Contacts of the helix formed by residues 476 - 484 (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 TYR 476 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358D TRP* 3.9 22.2 - + - -
473D TRP* 3.4 28.4 - - + +
474D ASP 3.0 0.8 - - - -
475D GLU* 1.3 82.6 - - + +
477D LYS* 1.3 64.5 + - - +
478D ASP 2.7 6.5 - - - -
479D TYR* 2.5 54.2 + + - +
480D PHE 3.4 5.4 + - - -
510D PHE* 3.5 23.6 - + + -
511D LYS* 4.0 29.9 + - + +
514D MET* 3.5 30.2 - - + +
515D GLU* 5.2 5.5 + - - +
522D THR* 5.9 2.0 - - + -
527D LEU* 5.1 7.2 - - + +
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Residues in contact with LYS 477 (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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469D VAL* 3.5 29.2 - - + -
470D GLU* 3.2 48.4 + - - +
473D TRP* 4.1 3.1 - - - +
474D ASP* 2.5 39.3 + - - +
475D GLU 4.3 1.8 - - - -
476D TYR* 1.3 72.9 - - - +
478D ASP* 1.3 62.3 + - - +
480D PHE* 3.2 2.3 + - - +
481D TYR* 2.9 45.4 + - + -
499D LYS* 4.7 7.0 - - - +
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Residues in contact with ASP 478 (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 3.5 15.8 - - - +
476D TYR* 2.5 3.8 + - - -
477D LYS* 1.3 81.8 - - - +
479D TYR* 1.3 69.7 + - + +
481D TYR* 4.0 8.2 - - - +
482D ALA* 3.1 23.9 + - - +
530D LYS* 6.1 3.7 - - + +
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Residues in contact with TYR 479 (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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358D TRP* 4.3 17.7 - + + -
475D GLU* 5.1 4.0 - - + -
476D TYR* 2.5 57.7 + + - +
478D ASP* 1.3 74.0 - - + +
480D PHE* 1.3 63.8 + - - +
482D ALA* 3.3 5.0 + - + +
483D SER* 3.1 25.3 + - - -
527D LEU* 3.6 32.6 - - + +
528D PRO* 3.4 40.4 - - + +
530D LYS* 6.5 1.3 - - + -
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Residues in contact with PHE 480 (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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358D TRP 3.2 21.5 - - - -
359D SER* 3.6 14.4 - - - -
360D MET* 4.3 8.7 - - + -
462D LEU* 4.4 2.2 - - + -
465D TYR* 3.8 19.3 - - + -
466D VAL* 3.9 12.3 - - + -
469D VAL* 3.7 26.0 - - + -
473D TRP* 3.5 23.1 - + + -
476D TYR 3.4 2.2 + - - -
477D LYS 3.2 8.3 + - - +
479D TYR* 1.3 78.8 - - - +
481D TYR* 1.3 71.2 + + - +
483D SER* 3.1 5.0 + - - -
484D ARG* 2.8 57.2 + - - +
487D SER* 3.6 24.7 - - - -
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Residues in contact with TYR 481 (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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146A VAL* 6.1 5.9 - - + +
466D VAL* 3.6 12.4 - - + +
469D VAL* 5.4 1.6 - - + -
470D GLU* 2.4 40.8 + - - +
477D LYS* 2.9 35.4 + - + +
478D ASP* 4.1 8.7 - - - +
480D PHE* 1.3 92.8 - + - +
482D ALA* 1.3 62.3 + - - +
484D ARG 3.0 6.6 - - - -
485D PRO* 3.0 28.6 - - - +
487D SER* 4.0 17.3 - - - -
488D GLN* 4.0 52.8 + - + +
492D TYR* 4.9 2.8 - - - -
531D ASN* 4.3 0.3 + - - -
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Residues in contact with ALA 482 (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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478D ASP 3.1 18.4 + - - +
479D TYR* 3.5 8.7 - - + +
481D TYR* 1.3 78.2 - - - +
483D SER* 1.3 60.4 + - - +
484D ARG 3.5 0.2 + - - -
485D PRO* 3.7 1.4 - - - +
528D PRO* 4.6 8.3 - - + +
529D PRO 4.1 20.4 - - - +
530D LYS* 4.6 10.3 - - + -
531D ASN* 2.9 31.3 + - - +
572D ARG* 3.4 12.3 + - - -
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Residues in contact with SER 483 (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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358D TRP* 3.6 24.6 - - - +
359D SER* 3.9 12.6 + - - -
479D TYR 3.1 11.0 + - - -
480D PHE 3.4 8.1 - - - -
482D ALA* 1.3 81.1 - - - +
484D ARG* 1.3 60.5 + - - +
485D PRO* 3.7 5.4 - - - +
486D GLU* 4.8 1.0 - - - +
528D PRO* 3.5 17.7 - - - +
572D ARG* 3.7 28.9 + - - +
582D TYR* 6.0 0.5 - - - -
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Residues in contact with ARG 484 (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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359D SER* 2.6 46.4 + - - -
361D LEU* 4.3 11.3 - - - +
462D LEU* 3.8 17.5 - - - +
465D TYR* 3.6 21.4 - - - -
480D PHE* 2.8 39.7 + - + +
481D TYR* 3.0 11.2 - - - +
483D SER* 1.3 83.9 - - - +
485D PRO* 1.4 68.2 - - - +
486D GLU* 3.1 21.5 + - - +
487D SER* 3.0 26.1 + - - -
488D GLN* 3.9 1.2 + - - +
582D TYR* 5.4 11.1 - - - -
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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