Contacts of the helix formed by residues 473 - 492 (chain A) in PDB entry 4FYT
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 ASP 473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442A ARG* 5.0 0.9 - - - -
453A HIS* 2.6 30.6 + - - -
470A GLU* 3.4 17.7 - - - +
471A LEU* 2.8 15.7 + - - +
472A PHE* 1.3 75.6 - - - +
474A ALA* 1.3 67.4 + - - +
475A ILE* 3.1 7.6 + - - +
476A SER* 2.9 22.5 + - - -
477A TYR* 3.1 26.0 + - - +
899A SER* 6.5 0.9 - - - -
935A ARG* 5.5 0.9 - - - -
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Residues in contact with ALA 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A ARG* 3.7 34.3 - - + +
443A VAL* 3.3 22.3 - - + +
446A VAL* 4.2 16.4 - - + -
473A ASP* 1.3 76.2 - - - +
475A ILE* 1.3 58.2 + - - +
478A SER* 2.8 25.5 + - - -
479A LYS 3.0 6.8 + - - -
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Residues in contact with ILE 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A VAL* 3.6 22.0 - - + -
446A VAL* 4.4 9.0 - - + -
447A ASP* 3.5 31.6 - - + +
452A SER* 3.5 10.3 - - - +
453A HIS* 3.5 42.4 - - + +
455A LEU* 3.3 30.6 - - + +
473A ASP* 3.1 9.7 + - - +
474A ALA* 1.3 77.6 - - - +
476A SER* 1.3 63.6 + - - +
479A LYS* 3.2 13.5 + - + +
480A GLY 3.0 21.8 + - - -
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Residues in contact with SER 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A LEU* 4.2 19.9 - - - +
408A TRP* 3.5 25.4 + - - +
411A GLU* 4.4 0.7 - - - -
412A GLY* 3.2 26.3 + - - -
453A HIS* 4.6 7.1 - - - -
455A LEU* 4.3 6.9 + - - -
471A LEU* 2.7 34.1 + - - +
473A ASP* 2.9 11.5 + - - -
475A ILE* 1.3 73.7 - - - +
477A TYR* 1.3 62.7 + - - +
480A GLY* 3.8 1.0 - - - -
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Residues in contact with TYR 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A HIS* 3.9 5.4 - + - -
411A GLU* 3.2 36.1 + - + -
412A GLY* 3.6 0.9 - - - -
415A SER* 3.3 36.0 - - - +
439A ASP* 5.7 0.2 - - - +
442A ARG* 4.3 12.1 - - - +
472A PHE* 3.5 36.2 - - + -
473A ASP 3.1 30.7 + - - +
476A SER* 1.3 80.1 - - - +
478A SER* 1.3 62.8 + - - +
479A LYS 3.6 0.2 - - - -
480A GLY 3.9 0.2 - - - -
481A ALA 2.9 21.1 + - - -
1B L2O 2.7 40.6 + - - +
2B VAL* 4.5 6.3 - - + -
3B VAL* 4.0 10.4 - - + +
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Residues in contact with SER 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ASN 3.6 0.7 + - - -
439A ASP* 3.0 42.2 + - - +
442A ARG* 2.8 34.3 + - - -
443A VAL* 3.8 7.0 - - - -
474A ALA 2.8 16.3 + - - -
477A TYR* 1.3 73.3 - - - +
479A LYS* 1.3 60.5 + - - -
481A ALA* 3.8 1.4 - - - +
482A SER* 2.7 32.6 + - - -
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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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443A VAL* 3.7 21.8 - - + +
447A ASP* 3.1 22.7 + - - +
453A HIS 5.4 0.4 + - - -
455A LEU* 4.2 11.7 - - + +
474A ALA 3.0 7.1 + - - -
475A ILE* 3.2 23.6 - - + +
478A SER* 1.3 73.6 - - - +
480A GLY* 1.3 66.4 + - - +
482A SER* 3.1 3.5 + - - -
483A VAL* 2.9 32.3 + - + +
543A TRP* 3.4 27.6 + - - +
546A GLN 3.9 8.7 + - - -
547A MET* 4.0 1.8 - - - +
