Contacts of the helix formed by residues 449 - 463 (chain D) in PDB entry 1FSJ
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 449 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405D ARG 3.7 9.0 - - - -
406D ASN* 4.3 14.4 - - - -
407D LYS 4.2 1.3 - - - -
447D PHE* 3.3 2.3 - - - +
448D LYS* 1.3 81.4 - - - +
450D PHE* 1.3 66.4 + - - +
451D ASP* 3.5 9.5 + - - +
452D ASP* 3.1 28.9 + - - +
453D PHE 3.1 9.7 + - - -
514D TYR* 3.0 17.9 + - - -
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Residues in contact with PHE 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405D ARG* 2.8 48.3 + - + +
449D SER* 1.3 72.1 - - - +
451D ASP* 1.3 60.1 + - - +
453D PHE* 3.2 23.4 + + + +
454D ARG* 2.9 27.8 + - + +
501D LEU* 3.8 42.6 - - + -
503D HIS* 3.5 22.0 - + - -
513D VAL* 3.3 42.8 - - + -
514D TYR* 3.3 8.3 + + - -
519D ILE* 3.8 10.1 - - + -
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Residues in contact with ASP 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406D ASN* 6.1 0.8 - - - +
449D SER* 3.1 8.8 + - - +
450D PHE* 1.3 81.4 - - - +
452D ASP* 1.3 56.3 + - - +
454D ARG* 2.9 39.4 + - - +
455D LYS* 3.0 27.0 + - - +
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Residues in contact with ASP 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446D GLU 5.1 0.2 - - - +
447D PHE* 3.8 13.3 - - - +
448D LYS* 3.2 36.9 + - + +
449D SER* 3.1 25.5 + - - +
451D ASP* 1.3 80.2 - - - +
453D PHE* 1.3 60.4 + - - +
455D LYS* 3.4 18.9 + - - +
456D ALA* 3.1 21.0 + - - +
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Residues in contact with PHE 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411D ALA* 4.1 8.3 - - + -
434D ILE* 5.1 4.0 - - + -
442D LEU* 3.8 17.5 - - + -
447D PHE* 3.7 33.2 - + + -
449D SER 3.1 5.5 + - - -
450D PHE* 3.2 25.1 + + - +
452D ASP* 1.3 73.2 - - - +
454D ARG* 1.3 64.3 + - - +
456D ALA* 3.1 3.8 + - - +
457D VAL* 2.9 49.8 + - + +
501D LEU* 4.2 7.0 - - + -
514D TYR* 3.9 28.9 - + + -
516D MET* 3.7 33.4 - - + -
519D ILE* 3.6 23.1 - - + -
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Residues in contact with ARG 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450D PHE* 2.9 18.0 + - + +
451D ASP* 2.9 45.8 + - - +
453D PHE* 1.3 76.8 - - - +
455D LYS* 1.3 78.8 + - - +
457D VAL* 3.2 10.7 + - - +
458D TRP* 3.2 35.2 + - + +
482D GLY 2.9 29.3 + - - -
483D TYR* 4.2 4.4 - - - +
484D SER* 3.2 27.3 + - - +
499D TYR 6.0 0.4 - - - -
501D LEU* 3.8 34.5 - - + +
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Residues in contact with LYS 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451D ASP* 3.0 14.5 + - - +
452D ASP* 3.5 20.1 + - - +
454D ARG* 1.3 88.9 - - - +
456D ALA* 1.3 57.6 + - - +
458D TRP 3.4 0.3 + - - -
459D GLU* 2.6 63.1 + - - +
481D LYS 4.1 11.7 - - - -
482D GLY* 3.6 23.6 - - - +
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Residues in contact with ALA 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442D LEU* 4.0 14.1 - - + -
447D PHE* 3.5 31.9 - - + -
452D ASP 3.1 7.7 + - - +
453D PHE 3.1 6.7 + - - +
455D LYS* 1.3 74.4 - - - +
457D VAL* 1.3 65.5 - - - +
459D GLU* 3.8 13.1 - - - +
460D GLU* 2.9 30.6 + - + +
