Contacts of the strand formed by residues 459 - 469 (chain D) in PDB entry 1F6A
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 LYS 459 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452D GLU* 5.5 2.1 - - - -
453D TRP 5.8 0.3 + - - -
456D SER* 3.6 33.9 + - - +
457D ARG 3.7 1.0 - - - -
458D ASP* 1.3 85.7 - - + +
460D ARG* 1.3 67.7 + - - +
461D THR* 5.6 0.2 - - - -
511D VAL 3.8 9.9 - - - +
512D THR* 5.8 2.2 - - + +
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Residues in contact with ARG 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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450D THR* 3.6 22.1 + - - +
451D PRO* 4.2 5.7 - - - +
452D GLU* 3.0 61.5 + - + +
457D ARG 5.6 4.0 + - - +
458D ASP 4.3 0.4 - - - -
459D LYS* 1.3 79.6 - - - +
461D THR* 1.3 62.9 + - - +
462D LEU* 5.1 3.3 - - + +
510D GLU* 5.1 0.7 - - - -
511D VAL* 3.1 37.8 + - + +
516D TRP* 4.3 30.6 - - + -
543D VAL* 2.9 40.3 - - + +
544D ASN* 4.6 7.3 + - - +
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Residues in contact with THR 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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465B LEU* 4.3 8.3 - - + -
467B GLN* 3.0 41.8 + - - +
449D ALA* 3.8 0.3 - - - -
450D THR* 3.0 46.7 + - - +
459D LYS 5.4 0.5 + - - -
460D ARG* 1.3 74.8 - - - +
462D LEU* 1.3 75.9 + - - +
508D ARG* 3.8 21.9 + - + +
510D GLU* 4.6 12.5 - - + +
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Residues in contact with LEU 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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465B LEU* 5.6 0.2 - - - -
448D PHE 3.4 17.9 - - - +
449D ALA* 3.6 18.6 - - + -
460D ARG* 5.2 3.6 - - + +
461D THR* 1.3 86.2 - - - +
463D ALA* 1.3 61.1 + - - +
478D TRP* 3.8 29.2 - - + -
508D ARG* 3.4 5.4 - - - +
509D LEU* 3.1 40.0 + - + +
511D VAL* 4.2 11.0 - - + -
522D PHE* 3.4 38.1 - - + -
541D VAL* 4.0 9.4 - - + -
542D SER* 6.0 1.3 - - - +
543D VAL* 5.5 7.2 - - + -
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Residues in contact with ALA 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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448B PHE* 5.7 7.0 - - + -
465B LEU* 4.5 8.1 - - + -
506B PHE* 3.8 28.5 - - + -
447D ALA* 3.7 1.7 - - - +
448D PHE* 2.9 44.9 + - + +
462D LEU* 1.3 77.0 - - - +
464D CYS* 1.3 62.4 + - - +
465D LEU 4.3 0.2 - - - -
478D TRP* 4.3 3.5 - - - -
506D PHE* 6.1 1.8 - - + -
507D SER 3.2 6.3 - - - -
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Residues in contact with CYS 464 (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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445D VAL* 3.5 24.7 - - - -
446D TYR 3.8 5.4 - - - -
447D ALA* 4.7 4.0 - - - -
463D ALA* 1.3 77.7 - - - +
465D LEU* 1.3 59.7 + - - +
466D ILE* 4.0 7.2 + - - +
478D TRP* 3.8 14.8 - - + -
505D VAL 3.9 1.4 - - - +
506D PHE* 3.7 5.1 - - - -
507D SER* 3.0 34.5 + - - -
524D CYS* 2.0 49.4 - - + -
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Residues in contact with LEU 465 (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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450B THR* 5.0 8.3 - - - +
461B THR* 4.3 14.4 - - + +
463B ALA* 4.5 9.2 - - + -
508B ARG* 4.7 2.9 - - - -
444D GLU 3.4 1.7 - - - +
445D VAL* 3.2 3.6 - - - -
446D TYR* 3.0 40.7 + - + +
448D PHE* 5.0 9.1 - - + -
463D ALA 4.3 0.2 - - - -
464D CYS* 1.3 71.0 - - - +
466D ILE* 1.3 86.2 + - - +
467D GLN* 3.9 30.3 - - + +
504D PHE* 4.4 10.8 - - + -
505D VAL 3.8 4.5 - - - +
506D PHE* 3.1 39.5 - - + -
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Residues in contact with ILE 466 (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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443D PRO* 3.6 24.2 - - + -
444D GLU 3.2 6.7 - - - +
445D VAL* 4.2 12.6 - - + -
464D CYS* 4.4 12.8 - - - +
465D LEU* 1.3 79.3 - - - +
467D GLN* 1.3 61.4 + - - +
469D PHE* 3.3 4.6 - - + -
474D ILE* 3.6 21.1 - - + -
476D VAL* 3.5 37.5 - - + -
504D PHE* 3.2 2.1 - - - -
505D VAL* 2.9 43.7 + - + +
507D SER* 6.2 0.4 - - - -
524D CYS* 4.7 0.2 - - - -
525D ARG 4.5 2.5 - - - +
526D ALA* 3.7 21.8 - - + -
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Residues in contact with GLN 467 (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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461B THR* 3.1 33.1 + - - +
508B ARG* 3.0 29.5 + - - +
443D PRO* 3.7 0.2 - - - +
444D GLU* 2.8 47.8 + - + +
446D TYR* 4.2 13.2 + - + -
465D LEU* 3.9 13.9 - - + +
466D ILE* 1.3 76.1 - - - +
468D ASN* 1.3 94.8 + - - +
469D PHE* 3.2 5.7 + - - -
503D PHE 3.3 8.1 - - - -
504D PHE* 3.7 15.5 - - + -
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Residues in contact with ASN 468 (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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508B ARG* 4.2 9.0 + - - -
510B GLU* 4.7 4.0 - - - +
441D ALA* 4.0 8.7 - - - +
442D ALA 2.8 16.3 - - - +
444D GLU* 2.6 40.5 + - - +
467D GLN* 1.3 99.6 + - - +
469D PHE* 1.3 55.2 + - - +
470D MET* 5.8 0.2 - - - -
498D THR* 4.2 12.3 + - - -
500D GLY* 5.3 7.3 - - - +
502D GLY* 4.3 12.7 - - - -
503D PHE 2.9 9.3 + - - -
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Residues in contact with PHE 469 (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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441D ALA 3.1 13.5 - - - +
442D ALA 3.8 5.8 - - - +
443D PRO* 3.8 10.3 - - + -
466D ILE* 3.3 23.8 - - + -
467D GLN* 3.5 11.9 - - - -
468D ASN* 1.3 77.5 - - - +
470D MET* 1.3 67.9 + - - +
471D PRO 3.4 11.7 - - - -
472D GLU 4.0 8.3 - - - -
474D ILE* 3.8 37.5 - - + -
495D PRO* 4.9 4.0 - - + -
502D GLY* 3.4 1.2 - - - -
503D PHE* 2.8 72.2 + - + +
504D PHE* 3.6 4.0 - - - -
505D VAL* 4.3 7.9 - - + -
528D HIS* 3.2 31.6 - + + +
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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