Contacts of the helix formed by residues 509 - 517 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425D GLN* 3.7 0.4 - - - -
474D ASP* 4.0 6.7 - - - -
475D GLU* 5.8 0.4 - - - -
502D ARG* 3.7 9.6 - - - +
507D CYS 3.9 0.6 + - - -
508D LYS* 1.3 77.3 - - - +
510D PHE* 1.3 64.0 + - - +
511D LYS* 3.8 11.9 - - - +
512D TRP* 3.1 25.8 + - - +
513D PHE* 3.1 19.6 + - - +
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Residues in contact with PHE 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D TRP* 4.2 5.4 - + - -
358D TRP* 4.7 1.8 - + - -
421D TYR* 3.8 13.7 - + - -
425D GLN* 3.5 19.5 + - - -
472D TRP 3.3 24.9 - - - +
473D TRP* 3.4 57.4 - + - +
474D ASP* 3.4 10.0 + - + -
476D TYR* 3.5 28.9 - + + -
509D SER* 1.3 72.4 - - - +
511D LYS* 1.3 59.1 + - - +
513D PHE* 3.0 19.5 + + - +
514D MET* 2.8 61.4 + - + +
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Residues in contact with LYS 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475D GLU* 3.7 38.2 + - - +
476D TYR* 4.0 25.7 - - + +
509D SER* 3.1 9.2 - - - +
510D PHE* 1.3 80.0 - - - +
512D TRP* 1.3 62.1 + - - +
514D MET* 3.3 1.7 + - - +
515D GLU* 3.3 43.0 + - - +
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Residues in contact with TRP 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424D TRP* 3.7 29.8 - + - -
425D GLN* 4.3 3.6 - - + -
508D LYS* 3.7 47.7 - - + +
509D SER* 3.1 27.8 + - - +
511D LYS* 1.3 74.4 - - - +
513D PHE* 1.3 97.9 + + + +
515D GLU* 3.2 4.4 + - - -
516D GLU* 2.9 47.6 + - + +
517D ILE* 3.9 22.4 - - + -
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Residues in contact with PHE 513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D TRP* 3.5 27.8 - + - -
385D PRO 3.9 14.4 - - - -
421D TYR* 3.9 17.9 - + - -
424D TRP* 3.3 28.5 - + + -
425D GLN* 4.1 10.1 - - + -
509D SER 3.1 11.9 + - - +
510D PHE* 3.0 25.0 + + - +
512D TRP* 1.3 93.8 - + + +
514D MET* 1.3 72.5 + - + +
517D ILE* 3.1 47.3 + - + +
518D ALA* 3.0 26.4 + - + -
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Residues in contact with MET 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D TRP* 3.2 33.7 - - + -
358D TRP* 3.5 30.1 - - - -
476D TYR* 3.5 28.0 - - + +
510D PHE* 2.8 32.8 + - + +
511D LYS 3.3 2.7 + - - +
512D TRP 3.2 0.4 - - - -
513D PHE* 1.3 87.2 - - + +
515D GLU* 1.3 61.8 + - + +
518D ALA* 3.3 32.3 - - + +
519D TYR* 3.3 23.4 + - - -
521D ILE* 4.3 5.6 - - + -
522D THR* 5.6 4.5 - - - -
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Residues in contact with GLU 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476D TYR* 5.2 4.8 + - - +
511D LYS* 3.3 30.1 + - - +
512D TRP* 3.2 4.4 + - - +
514D MET* 1.3 87.0 - - + +
516D GLU* 1.3 62.6 + - - +
519D TYR* 4.1 14.6 - - - +
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Residues in contact with GLU 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D ARG* 4.1 20.0 + - - +
512D TRP* 2.9 46.3 + - + +
515D GLU* 1.3 79.7 - - - +
517D ILE* 1.3 68.9 + - + +
519D TYR* 3.2 20.1 - - - -
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Residues in contact with ILE 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D ARG* 3.3 25.4 + - - +
383D ARG* 4.2 16.1 - - + +
384D SER 4.6 0.2 - - - -
385D PRO* 3.6 18.6 - - + +
424D TRP* 3.5 43.3 - - + -
512D TRP* 3.9 27.6 - - + -
513D PHE* 3.1 45.6 + - + +
516D GLU* 1.3 88.9 - - + +
518D ALA* 1.3 63.5 + - - +
519D TYR* 3.6 8.2 - - - -
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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