548A GLY 2.9 33.9 + - - +
629A TYR* 3.6 24.7 - - + -
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Residues in contact with GLY 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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408A TRP* 4.3 9.1 - - - -
412A GLY* 3.7 24.2 - - - -
455A LEU* 3.6 17.0 - - - +
475A ILE 3.0 11.5 + - - -
476A SER 3.8 1.3 - - - -
477A TYR 3.6 1.0 + - - -
478A SER 3.3 0.4 - - - -
479A LYS* 1.3 75.9 - - - +
481A ALA* 1.3 61.4 + - - +
483A VAL* 3.4 1.9 + - - +
484A LEU* 3.1 27.9 + - - +
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Residues in contact with ALA 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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412A GLY 3.6 8.6 + - - -
415A SER* 3.7 9.0 - - - +
416A TYR* 3.7 31.2 - - + +
435A MET* 4.9 4.2 - - - +
439A ASP* 4.0 16.6 - - + +
477A TYR 2.9 18.8 + - - +
478A SER 3.8 4.7 - - - +
479A LYS 3.3 0.2 - - - -
480A GLY* 1.3 74.0 - - - +
482A SER* 1.3 57.2 + - - +
484A LEU* 3.3 3.1 + - - +
485A ARG* 2.9 30.1 + - - +
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Residues in contact with SER 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A MET* 6.2 0.2 - - - -
439A ASP* 3.8 1.9 + - - +
440A VAL* 3.4 38.0 + - - +
478A SER 2.7 25.2 + - - -
479A LYS 3.1 3.8 + - - -
481A ALA* 1.3 73.4 - - - +
483A VAL* 1.3 61.9 + - - +
485A ARG* 3.3 9.1 + - - +
486A MET* 3.0 28.1 + - - +
627A THR 4.4 1.7 - - - +
628A GLY 5.8 0.2 - - - -
629A TYR* 3.6 32.5 - - - +
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Residues in contact with VAL 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A TRP* 5.2 7.4 - - + -
455A LEU* 4.3 13.2 - - + -
479A LYS* 2.9 35.2 + - + +
480A GLY 4.0 3.1 - - - +
482A SER* 1.3 76.8 - - - +
484A LEU* 1.3 59.9 + - + +
486A MET* 3.4 13.5 + - + +
487A LEU* 2.9 26.9 + - - +
518A TRP* 5.4 0.7 - - + -
540A MET* 3.0 34.2 - - + +
543A TRP* 4.0 27.1 - - + +
544A THR* 4.9 2.7 - - - +
629A TYR* 4.7 8.1 - - + -
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Residues in contact with LEU 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A TRP* 3.9 19.3 - - + -
412A GLY 3.7 7.2 - - - +
413A PHE* 3.6 70.7 - - + +
416A TYR* 4.1 17.9 - - + -
480A GLY 3.1 14.3 + - - +
481A ALA 3.7 3.6 - - - +
483A VAL* 1.3 76.6 - - + +
485A ARG* 1.3 58.8 + - - +
487A LEU* 3.6 18.1 - - + +
488A SER* 2.8 31.9 + - - -
496A PHE* 3.9 18.1 - - + -
517A LEU* 4.7 0.9 - - + -
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Residues in contact with ARG 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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416A TYR* 3.7 14.5 - - + -
432A LYS* 3.8 11.7 + - - +
433A ASP* 5.4 3.2 + - - -
435A MET* 3.7 44.8 - - - +
436A VAL* 3.6 17.8 - - - +
440A VAL* 4.4 14.1 - - - +
481A ALA 2.9 14.2 + - - +
482A SER* 3.4 9.4 - - - +
484A LEU* 1.3 75.5 - - - +
486A MET* 1.3 57.9 + - - +
488A SER* 3.5 2.1 + - - -
489A SER* 3.0 28.4 + - - -
625A ASN* 2.8 30.1 + - - +
626A VAL 3.0 19.1 + - - -
627A THR* 3.7 21.9 - - + +
656A ILE* 4.8 4.8 - - - +
