Contacts of the helix formed by residues 412 - 419 (chain B) in PDB entry 1Q6X
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 GLY 412 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411B TYR* 1.3 82.1 - - - +
413B LYS* 1.3 64.1 + - - -
414B THR* 3.4 0.8 + - - -
415B PHE* 3.4 5.7 + - - +
416B ILE* 3.3 30.3 + - - +
577B GLN 3.5 7.9 - - - -
578B PRO 3.4 14.7 + - - -
579B GLU* 3.7 1.2 + - - +
580B ALA 3.8 2.9 - - - -
581B ILE* 4.2 10.8 - - - -
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Residues in contact with LYS 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B GLY* 1.3 68.5 - - - -
414B THR* 1.3 62.5 + - + +
416B ILE* 3.9 7.9 - - + +
417B LYS* 2.8 57.9 + - - +
423B PRO* 4.3 19.8 - - + +
576B PRO* 3.4 39.9 + - + +
577B GLN* 2.9 23.0 + - - +
578B PRO* 3.1 11.9 + - + +
581B ILE* 5.4 0.4 - - - +
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Residues in contact with THR 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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412B GLY 5.4 0.3 + - - -
413B LYS* 1.3 76.0 - - + +
415B PHE* 1.3 66.3 + - - +
417B LYS* 3.8 7.9 - - - +
418B LYS* 3.1 44.6 + - - +
578B PRO* 3.2 27.9 + - + +
579B GLU* 2.9 25.3 + - - +
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Residues in contact with PHE 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B TYR* 3.7 39.0 - + + -
412B GLY 3.4 9.0 + - - +
413B LYS 3.3 0.4 - - - -
414B THR* 1.3 82.2 + - - +
416B ILE* 1.3 69.2 + - + +
418B LYS* 3.1 21.3 + - + +
419B GLN* 2.9 44.4 + - + +
426B PHE* 4.9 7.9 - + - -
611B ARG* 3.4 50.3 - - + -
614B CYS* 4.4 2.7 - - + -
615B SER* 4.9 4.7 - - - -
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Residues in contact with ILE 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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411B TYR* 4.1 15.0 - - + -
412B GLY 3.3 23.3 + - - +
413B LYS* 3.9 3.8 - - + +
415B PHE* 1.3 79.5 - - + +
417B LYS* 1.3 62.8 + - - +
419B GLN* 3.1 16.6 + - - +
421B TYR* 3.3 29.9 + - + +
422B SER 4.0 0.2 - - - +
423B PRO* 3.8 27.6 - - + +
426B PHE* 3.7 54.5 - - + -
427B ILE* 4.6 8.5 - - + -
581B ILE* 4.6 6.5 - - + -
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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
----------------------------------------------------------
413B LYS* 2.8 54.0 + - - +
414B THR* 3.8 7.6 - - - +
416B ILE* 1.3 77.4 - - - +
418B LYS* 1.3 57.4 + - + +
420B LYS* 2.9 21.5 + - - +
421B TYR 4.0 8.5 - - - +
423B PRO* 4.9 14.6 - - + +
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Residues in contact with LYS 418 (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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414B THR* 3.1 33.7 + - - +
415B PHE* 3.1 12.3 + - + +
417B LYS* 1.3 75.7 - - + +
419B GLN* 1.3 67.0 + - - +
420B LYS* 3.1 9.1 + - - +
617B ARG* 5.2 0.3 + - - -
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Residues in contact with GLN 419 (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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415B PHE* 2.9 48.2 + - + +
416B ILE* 3.1 13.2 + - - +
417B LYS 3.1 1.0 - - - -
418B LYS* 1.3 84.9 - - - +
420B LYS* 1.3 82.7 + - - +
421B TYR* 3.4 22.4 + - + -
426B PHE* 5.8 1.1 - - + -
614B CYS* 3.1 37.0 - - - +
615B SER* 5.5 0.6 + - - +
617B ARG* 3.2 27.3 + - - +
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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