Contacts of the helix formed by residues 476 - 484 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A TRP* 3.8 22.4 - + - -
473A TRP* 3.3 29.6 - - + +
474A ASP 2.9 0.2 + - - -
475A GLU* 1.3 85.5 - - + +
477A LYS* 1.3 63.7 + - - +
478A ASP 2.5 7.4 + - - -
479A TYR* 2.5 50.0 + + - +
480A PHE 3.4 5.2 + - - -
510A PHE* 3.5 25.8 - + + -
511A LYS* 3.3 46.3 + - + +
514A MET* 3.7 27.0 - - + +
515A GLU* 5.3 0.3 - - - +
522A THR* 5.7 2.3 - - + +
527A LEU* 4.5 11.2 - - + +
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Residues in contact with LYS 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A VAL* 3.5 28.7 - - + -
470A GLU* 3.2 47.1 + - - +
473A TRP* 4.1 2.7 - - - +
474A ASP* 2.4 46.8 + - - +
475A GLU* 4.4 2.5 - - - -
476A TYR* 1.3 72.9 - - - +
478A ASP* 1.3 64.2 + - - +
480A PHE* 3.2 2.6 + - - +
481A TYR* 2.9 44.6 + - + -
499A LYS* 4.7 7.0 - - - +
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Residues in contact with ASP 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A GLU* 3.6 18.6 - - - +
476A TYR 2.5 4.0 + - - -
477A LYS* 1.3 81.9 - - - +
479A TYR* 1.3 69.9 + - + +
481A TYR* 3.4 9.1 + - - +
482A ALA* 3.3 22.3 + - - +
530A LYS* 6.1 4.1 - - + +
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Residues in contact with TYR 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A TRP* 4.3 17.3 - - + -
475A GLU 4.7 4.5 - - - -
476A TYR* 2.5 56.5 + + - +
478A ASP* 1.3 74.7 - - + +
480A PHE* 1.3 64.4 + - - +
482A ALA* 3.5 2.0 + - - -
483A SER* 3.2 25.5 + - - -
527A LEU* 3.5 34.0 - - + +
528A PRO* 3.3 41.9 - - + +
530A LYS* 6.5 1.3 - - + -
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Residues in contact with PHE 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A TRP 3.2 20.6 - - - -
359A SER 3.6 14.4 - - - -
360A MET* 4.3 7.9 - - + -
462A LEU* 4.3 5.4 - - + -
465A TYR* 3.9 19.7 - - + -
466A VAL* 3.9 23.8 - - + -
469A VAL* 3.7 26.2 - - + -
473A TRP* 3.5 23.6 - + + -
476A TYR 3.4 2.4 + - - -
477A LYS 3.2 7.9 + - - +
479A TYR* 1.3 79.8 - - - +
481A TYR* 1.3 71.3 + + - +
483A SER* 3.2 3.1 + - - -
484A ARG* 2.9 58.1 + - + +
487A SER* 4.0 9.6 - - - -
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Residues in contact with TYR 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A VAL* 3.5 18.1 - - + +
469A VAL* 5.5 1.6 - - + -
470A GLU* 2.5 35.0 + - - +
477A LYS* 2.9 34.1 + - + +
478A ASP* 3.4 9.2 + - - +
479A TYR 3.3 0.2 - - - -
480A PHE* 1.3 94.9 - + - +
482A ALA* 1.3 57.6 + - - +
484A ARG 2.5 23.1 - - - +
485A PRO* 2.9 12.6 - - - +
487A SER* 3.8 21.3 - - - -
488A GLN* 3.9 48.1 + - - +
492A TYR* 4.8 3.5 - - - -
531A ASN* 4.4 0.2 + - - -
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Residues in contact with ALA 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A ASP 3.3 15.2 + - - +
479A TYR* 3.5 2.9 + - - +
480A PHE 3.3 0.4 - - - -
481A TYR* 1.3 74.9 - - - +
483A SER* 1.3 62.6 + - - +
484A ARG 4.4 0.2 - - - -
485A PRO* 4.0 0.7 - - - +
528A PRO* 5.4 6.7 - - + +
529A PRO 4.2 16.2 - - - +
530A LYS* 4.4 4.9 - - + -
531A ASN* 3.0 42.8 + - - +
572A ARG* 3.1 19.0 + - - -
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Residues in contact with SER 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A TRP* 3.8 24.8 - - - +
359A SER* 4.0 12.1 - - - -
479A TYR 3.2 13.5 + - - -
480A PHE 3.2 8.1 + - - -
482A ALA* 1.3 78.3 - - - +
484A ARG* 1.3 64.8 + - - +
485A PRO* 4.0 3.0 - - - +
486A GLU* 4.8 1.4 - - - +
528A PRO* 3.4 19.4 - - - +
572A ARG* 3.9 26.2 + - - +
582A TYR* 5.8 1.6 - - - -
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Residues in contact with ARG 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A SER* 2.9 36.8 + - - -
361A LEU* 4.2 9.7 - - - +
462A LEU* 3.3 25.1 - - - +
465A TYR* 3.7 17.9 - - - -
480A PHE* 2.9 37.0 + - + +
481A TYR* 2.5 22.0 - - - +
483A SER* 1.3 83.7 - - - +
485A PRO* 1.4 60.0 - - - +
486A GLU* 3.2 26.5 + - - +
487A SER* 2.7 27.7 + - - +
582A TYR* 5.9 5.7 - - - -
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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