Contacts of the helix formed by residues 509 - 517 (chain B) in PDB entry 6IWQ
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 SER 509 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425B GLN* 3.5 1.2 - - - +
474B ASP* 3.9 7.9 - - - -
475B GLU* 6.0 0.2 - - - -
502B ARG* 3.4 11.9 - - - +
507B CYS 3.9 0.4 + - - -
508B LYS* 1.3 76.8 - - - +
510B PHE* 1.3 63.7 + - - +
511B LYS* 3.7 10.9 - - - +
512B TRP* 2.8 26.2 + - - +
513B PHE* 3.1 17.5 + - - +
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Residues in contact with PHE 510 (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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356B TRP* 4.2 6.5 - + - -
358B TRP* 4.6 2.0 - + - -
421B TYR* 3.8 12.8 - + - -
425B GLN* 3.4 19.6 + - - -
472B TRP 3.2 24.2 - - - +
473B TRP* 3.4 52.0 - + - +
474B ASP* 3.3 8.8 + - + -
476B TYR* 3.4 37.5 - + + -
509B SER* 1.3 74.1 - - - +
511B LYS* 1.3 57.3 + - - +
513B PHE* 3.1 20.6 + + - +
514B MET* 2.9 59.6 + - + +
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Residues in contact with LYS 511 (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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474B ASP* 4.7 0.8 + - - -
475B GLU* 3.4 31.9 + - - +
476B TYR* 3.2 31.5 + - + +
509B SER* 3.0 9.3 - - - +
510B PHE* 1.3 75.8 - - - +
512B TRP* 1.3 68.4 + - - +
514B MET* 3.2 8.7 + - - -
515B GLU* 2.8 46.9 + - - +
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Residues in contact with TRP 512 (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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424B TRP* 3.5 36.1 - + - -
425B GLN* 4.1 5.4 - - + -
508B LYS* 3.6 43.5 - - + +
509B SER* 2.8 27.5 + - - +
511B LYS* 1.3 70.0 - - - +
513B PHE* 1.3 98.3 + + + +
515B GLU* 3.0 4.6 + - - -
516B GLU* 2.8 49.7 + - + +
517B ILE* 3.7 26.2 - - + -
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Residues in contact with PHE 513 (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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356B TRP* 3.5 27.8 - + - -
385B PRO 3.9 15.3 - - - -
421B TYR* 3.9 17.5 - + - -
424B TRP* 3.3 28.5 - + + -
425B GLN* 4.1 9.4 - - + -
509B SER 3.1 8.4 + - - +
510B PHE* 3.1 24.8 + + - +
512B TRP* 1.3 96.6 - + + +
514B MET* 1.3 72.2 + - + +
517B ILE* 3.1 48.5 + - + +
518B ALA* 3.0 27.2 + - + -
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Residues in contact with MET 514 (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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356B TRP* 3.2 33.0 - - + -
358B TRP* 3.5 29.4 - - - -
476B TYR* 3.4 30.5 - - + +
510B PHE* 2.9 33.3 + - + +
511B LYS 3.9 2.7 - - - +
512B TRP 3.1 0.4 - - - -
513B PHE* 1.3 87.7 - - + +
515B GLU* 1.3 61.6 + - + +
518B ALA* 3.3 32.3 - - + +
519B TYR* 3.3 23.4 + - - -
521B ILE* 4.3 4.3 - - + -
522B THR* 5.0 8.4 - - + +
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Residues in contact with GLU 515 (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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476B TYR* 5.0 0.2 - - - +
511B LYS* 2.8 53.6 + - - +
512B TRP* 3.0 5.4 + - - +
514B MET* 1.3 84.8 - - + +
516B GLU* 1.3 62.5 + - - +
519B TYR* 4.1 14.9 - - - +
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Residues in contact with GLU 516 (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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370B GLN* 4.7 2.4 - - - +
383B ARG* 3.9 18.1 + - - +
512B TRP* 2.8 46.6 + - + +
515B GLU* 1.3 80.1 - - - +
517B ILE* 1.3 68.0 + - + +
519B TYR* 3.2 19.7 - - - -
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Residues in contact with ILE 517 (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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353B ARG* 3.3 25.7 + - - +
371B GLU* 4.8 0.2 - - - +
383B ARG* 3.6 24.9 - - + +
384B SER 4.2 0.9 - - - +
385B PRO* 3.7 18.8 - - + +
424B TRP* 3.5 36.6 - - + -
512B TRP* 3.7 33.7 - - + -
513B PHE* 3.1 44.5 + - + +
516B GLU* 1.3 81.4 - - + +
518B ALA* 1.3 62.1 + - - +
519B TYR* 3.6 8.6 - - - -
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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