Contacts of the helix formed by residues 458 - 479 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B LEU* 4.6 3.8 - - - +
455B SER* 3.1 31.6 + - - -
456B PHE 4.5 1.0 - - - +
457B ALA* 1.3 82.0 - - - +
459B ALA* 1.3 61.8 + - - +
460B GLU* 3.7 8.8 + - - +
461B TYR* 3.1 20.4 + - - +
462B GLN* 3.2 19.8 + - - +
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Residues in contact with ALA 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B ALA 4.0 0.4 + - - -
458B SER* 1.3 72.3 - - - +
460B GLU* 1.3 60.4 + - - +
462B GLN* 3.4 14.9 + - - +
463B GLU* 3.0 29.8 + - - +
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Residues in contact with GLU 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B HIS* 2.7 34.2 + - + +
443B HIS* 3.3 6.7 - - - -
446B ARG* 2.8 40.7 + - - -
454B LEU* 3.7 11.9 - - + +
458B SER* 3.2 8.6 + - - +
459B ALA* 1.3 75.7 - - - +
461B TYR* 1.3 66.0 + - - +
463B GLU* 3.5 6.1 + - - +
464B ALA* 3.0 24.1 + - - +
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Residues in contact with TYR 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B LEU* 3.5 13.0 - - + +
439B PRO* 2.6 49.9 + - + +
441B ILE* 3.5 30.9 - - + +
454B LEU* 4.1 20.5 - - + +
455B SER 3.4 15.9 - - - +
456B PHE* 3.6 36.5 - + - +
458B SER* 3.1 23.5 + - - +
460B GLU* 1.3 76.1 - - - +
462B GLN* 1.3 55.3 - - - +
464B ALA* 3.2 3.5 + - - +
465B LEU* 2.7 61.2 + - + +
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Residues in contact with GLN 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B PHE 6.1 0.4 - - - +
458B SER 3.2 10.6 + - - +
459B ALA* 3.8 15.6 + - - +
460B GLU 3.4 0.2 - - - -
461B TYR* 1.3 84.0 - - + +
463B GLU* 1.3 62.6 + - - +
465B LEU* 3.6 8.3 - - + +
466B SER* 3.1 34.7 + - - +
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Residues in contact with GLU 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B HIS* 4.7 6.1 - - - -
459B ALA 3.0 17.8 + - - +
460B GLU* 3.9 6.0 - - - +
462B GLN* 1.3 76.4 - - - +
464B ALA* 1.3 63.7 + - - +
466B SER* 3.5 3.6 + - - -
467B ARG* 2.8 66.2 + - - +
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Residues in contact with ALA 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B HIS* 3.7 39.9 - - + +
441B ILE* 4.1 14.8 - - + -
460B GLU 3.0 18.3 + - - +
461B TYR 3.7 2.5 - - - +
463B GLU* 1.3 78.0 + - - +
465B LEU* 1.3 60.6 + - - +
467B ARG* 3.8 6.7 - - - +
468B ILE* 2.9 37.3 + - + +
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Residues in contact with LEU 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437B LYS 5.8 2.0 - - - +
438B LEU* 5.7 3.6 - - + -
439B PRO* 3.7 32.8 - - + -
441B ILE* 3.7 12.3 - - + +
461B TYR* 2.7 42.3 + - + +
462B GLN* 3.6 9.6 - - + +
464B ALA* 1.3 72.7 - - - +
466B SER* 1.3 54.8 + - - +
468B ILE* 4.3 1.7 - - - +
469B THR* 2.6 64.9 + - + +
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Residues in contact with SER 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B GLN* 3.1 23.2 + - - +
463B GLU* 4.1 4.5 - - - -
465B LEU* 1.3 77.3 - - - +
467B ARG* 1.3 64.3 + - - +
469B THR* 3.3 6.5 + - - -
470B SER* 3.1 25.6 + - - -
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Residues in contact with ARG 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ASP* 5.6 6.8 + - - -
395B LEU* 2.8 66.2 + - + +
396B GLY* 3.9 6.9 - - - +
397B GLN 4.4 0.8 - - - +
398B HIS* 3.9 17.4 + - - +
463B GLU* 2.8 60.8 + - - +
464B ALA* 3.8 11.9 - - - +
466B SER* 1.3 77.3 - - - +
468B ILE* 1.3 64.1 + - - +
470B SER* 3.8 4.0 - - - -
471B VAL* 3.6 14.8 + - + +
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Residues in contact with ILE 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ALA* 3.8 29.6 - - + +
395B LEU* 3.9 20.0 - - + +
398B HIS* 3.7 37.5 - - + +
399B LYS 4.4 0.2 - - - -
400B ALA* 3.9 35.0 - - + +
402B PHE* 4.3 4.0 - - + -
441B ILE* 5.0 1.3 - - + -
464B ALA* 2.9 24.4 + - + +
465B LEU* 4.3 2.0 - - - +
467B ARG* 1.3 77.7 - - + +
469B THR* 1.3 65.6 + - + +
471B VAL* 3.2 11.8 - - + +
472B VAL* 3.0 25.8 + - + +
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Residues in contact with THR 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B PHE* 4.3 20.0 - - + -
