Contacts of the helix formed by residues 474 - 489 (chain A) in PDB entry 4HPF
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 CYS 474 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449A ILE* 3.6 19.3 - - + +
450A LEU 3.8 15.5 - - - -
452A SER* 3.9 20.4 - - - -
455A LYS* 4.0 19.0 - - - +
472A ILE 4.3 0.8 + - - -
473A ILE* 1.3 77.9 - - - +
475A PHE* 1.3 65.4 + - - +
476A ALA* 3.9 3.4 - - - -
477A GLU* 2.8 43.8 + - + +
478A LEU* 3.1 15.8 + - - +
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Residues in contact with PHE 475 (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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448A GLN* 3.2 35.3 - - + +
449A ILE 4.6 2.0 + - - -
473A ILE* 3.8 21.9 - - + +
474A CYS* 1.3 70.2 - - - +
476A ALA* 1.3 56.0 + - - +
478A LEU* 3.0 5.1 + - - +
479A LYS* 2.7 58.5 + - + +
906A LEU* 3.1 36.1 - - + -
907A ASP* 4.5 17.5 - - - -
909A LEU* 3.9 15.7 - - + -
910A LEU* 5.2 8.5 - - + -
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Residues in contact with ALA 476 (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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450A LEU 3.8 22.2 + - - +
451A GLN* 5.5 1.1 - - - -
474A CYS* 3.9 3.8 - - - -
475A PHE* 1.3 76.8 - - - +
477A GLU* 1.3 62.6 + - - +
479A LYS* 3.8 10.5 - - - +
480A LEU* 3.2 31.7 + - + +
730A GLY* 4.9 10.8 - - - +
733A ASN* 3.8 12.6 + - - +
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Residues in contact with GLU 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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452A SER* 4.5 4.3 - - - -
455A LYS* 3.2 40.0 + - - +
474A CYS* 2.8 23.4 + - - +
476A ALA* 1.3 81.2 - - - +
478A LEU* 1.3 71.8 + - - +
481A GLY* 3.3 19.9 + - - -
733A ASN* 3.4 33.8 - - + +
924A GLN* 3.9 12.2 + - - -
928A THR* 4.1 22.9 - - + +
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Residues in contact with LEU 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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473A ILE* 5.1 2.7 - - + -
474A CYS 3.1 15.9 + - - +
475A PHE* 3.0 5.5 + - - +
477A GLU* 1.3 96.8 - - - +
479A LYS* 1.3 65.4 + - - +
480A LEU 3.2 0.2 - - - -
481A GLY* 3.0 9.7 + - - -
482A PHE* 3.1 26.9 + - + -
906A LEU* 4.1 12.8 - - + -
909A LEU* 3.3 34.3 - - + -
920A LEU* 5.4 7.4 - - + -
923A LEU* 4.4 17.5 - - + -
924A GLN* 4.7 17.9 - - + +
927A VAL* 3.7 5.8 - - + +
928A THR* 4.4 12.1 - - + -
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Residues in contact with LYS 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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475A PHE* 2.7 48.0 + - + +
476A ALA* 3.8 8.2 - - - +
478A LEU* 1.3 73.1 - - - +
480A LEU* 1.3 61.9 + - + +
481A GLY 3.5 0.2 + - - -
482A PHE* 3.8 1.0 + - - -
483A ILE* 3.6 26.0 + - - +
864A GLU* 4.5 17.0 - - - +
866A LYS* 6.3 2.5 - - - -
901A PHE* 3.8 14.9 - - + -
903A GLY* 4.0 25.6 - - - +
906A LEU* 3.5 23.1 - - + -
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Residues in contact with LEU 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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476A ALA* 3.2 16.8 + - + +
479A LYS* 1.3 77.9 - - + +
481A GLY* 1.3 60.4 + - - +
483A ILE* 3.6 18.1 + - + +
484A ALA* 3.0 26.9 + - - +
729A MET* 5.1 7.6 - - + -
730A GLY* 2.7 39.3 - - - +
731A LEU* 4.2 5.4 - - + -
733A ASN* 3.9 16.2 - - + +
734A PHE* 3.7 30.6 - - + +
800A LEU* 4.3 21.3 - - + -
864A GLU* 5.9 1.8 - - - +
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Residues in contact with GLY 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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477A GLU 3.3 10.2 + - - -
478A LEU 3.0 3.8 + - - -
480A LEU* 1.3 75.4 - - - +
482A PHE* 1.3 66.5 + - - +
484A ALA* 2.9 17.1 + - - +
485A GLN* 3.0 16.5 + - - +
733A ASN 4.2 5.1 + - - -
737A PRO* 4.5 2.9 - - - -
927A VAL* 3.2 30.5 - - - +
928A THR* 5.3 0.4 - - - -
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Residues in contact with PHE 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 LEU* 3.1 33.3 + - + -
479A LYS* 4.0 1.6 - - - +
481A GLY* 1.3 74.2 - - - +
