Contacts of the helix formed by residues 458 - 478 (chain A) in PDB entry 4FDI
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 SER 458 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A LEU* 4.7 3.1 - - - +
455A SER* 2.9 33.5 + - - -
456A PHE 3.4 1.1 - - - +
457A ALA* 1.3 83.0 - - - +
459A ALA* 1.3 64.1 + - - +
460A GLU* 3.9 9.0 + - - +
461A TYR* 3.3 15.2 + - - +
462A GLN* 3.3 19.9 + - - +
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Residues in contact with ALA 459 (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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457A ALA 3.9 1.0 + - - -
458A SER* 1.3 70.8 - - - +
460A GLU* 1.3 58.7 + - - +
462A GLN* 3.4 14.0 + - - +
463A GLU* 3.0 30.0 + - - +
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Residues in contact with GLU 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A HIS* 2.7 34.6 + - + +
443A HIS* 3.4 6.1 - - - -
446A ARG* 2.8 41.6 + - - -
454A LEU* 3.8 9.3 - - + +
458A SER* 3.2 8.0 - - - +
459A ALA* 1.3 77.6 - - - +
461A TYR* 1.3 58.9 + - - +
463A GLU* 3.5 7.0 + - - +
464A ALA* 3.0 29.1 + - - +
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Residues in contact with TYR 461 (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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438A LEU* 3.5 17.8 - - + +
439A PRO* 2.7 46.9 + - - +
441A ILE* 3.5 30.4 - - + +
454A LEU* 4.1 18.5 - - + +
455A SER 3.2 26.7 - - - +
456A PHE* 3.4 36.6 - + - -
458A SER* 3.3 11.2 + - - +
459A ALA 3.3 0.2 - - - -
460A GLU* 1.3 78.5 - - - +
462A GLN* 1.3 57.9 + - + +
464A ALA* 3.1 4.1 + - - +
465A LEU* 2.7 59.6 + - + +
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Residues in contact with GLN 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A PHE 5.8 0.7 - - - +
458A SER 3.3 10.0 + - - +
459A ALA* 3.7 13.9 - - - +
460A GLU 3.4 0.2 - - - -
461A TYR* 1.3 85.1 - - + +
463A GLU* 1.3 62.4 + - - +
465A LEU* 3.8 7.8 - - + +
466A SER* 3.1 35.0 + - - +
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Residues in contact with GLU 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A HIS* 4.4 7.4 - - - -
459A ALA 3.0 17.7 + - - +
460A GLU* 3.8 8.5 - - - +
462A GLN* 1.3 74.5 + - - +
464A ALA* 1.3 69.5 + - - +
466A SER* 3.9 3.7 - - - -
467A ARG* 2.8 67.1 + - - +
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Residues in contact with ALA 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A HIS* 3.8 38.1 - - + +
441A ILE* 4.1 15.5 - - + -
460A GLU 3.0 18.7 + - - +
461A TYR 3.6 3.1 - - - +
463A GLU* 1.3 76.0 + - - +
465A LEU* 1.3 59.3 + - - +
467A ARG* 3.3 11.3 + - - +
468A ILE* 2.9 37.2 + - + +
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Residues in contact with LEU 465 (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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400A ALA* 6.0 0.7 - - + -
437A LYS 5.6 2.7 - - - +
438A LEU* 5.5 4.3 - - + -
439A PRO* 3.7 33.0 - - + -
441A ILE* 3.8 10.9 - - + +
461A TYR* 2.7 43.7 + - + +
462A GLN* 3.8 8.5 - - + +
464A ALA* 1.3 72.7 - - - +
466A SER* 1.3 53.4 + - - +
468A ILE* 5.1 1.3 - - - -
469A THR* 2.6 65.1 + - + +
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Residues in contact with SER 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A GLN* 3.1 23.3 + - - +
463A GLU* 4.0 4.0 - - - -
465A LEU* 1.3 78.5 - - - +
467A ARG* 1.3 62.5 + - - +
469A THR* 3.5 5.6 + - - -
470A SER* 3.2 25.8 + - - -
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Residues in contact with ARG 467 (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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379A ASP* 5.7 5.4 + - - -
395A LEU* 2.8 54.2 + - + +
396A GLY* 4.1 5.7 - - - +
397A GLN 4.5 0.6 - - - +
398A HIS* 3.8 17.8 + - - +
463A GLU* 2.8 65.8 + - - +
464A ALA* 3.7 11.6 - - - +
466A SER* 1.3 78.1 - - - +
468A ILE* 1.3 62.7 + - - +
470A SER* 3.8 3.4 - - - -
471A VAL* 3.4 27.3 + - + +
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Residues in contact with ILE 468 (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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393A ALA* 3.8 33.0 - - + +
394A THR 5.6 0.2 - - - -
395A LEU* 4.1 24.9 - - + +
398A HIS* 3.8 37.0 - - + +
399A LYS 4.4 0.4 - - - -
400A ALA* 4.0 24.9 - - + +
402A PHE* 4.1 11.4 - - + -
