Contacts of the helix formed by residues 476 - 484 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358F TRP* 3.8 22.9 - + - -
473F TRP* 3.3 24.2 - - + +
474F ASP 2.9 0.2 + - - -
475F GLU* 1.3 88.4 - - + +
477F LYS* 1.3 64.1 + - - +
478F ASP 2.5 8.0 + - - -
479F TYR* 2.5 51.5 + + + +
480F PHE 3.4 5.5 + - - -
510F PHE* 3.4 30.5 - + + -
511F LYS* 4.3 22.5 - - + +
514F MET* 3.7 29.2 - - + +
515F GLU* 5.2 5.2 + - - +
522F THR* 5.7 3.1 - - + +
527F LEU* 4.5 11.0 - - + +
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Residues in contact with LYS 477 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469F VAL* 3.5 29.8 - - + -
470F GLU* 3.2 49.0 + - - +
473F TRP* 4.1 2.3 - - - +
474F ASP* 2.4 46.0 + - - +
475F GLU* 4.4 2.2 - - - -
476F TYR* 1.3 73.8 - - - +
478F ASP* 1.3 61.7 + - - +
480F PHE* 3.2 2.9 + - - +
481F TYR* 2.9 45.0 + - + -
499F LYS* 4.7 6.5 - - - +
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Residues in contact with ASP 478 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475F GLU* 3.6 18.0 - - - +
476F TYR 2.5 4.0 + - - -
477F LYS* 1.3 81.3 - - - +
479F TYR* 1.3 70.0 + - + +
481F TYR* 3.4 8.9 + - - +
482F ALA* 3.3 22.5 + - - +
530F LYS* 6.3 2.7 - - + -
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Residues in contact with TYR 479 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358F TRP* 4.3 16.4 - - + -
475F GLU 4.7 4.7 - - - -
476F TYR* 2.5 57.8 + + - +
478F ASP* 1.3 75.4 - - + +
480F PHE* 1.3 63.4 + - - +
482F ALA* 3.5 2.0 + - - -
483F SER* 3.2 26.1 + - - -
527F LEU* 3.6 32.8 - - + +
528F PRO* 3.5 42.8 - - + +
530F LYS* 6.4 2.0 - - - -
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Residues in contact with PHE 480 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358F TRP 3.2 21.5 - - - -
359F SER 3.6 14.1 - - - -
360F MET* 4.3 7.0 - - + -
462F LEU* 4.5 4.0 - - + -
465F TYR* 3.8 20.9 - - + -
466F VAL* 3.9 23.6 - - + -
469F VAL* 3.7 26.2 - - + -
473F TRP* 3.5 23.6 - + + -
476F TYR 3.4 2.0 + - - -
477F LYS 3.2 7.3 + - - +
479F TYR* 1.3 79.2 - - - +
481F TYR* 1.3 71.6 + + - +
483F SER* 3.2 3.3 + - - -
484F ARG* 2.9 58.2 + - + +
487F SER* 4.0 10.3 - - - -
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Residues in contact with TYR 481 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466F VAL* 3.5 18.3 - - + +
469F VAL* 5.5 1.6 - - + -
470F GLU* 2.5 34.3 + - - +
477F LYS* 2.9 34.1 + - + +
478F ASP* 4.0 8.7 - - - +
479F TYR 3.3 0.4 - - - -
480F PHE* 1.3 95.7 - + - +
482F ALA* 1.3 57.4 + - - +
484F ARG 2.5 23.2 - - - +
485F PRO* 2.9 11.8 - - - +
487F SER* 3.8 21.3 - - - -
488F GLN* 3.9 48.9 + - - +
492F TYR* 4.8 3.3 - - - -
531F ASN* 4.4 0.2 + - - -
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Residues in contact with ALA 482 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478F ASP 3.3 15.2 + - - +
479F TYR* 4.3 2.9 - - - +
480F PHE 3.3 0.4 - - - -
481F TYR* 1.3 75.9 - - - +
483F SER* 1.3 61.6 + - - +
484F ARG 4.4 0.2 - - - -
485F PRO* 4.0 0.7 - - - +
488F GLN* 6.0 0.2 - - - +
528F PRO* 5.2 4.9 - - + +
529F PRO 3.9 21.5 - - - +
530F LYS* 4.4 4.0 - - + -
531F ASN* 3.0 40.8 + - + +
572F ARG* 3.1 18.2 + - - -
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Residues in contact with SER 483 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358F TRP* 3.8 22.6 - - - +
359F SER* 4.0 12.8 + - - -
479F TYR 3.2 13.6 + - - -
480F PHE 3.2 8.1 + - - -
482F ALA* 1.3 78.2 - - - +
484F ARG* 1.3 64.9 + - - +
485F PRO* 4.0 3.8 - - - +
486F GLU* 4.8 1.4 - - - +
528F PRO* 3.3 21.3 - - - +
572F ARG* 3.8 27.4 + - - +
582F TYR* 5.8 1.4 - - - -
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Residues in contact with ARG 484 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359F SER* 2.9 36.0 + - - -
361F LEU* 4.3 10.1 - - - +
462F LEU* 3.6 23.8 - - - +
465F TYR* 3.7 18.2 - - - -
480F PHE* 2.9 37.4 + - + +
481F TYR* 2.5 22.7 - - - +
483F SER* 1.3 82.9 - - - +
485F PRO* 1.4 60.3 - - - +
486F GLU* 3.5 27.4 + - - +
487F SER* 2.7 28.2 + - - +
582F 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