483A ILE* 1.3 63.2 + - - +
485A GLN* 3.3 7.2 + - - +
486A GLY 3.2 16.1 + - - -
493A CYS* 3.4 15.2 - - - +
496A LEU* 3.8 32.5 - - + -
497A THR* 3.6 26.9 - - - -
500A PHE* 4.3 4.5 - + - -
901A PHE* 3.6 28.9 - + + -
905A PHE* 3.8 24.2 - + - -
906A LEU* 4.2 12.3 - - + -
923A LEU* 3.5 25.6 - - + -
927A VAL* 3.5 17.9 - - + +
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Residues in contact with ILE 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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479A LYS 3.6 16.6 + - - +
480A LEU* 3.6 15.9 + - + +
481A GLY 3.2 0.2 - - - -
482A PHE* 1.3 77.1 - - - +
484A ALA* 1.3 68.4 + - - +
486A GLY* 2.8 13.3 + - - -
487A CYS* 3.1 10.2 + - - -
493A CYS* 4.3 0.9 - - - -
734A PHE* 4.0 20.2 - - + -
798A ALA* 4.2 7.6 - - + -
800A LEU* 4.1 22.9 - - + -
862A LEU* 3.9 23.4 - - + +
864A GLU* 4.0 36.6 - - + -
901A PHE* 3.9 20.2 - - + -
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Residues in contact with ALA 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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480A LEU 3.0 14.9 + - - +
481A GLY 2.9 10.0 + - - +
483A ILE* 1.3 73.6 - - - +
485A GLN* 1.3 55.5 + - - +
487A CYS* 2.7 28.7 + - - +
488A LEU 3.0 8.7 + - - -
734A PHE* 3.8 25.1 - - + +
737A PRO* 3.7 28.9 - - + -
738A LEU* 3.3 15.6 - - + +
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Residues in contact with GLN 485 (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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481A GLY 3.0 6.4 + - - +
482A PHE 3.6 7.0 - - - +
484A ALA* 1.3 77.6 - - - +
486A GLY* 1.3 57.7 + - - +
488A LEU* 3.1 23.1 + - - +
489A VAL* 2.9 30.3 + - - +
492A LEU* 3.5 25.7 - - + +
493A CYS 5.0 0.2 - - - +
496A LEU* 3.9 23.8 - - + -
737A PRO* 3.8 18.6 + - - +
743A TYR* 5.0 1.7 + - - -
926A LEU 3.5 18.5 + - - +
927A VAL* 2.9 29.5 + - - +
929A GLY* 4.8 4.9 - - - +
963A LEU* 5.5 2.3 - - - +
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Residues in contact with GLY 486 (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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482A PHE 3.2 7.3 + - - -
483A ILE 2.8 9.5 + - - -
485A GLN* 1.3 76.5 - - - +
487A CYS* 1.3 60.9 + - - +
489A VAL 3.5 19.9 - - - +
490A PRO* 4.0 2.9 - - - +
491A GLY 4.6 1.9 + - - -
492A LEU 4.8 0.2 - - - -
493A CYS* 3.8 22.6 - - - +
796A MET* 4.0 16.7 - - - +
862A LEU* 4.2 9.9 - - - -
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Residues in contact with CYS 487 (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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483A ILE* 3.1 16.4 + - - -
484A ALA 2.7 17.1 + - - +
486A GLY* 1.3 71.0 - - - +
488A LEU* 1.3 63.0 + - - +
490A PRO* 5.3 1.7 - - - +
716A ILE* 3.7 40.0 - - + +
734A PHE* 4.3 9.9 - - - -
738A LEU* 4.2 3.4 - - + -
749A LYS* 4.6 10.6 + - - +
796A MET* 4.0 31.5 - - + +
798A ALA* 4.1 23.6 - - - -
862A LEU* 4.8 2.7 - - - -
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Residues in contact with LEU 488 (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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484A ALA 3.0 5.4 + - - +
485A GLN* 3.1 33.4 + - - +
487A CYS* 1.3 80.6 - - - +
489A VAL* 1.3 71.4 - - + +
490A PRO* 3.8 7.0 - - - +
716A ILE* 5.5 2.7 - - + -
737A PRO 3.7 20.4 - - - +
738A LEU* 3.4 30.7 - - + +
743A TYR* 3.5 39.9 - - + +
749A LYS* 5.1 13.5 + - + -
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Residues in contact with VAL 489 (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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485A GLN 2.9 12.1 + - - +
486A GLY 3.5 6.3 - - - +
488A LEU* 1.3 84.5 - - + +
490A PRO* 1.3 73.3 - - + +
491A GLY 3.1 0.5 + - - -
492A LEU* 2.9 40.4 + - + +
743A TYR* 4.7 4.0 - - - +
963A LEU 3.4 23.6 - - - +
964A GLY* 4.2 7.0 - - - -
965A LEU* 3.8 33.7 - - + +
1034A PHE* 4.1 7.0 - - + -
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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
------------------------------------------------------------
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