Contacts of the helix formed by residues 450 - 464 (chain A) in PDB entry 6FWF
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 ASN 450 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445A LYS* 4.2 18.8 - - + +
446A GLY 5.2 0.4 - - - +
447A VAL* 3.5 37.3 + - + +
449A LYS* 1.3 79.2 - - - +
451A LEU* 1.3 72.2 + - - +
452A LEU* 3.2 14.0 + - - +
453A ALA* 2.8 24.9 + - - +
454A ILE* 2.8 19.6 + - - +
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Residues in contact with LEU 451 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450A ASN* 1.3 82.7 + - - +
452A LEU* 1.3 56.1 + - + +
453A ALA 3.2 0.3 + - - -
454A ILE* 4.0 12.1 - - + -
455A PHE* 2.8 44.2 + - + +
503A ALA 3.5 24.9 - - - +
506A ALA* 4.0 18.4 - - + +
507A PHE* 3.9 36.3 - - + +
510A TYR* 4.6 16.2 - - + -
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Residues in contact with LEU 452 (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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358A VAL* 3.6 33.4 - - + +
441A ALA* 3.7 36.1 - - + +
442A PHE* 5.0 0.2 - - - -
444A GLU* 4.0 16.6 - - + +
445A LYS* 3.2 23.7 - - + +
450A ASN* 3.2 7.8 + - + +
451A LEU* 1.3 78.1 - - + +
453A ALA* 1.3 55.1 + - - +
455A PHE* 5.0 3.4 - - + -
456A VAL* 3.1 28.7 - - + +
507A PHE* 4.1 20.9 - - + -
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Residues in contact with ALA 453 (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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445A LYS* 3.8 16.7 - - + +
448A ASP 3.4 26.0 - - - +
449A LYS* 4.0 7.4 + - + +
450A ASN 2.8 20.7 + - - +
452A LEU* 1.3 78.4 - - - +
454A ILE* 1.3 58.1 + - - +
455A PHE 3.6 0.2 - - - -
456A VAL* 3.5 8.3 - - - +
457A ALA* 2.8 28.6 + - - +
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Residues in contact with ILE 454 (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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11A LEU* 4.1 26.0 - - + -
449A LYS* 4.1 17.4 - - - +
450A ASN 2.8 12.8 + - - +
451A LEU* 3.5 21.8 - - + +
453A ALA* 1.3 69.6 - - - +
455A PHE* 1.3 60.9 + - - +
456A VAL 3.1 4.3 - - - -
457A ALA* 3.1 7.5 + - + +
458A SER* 2.8 30.3 + - - -
499A VAL* 5.4 6.5 - - + +
503A ALA* 3.8 19.7 - - + +
506A ALA* 6.4 0.4 - - + -
528A ALA* 5.7 11.2 - - + -
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Residues in contact with PHE 455 (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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351A GLY* 5.3 0.4 - - - -
354A LEU* 5.3 9.2 - - + -
358A VAL* 3.8 28.7 - - + -
434A MET* 3.6 33.7 - - + -
438A THR* 4.8 2.7 - - + -
451A LEU* 2.8 25.8 + - + +
452A LEU* 5.0 2.5 - - + -
454A ILE* 1.3 73.2 - - - +
456A VAL* 1.3 64.2 + - + +
458A SER* 3.2 13.6 + - - -
459A MET* 3.9 8.9 + - - +
500A PHE* 4.1 17.7 - + - -
503A ALA* 3.4 39.7 - - + +
504A ALA* 3.5 24.7 - - + -
507A PHE* 4.9 9.9 - + + -
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Residues in contact with VAL 456 (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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358A VAL* 5.3 1.3 - - + -
435A LEU* 5.8 1.1 - - + -
438A THR* 4.0 30.5 - - + +
441A ALA* 5.3 1.3 - - + -
442A PHE* 4.3 25.1 - - + +
445A LYS* 4.5 0.2 - - - -
452A LEU* 3.1 33.0 + - + +
453A ALA* 3.5 12.1 - - - +
454A ILE 3.1 0.6 - - - -
455A PHE* 1.3 85.8 - - + +
457A ALA* 1.3 57.7 + - - +
458A SER 3.5 0.2 - - - -
459A MET* 3.8 22.3 - - + +
460A VAL* 3.1 27.4 - - - +
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Residues in contact with ALA 457 (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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11A LEU* 5.6 5.4 - - + -