436B THR 6.1 0.2 - - - +
439B PRO* 5.2 0.4 - - + -
465B LEU* 2.6 49.3 + - + +
466B SER* 3.3 11.1 + - - -
468B ILE* 1.3 77.3 - - + +
470B SER* 1.3 58.4 + - - +
472B VAL* 3.8 6.4 - - - +
473B GLN* 2.9 51.5 + - - +
605B GOL 6.0 0.7 - - - +
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Residues in contact with SER 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B SER 3.1 20.0 + - - -
467B ARG* 3.8 6.3 - - - -
468B ILE 3.2 0.2 - - - -
469B THR* 1.3 78.5 + - - +
471B VAL* 1.3 60.4 + - - +
473B GLN* 3.4 8.2 + - - +
474B GLN* 3.0 49.8 + - - +
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Residues in contact with VAL 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B PRO* 4.1 22.9 - - + -
383B PHE* 3.8 5.0 - - + -
393B ALA* 5.8 0.7 - - + -
395B LEU* 3.7 35.0 - - + -
467B ARG* 3.6 10.3 + - + +
468B ILE* 3.2 17.2 + - + +
470B SER* 1.3 77.0 - - - +
472B VAL* 1.3 68.5 + - + +
474B GLN* 3.6 17.7 + - - +
475B HIS* 3.1 22.7 + - - +
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Residues in contact with VAL 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B PHE* 3.9 14.6 - - + -
390B LEU* 4.0 17.3 - - + -
393B ALA* 3.7 30.1 - - + -
402B PHE* 3.9 16.6 - - + -
468B ILE* 3.0 21.6 + - + +
469B THR* 3.8 6.1 - - - +
471B VAL* 1.3 75.6 - - + +
473B GLN* 1.3 55.9 + - + +
475B HIS* 3.1 4.2 + - - +
476B GLN* 2.8 50.5 + - - +
605B GOL 4.0 17.3 - - - -
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Residues in contact with GLN 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B THR* 2.9 38.6 + - - +
470B SER* 3.6 7.1 - - - +
472B VAL* 1.3 77.9 - - + +
474B GLN* 1.3 57.5 + - + +
476B GLN* 3.2 7.6 + - - +
477B GLU* 2.8 53.0 + - - +
605B GOL 6.4 1.6 - - - -
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Residues in contact with GLN 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470B SER* 3.0 35.3 + - - +
471B VAL* 3.7 21.2 - - - +
473B GLN* 1.3 75.7 - - + +
475B HIS* 1.3 62.7 + - - +
477B GLU* 4.1 6.5 - - - +
478B ALA* 3.3 24.4 + - - +
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Residues in contact with HIS 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 3.7 20.2 - - + -
93B ILE* 5.2 0.7 - - + -
94B ARG* 3.4 33.2 + - - +
383B PHE* 3.5 26.4 - + + -
385B TYR* 2.7 33.1 + + - -
390B LEU* 3.8 20.0 - - + -
471B VAL 3.1 15.3 + - - +
472B VAL 3.1 6.3 + - - +
474B GLN* 1.3 76.4 - - - +
476B GLN* 1.3 69.8 + - + +
478B ALA* 3.4 5.3 + - - +
479B LEU* 3.2 31.1 + - + +
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Residues in contact with GLN 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B TYR* 5.0 4.1 + - - +
390B LEU* 4.2 12.6 - - + +
472B VAL* 2.8 31.0 + - + +
473B GLN* 3.9 7.6 - - - +
475B HIS* 1.3 87.0 - - + +
477B GLU* 1.3 62.0 + - + +
479B LEU* 3.3 27.9 + - + +
605B GOL 3.1 46.0 + - - -
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Residues in contact with GLU 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473B GLN* 2.8 40.7 + - - +
474B GLN* 4.1 6.5 - - - +
476B GLN* 1.3 77.4 - - + +
478B ALA* 1.3 58.9 + - - +
479B LEU 3.7 2.1 + - - +
480B VAL* 6.1 0.2 - - - +
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Residues in contact with ALA 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ARG* 4.8 5.6 + - - +
474B GLN 3.3 15.6 + - - +
475B HIS* 3.8 4.3 - - - +
476B GLN 3.3 0.4 - - - -
477B GLU* 1.3 77.6 - - - +
479B LEU* 1.3 60.4 + - - +
480B VAL* 3.7 5.9 + - - +
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Residues in contact with LEU 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ILE* 4.0 23.6 - - + -
94B ARG* 3.4 41.7 - - + +
385B TYR* 3.6 24.2 - - + +
475B HIS* 3.2 22.1 + - + +
476B GLN* 3.3 20.7 + - + +
477B GLU 3.3 2.0 - - - +
478B ALA* 1.3 76.4 - - - +
480B VAL* 1.3 76.7 + - - +
481B PRO* 3.8 20.0 - - + +
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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
------------------------------------------------------------
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