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Residues in contact with MET 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 SER 3.0 10.6 + - - +
483A VAL* 3.5 17.5 - - + +
484A LEU 3.2 0.2 - - - -
485A ARG* 1.3 76.5 - - - +
487A LEU* 1.3 62.4 + - - +
489A SER* 3.1 5.7 + - - -
490A PHE* 3.0 28.6 + - + +
540A MET* 4.7 5.4 - - + -
543A TRP* 3.5 50.7 - - + +
587A PRO* 3.9 35.2 - - + +
627A THR 3.2 19.9 + - - +
628A GLY* 3.8 7.0 - - - -
629A TYR* 3.6 26.5 - - + +
630A TYR* 5.2 0.7 - - - -
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Residues in contact with LEU 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 VAL 2.9 14.8 + - - +
484A LEU* 3.6 20.9 - - + +
486A MET* 1.3 75.7 - - - +
488A SER* 1.3 62.2 + - - +
490A PHE* 3.3 34.0 + - + -
491A LEU* 3.0 49.7 + - + +
496A PHE* 3.9 19.1 - - + -
518A TRP* 4.2 8.3 - - + -
521A LEU* 3.8 24.0 - - + -
536A VAL* 4.5 4.0 - - + -
540A MET* 3.8 29.6 - - + -
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Residues in contact with SER 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A TYR* 3.2 19.6 + - - -
484A LEU 2.8 19.0 + - - -
485A ARG 3.7 4.5 - - - -
487A LEU* 1.3 73.2 - - - +
489A SER* 1.3 57.5 + - - +
492A SER* 2.8 32.6 + - - -
493A GLU* 2.7 35.8 + - - +
496A PHE* 3.7 17.6 - - - -
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Residues in contact with SER 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A ARG 3.0 14.7 + - - -
486A MET* 3.1 9.8 + - - -
488A SER* 1.3 78.2 - - - +
490A PHE* 1.3 60.6 + - - +
492A SER* 3.6 6.1 + - - -
589A THR* 5.2 6.4 - - - +
627A THR* 3.6 36.2 + - - +
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Residues in contact with PHE 490 (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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486A MET* 3.0 28.2 + - + +
487A LEU* 3.5 32.3 - - + -
489A SER* 1.3 77.1 - - - +
491A LEU* 1.3 85.2 + - + +
530A ILE* 5.6 2.8 - - - +
532A LEU* 4.1 19.2 - - + +
536A VAL* 5.7 2.5 - - + -
539A ILE* 4.1 11.4 - - + -
540A MET* 4.1 17.9 - - + -
587A PRO* 3.9 23.8 - - + -
599A ASP* 6.2 0.4 - - - -
601A TRP* 3.6 42.2 - + + -
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Residues in contact with LEU 491 (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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487A LEU* 3.0 39.6 + - + +
490A PHE* 1.3 103.4 - - + +
492A SER* 1.3 78.6 + - - +
495A VAL* 3.4 25.9 - - + +
496A PHE* 4.3 21.8 - - + +
521A LEU* 4.8 15.5 - - + -
525A VAL* 3.6 28.5 - - + -
530A ILE* 5.2 9.1 - - + +
532A LEU* 4.4 8.1 - - + -
536A VAL* 4.9 2.7 - - + -
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Residues in contact with SER 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A SER 2.8 14.6 + - - -
489A SER 3.6 5.5 + - - -
490A PHE 3.5 2.2 - - - -
491A LEU* 1.3 83.3 + - - +
493A GLU* 1.3 58.8 + - - +
494A ASP* 3.7 8.0 + - - +
495A VAL* 3.4 18.7 + - - +
496A PHE* 3.0 26.9 + - - +
528A ARG* 5.4 0.3 + - - -
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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
------------------------------------------------------------
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