449A LYS* 5.5 4.3 - - - +
453A ALA 2.8 18.0 + - - +
454A ILE* 3.1 17.2 + - + +
456A VAL* 1.3 77.3 - - - +
458A SER* 1.3 59.2 + - - +
460A VAL* 3.4 6.9 + - - +
461A GLY* 2.8 26.0 + - - -
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Residues in contact with SER 458 (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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454A ILE 2.8 15.7 + - - -
455A PHE* 3.2 20.7 + - - -
457A ALA* 1.3 74.5 - - - +
459A MET* 1.3 54.0 + - - +
461A GLY* 3.2 2.9 + - - -
462A VAL* 2.8 37.9 + - - +
495A GLY 4.6 1.7 - - - +
499A VAL* 3.5 29.1 - - - +
500A PHE* 3.3 37.5 - - - -
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Residues in contact with MET 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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430A TRP* 3.3 21.8 - - + -
431A LEU* 3.3 17.2 - - + +
434A MET* 3.4 21.5 - - - -
435A LEU* 3.7 34.3 - - + +
438A THR* 3.1 31.4 - - - +
455A PHE 3.9 5.6 - - - +
456A VAL* 3.8 33.2 - - + +
458A SER* 1.3 77.2 + - - +
460A VAL* 1.3 62.0 + - + +
462A VAL* 4.4 0.9 - - - +
463A GLY 2.8 29.1 + - - -
500A PHE* 3.6 19.3 - - + -
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Residues in contact with VAL 460 (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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431A LEU* 4.1 16.8 - - + -
435A LEU* 5.4 7.4 - - + -
456A VAL 3.1 19.0 + - - +
457A ALA* 3.4 9.1 + - - +
458A SER 3.3 0.4 - - - -
459A MET* 1.3 86.8 - - + +
461A GLY* 1.3 57.4 + - - +
464A VAL* 3.1 50.7 + - + +
465A PHE* 5.1 2.0 - - + -
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Residues in contact with GLY 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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457A ALA 2.8 18.1 + - - -
458A SER* 3.5 5.8 - - - -
460A VAL* 1.3 73.5 - - - +
462A VAL* 1.3 57.0 + - - +
465A PHE* 3.3 42.8 - - - +
492A TRP* 4.3 2.8 - - - -
495A GLY 4.1 11.2 - - - +
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Residues in contact with VAL 462 (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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348A LEU* 4.8 2.7 - - + -
427A LEU* 4.1 12.0 - - + +
430A TRP* 4.2 15.0 - - + -
458A SER 2.8 22.2 + - - +
459A MET* 3.7 6.7 - - - +
460A VAL 3.2 0.2 - - - -
461A GLY* 1.3 71.0 - - - +
463A GLY* 1.3 67.3 + - - +
464A VAL 3.0 5.9 + - - -
465A PHE 3.4 2.4 + - - -
466A TYR 4.0 0.5 + - - -
492A TRP* 2.9 38.2 + - + +
495A GLY 4.0 1.8 - - - +
496A PHE* 3.2 60.3 - - + -
500A PHE* 4.2 7.4 - - + -
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Residues in contact with GLY 463 (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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424A MET* 4.8 1.0 - - - +
427A LEU* 3.9 21.9 - - - +
428A LEU* 3.3 25.6 - - - +
430A TRP* 4.0 11.9 - - - -
431A LEU* 4.0 13.7 - - - -
459A MET 2.8 19.6 + - - -
462A VAL* 1.3 75.1 - - - +
464A VAL* 1.3 60.4 + - - +
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Residues in contact with VAL 464 (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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424A MET* 4.5 2.5 - - - +
428A LEU* 5.2 4.5 - - + -
431A LEU* 4.3 9.2 - - + -
460A VAL* 3.1 33.1 + - + +
462A VAL 3.1 0.6 - - - -
463A GLY* 1.3 79.9 - - - +
465A PHE* 1.3 71.8 + - + +
466A TYR* 2.9 4.3 + - - +
467A ALA* 2.8 44.5 + - + +
468A PRO* 5.6 1.3 - - + -
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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
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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