* 1.3 68.6 + - + +
408B ALA* 3.3 2.5 + - + +
409B GLU* 3.0 60.3 + - + +
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Residues in contact with GLU 406 (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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403B ASN* 3.5 33.1 + - - +
404B LEU 3.3 0.6 - - - -
405B LEU* 1.3 92.3 - - + +
407B LEU* 1.3 65.4 + - + +
408B ALA 3.4 0.3 + - - -
409B GLU* 3.6 13.4 + - - +
410B GLN 3.9 10.4 + - - +
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Residues in contact with LEU 407 (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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305B LEU* 4.0 21.1 - - + +
401B LEU* 3.6 41.7 - - + -
402B ASP* 4.0 9.4 - - + +
403B ASN* 3.1 32.5 - - - +
404B LEU* 3.1 8.1 + - - +
406B GLU* 1.3 79.8 - - + +
408B ALA* 1.3 62.3 + - - +
410B GLN 3.4 15.7 - - - +
411B PRO* 5.0 2.3 - - - +
416B LEU* 3.6 29.4 - - + +
418B ARG* 4.1 14.6 - - - +
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Residues in contact with ALA 408 (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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305B LEU* 3.1 32.6 - - + +
306B ARG* 3.8 21.9 - - - +
307B TYR* 3.8 18.8 - - + +
314B LEU* 5.0 3.6 - - + -
375B LEU* 5.8 0.4 - - + -
404B LEU 3.2 13.1 + - - +
405B LEU* 3.8 3.8 - - + +
407B LEU* 1.3 77.4 - - - +
409B GLU* 1.3 55.0 + - - +
410B GLN* 2.7 20.5 + - - -
411B PRO 4.6 3.1 - - - +
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Residues in contact with GLU 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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309B TYR* 3.9 22.2 + - - +
405B LEU* 3.0 42.6 + - + +
406B GLU* 3.6 9.9 + - - +
407B LEU 3.5 0.8 - - - -
408B ALA* 1.3 75.2 - - - +
410B GLN* 1.3 86.0 + - + +
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Residues in contact with GLN 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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406B GLU 3.9 7.8 + - - +
407B LEU* 3.4 13.2 - - - +
408B ALA 2.7 9.1 + - - -
409B GLU* 1.3 86.9 + - - +
411B PRO* 1.3 76.1 - - + +
412B PRO* 4.8 7.4 - - + -
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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