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Residues in contact with VAL 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422D TRP* 5.8 2.9 - - + -
434D ILE* 4.7 15.9 - - + -
435D PRO* 6.2 1.1 - - + -
438D ILE* 4.3 14.8 - - + +
442D LEU* 3.8 13.4 - - + +
453D PHE* 2.9 51.8 + - + +
454D ARG* 3.2 10.5 + - - +
456D ALA* 1.3 76.9 - - - +
458D TRP* 1.3 73.1 + - + +
460D GLU* 3.2 3.8 + - - +
461D VAL* 2.8 35.8 + - + +
501D LEU* 4.6 9.2 - - + -
521D VAL* 5.8 2.2 - - + -
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Residues in contact with TRP 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422D TRP* 4.5 10.5 - + - -
423D LEU* 4.4 11.0 - - + -
454D ARG* 3.2 48.9 + - + +
455D LYS 4.0 2.7 - - - +
457D VAL* 1.3 82.2 - - + +
459D GLU* 1.3 65.8 + - - +
461D VAL* 3.2 29.9 + - + +
462D SER 2.9 18.2 + - - -
471D LEU* 5.8 0.4 - - + -
479D VAL* 3.4 22.0 - - + +
482D GLY 4.1 6.5 - - - +
483D TYR 3.7 16.2 - - - +
484D SER* 3.4 17.1 + - - -
485D PRO* 3.6 29.8 - - + -
499D TYR* 3.8 27.0 + + + -
501D LEU* 4.7 13.0 - - + +
521D VAL* 4.1 24.7 - - + -
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Residues in contact with GLU 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455D LYS* 2.6 56.6 + - - +
456D ALA* 3.8 15.6 - - - +
458D TRP* 1.3 75.0 - - - +
460D GLU* 1.3 64.1 + - + +
462D SER* 2.6 22.3 + - - -
463D LYS* 3.3 31.4 + - - +
479D VAL 3.5 8.0 + - - +
480D SER 4.2 7.1 - - - +
481D LYS 4.3 4.0 - - - +
482D GLY* 3.6 15.9 - - - +
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Residues in contact with GLU 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438D ILE* 3.6 24.0 - - + +
441D LYS* 3.7 32.0 - - + +
442D LEU* 4.0 22.3 - - + +
445D LYS* 4.9 7.8 + - - -
456D ALA* 2.9 23.3 + - + +
457D VAL 3.6 1.3 - - - +
459D GLU* 1.3 73.2 - - + +
461D VAL* 1.3 67.9 + - - +
463D LYS* 3.1 33.6 + - - +
464D ASP* 3.2 14.4 + - - +
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Residues in contact with VAL 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422D TRP* 3.9 27.1 - - + -
423D LEU* 6.1 0.4 - - + -
438D ILE* 3.6 16.1 - - + +
457D VAL* 2.8 21.7 + - + +
458D TRP* 3.5 32.3 - - + +
460D GLU* 1.3 77.6 - - - +
462D SER* 1.3 62.3 + - - +
464D ASP* 3.1 24.5 + - - +
467D LEU* 4.1 23.6 - - + +
468D SER* 3.3 11.0 + - - -
471D LEU* 4.5 11.0 - - + -
479D VAL* 5.0 0.9 - - + -
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Residues in contact with SER 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458D TRP 2.9 6.5 + - - -
459D GLU* 2.6 19.7 + - - -
461D VAL* 1.3 76.5 - - - +
463D LYS* 1.3 66.1 + - - +
464D ASP 3.4 1.4 + - - -
465D PRO* 5.9 0.2 - - - +
468D SER* 4.1 12.2 + - - -
476D LYS 4.7 0.9 - - - -
479D VAL* 3.5 31.6 - - - +
480D SER* 3.4 29.7 - - - -
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Residues in contact with LYS 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459D GLU* 3.4 35.9 + - - +
460D GLU* 3.1 27.7 + - - +
462D SER* 1.3 84.3 - - - +
464D ASP* 1.3 58.2 + - - +
465D PRO* 3.4 11.3 - - - +
480D SER 5.5 4.0 - - - -
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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
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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