441A ILE* 5.0 1.3 - - + -
464A ALA* 2.9 26.1 + - + +
465A LEU* 4.5 1.3 - - - +
467A ARG* 1.3 77.8 - - + +
469A THR* 1.3 60.9 + - + +
471A VAL* 3.1 5.1 + - - +
472A VAL* 2.9 29.7 + - + +
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Residues in contact with THR 469 (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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402A PHE* 4.0 22.0 - - + -
439A PRO* 5.1 0.2 - - + -
465A LEU* 2.6 52.3 + - + +
466A SER* 3.5 7.6 + - - -
468A ILE* 1.3 75.5 - - + +
470A SER* 1.3 58.3 + - - +
472A VAL* 3.9 7.2 - - - +
473A GLN* 2.9 40.8 + - - +
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Residues in contact with SER 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A SER 3.2 18.4 + - - -
467A ARG* 3.8 6.1 - - - -
469A THR* 1.3 81.4 + - - +
471A VAL* 1.3 65.3 + - - +
473A GLN* 3.5 12.8 - - - +
474A GLN* 3.1 27.3 + - - +
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Residues in contact with VAL 471 (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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381A PRO* 3.7 39.0 - - + -
383A PHE* 4.1 4.9 - - + -
395A LEU* 3.6 20.2 - - + -
467A ARG* 3.4 15.9 + - + +
468A ILE* 3.1 7.6 + - + +
470A SER* 1.3 76.7 - - - +
472A VAL* 1.3 65.0 + - - +
474A GLN* 3.5 12.5 + - + +
475A HIS* 3.1 22.3 + - - +
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Residues in contact with VAL 472 (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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383A PHE* 3.8 14.8 - - + -
390A LEU* 4.1 11.7 - - + -
393A ALA* 3.6 31.0 - - + -
402A PHE* 3.8 15.7 - - + -
468A ILE 2.9 19.8 + - - +
469A THR* 3.9 6.7 - - - +
471A VAL* 1.3 76.2 - - - +
473A GLN* 1.3 59.4 + - + +
475A HIS* 3.1 5.2 + - - +
476A GLN* 2.9 37.8 + - - +
605A GOL 3.8 29.4 - - - -
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Residues in contact with GLN 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A THR* 2.9 27.9 + - - +
470A SER* 3.5 12.1 - - - +
472A VAL* 1.3 78.7 - - + +
474A GLN* 1.3 58.5 + - - +
476A GLN* 3.9 10.0 - - - +
477A GLU* 2.9 53.8 + - + +
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Residues in contact with GLN 474 (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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470A SER* 3.1 22.0 + - - +
471A VAL* 3.6 13.6 - - - +
473A GLN* 1.3 76.4 - - - +
475A HIS* 1.3 63.9 + - - +
477A GLU* 3.7 7.6 + - - +
478A ALA* 3.3 24.9 + - + +
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Residues in contact with HIS 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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91A LEU* 3.6 21.1 - - + -
93A ILE* 5.4 0.4 - - + -
94A ARG* 3.4 33.6 + - - +
383A PHE* 3.5 27.0 - + + -
385A TYR* 2.7 32.3 + - - -
390A LEU* 3.6 20.0 - - + -
471A VAL 3.1 13.8 + - - +
472A VAL 3.3 6.7 - - - +
474A GLN* 1.3 78.2 - - - +
476A GLN* 1.3 68.2 + - + +
478A ALA* 3.5 4.4 + - - +
479A LEU* 3.2 29.9 + - + +
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Residues in contact with GLN 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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385A TYR* 5.1 3.0 + - - +
390A LEU* 4.2 10.9 - - + +
472A VAL* 2.9 26.7 + - + +
473A GLN* 4.0 9.5 - - - +
475A HIS* 1.3 86.5 - - + +
477A GLU* 1.3 64.8 + - + +
479A LEU* 3.1 28.7 + - + +
605A GOL 3.2 44.8 + - - -
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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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473A GLN* 2.9 45.1 + - - +
474A GLN* 4.1 6.1 - - - +
476A GLN* 1.3 77.6 - - + +
478A ALA* 1.3 59.1 + - - +
479A LEU 3.7 1.7 + - - +
480A VAL* 6.1 0.2 - - - +
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Residues in contact with ALA 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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94A ARG* 4.9 5.4 + - - +
474A GLN* 3.3 17.6 + - + +
475A HIS* 3.8 4.0 - - - +
476A GLN 3.2 0.4 - - - -
477A GLU* 1.3 77.8 - - - +
479A LEU* 1.3 60.1 + - - +
480A VAL* 3.7 6.1 + - - +
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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
------------------------------------------------------------
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