Contacts of the strand formed by residues 459 - 469 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B GLU* 5.5 2.3 - - - -
453B TRP 5.8 0.2 + - - -
456B SER* 3.6 33.9 + - - +
457B ARG 3.7 1.6 - - - -
458B ASP* 1.3 86.8 - - + +
460B ARG* 1.3 68.8 + - - +
461B THR* 5.6 0.4 - - - -
511B VAL 3.8 10.1 - - - +
512B THR* 5.8 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B THR* 3.6 22.8 + - - +
451B PRO* 4.2 4.6 - - - +
452B GLU* 3.0 60.3 + - + +
457B ARG 5.6 3.1 + - - +
458B ASP 4.3 0.2 - - - -
459B LYS* 1.3 81.2 - - - +
461B THR* 1.3 62.5 + - - +
462B LEU* 5.2 3.7 - - + +
510B GLU* 5.1 0.4 - - - -
511B VAL* 3.1 36.8 + - + +
516B TRP* 4.4 30.8 - - + -
543B VAL* 2.9 40.7 - - + +
544B ASN* 4.6 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B ALA* 3.8 0.3 - - - -
450B THR* 3.1 45.5 + - - +
459B LYS 5.4 0.5 + - - -
460B ARG* 1.3 74.2 - - - +
462B LEU* 1.3 76.3 + - - +
508B ARG* 3.7 23.4 + - + +
510B GLU* 4.6 12.1 - - + +
465D LEU* 4.3 7.4 - - + -
467D GLN* 3.1 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B PHE 3.4 17.7 - - - +
449B ALA* 3.6 18.2 - - + -
460B ARG* 5.2 4.0 - - + +
461B THR* 1.3 86.2 - - - +
463B ALA* 1.3 61.6 + - - +
478B TRP* 3.8 28.9 - - + -
508B ARG* 3.4 5.5 - - - +
509B LEU* 3.1 40.3 + - + +
511B VAL* 4.2 10.8 - - + -
522B PHE* 3.4 39.0 - - + -
541B VAL* 4.0 9.4 - - + -
542B SER* 5.9 1.1 - - - +
543B VAL* 5.5 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B ALA* 3.7 1.9 - - - +
448B PHE* 2.9 44.2 + - + +
461B THR 4.4 0.2 + - - -
462B LEU* 1.3 76.5 - - - +
464B CYS* 1.3 63.0 + - - +
465B LEU 4.3 0.2 - - - -
478B TRP* 4.3 3.1 - - - -
506B PHE* 6.1 1.8 - - + -
507B SER 3.2 6.7 - - - -
448D PHE* 5.8 6.1 - - + -
465D LEU* 4.5 8.1 - - + -
506D PHE* 3.7 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 464 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B VAL* 3.5 24.7 - - - -
446B TYR 3.8 5.6 - - - -
447B ALA* 4.4 4.5 - - - +
463B ALA* 1.3 77.0 - - - +
465B LEU* 1.3 57.9 + - - +
466B ILE* 4.0 7.4 + - - +
478B TRP* 3.8 15.0 - - + -
505B VAL 3.9 1.2 - - - +
506B PHE* 3.7 5.4 - - - -
507B SER* 3.0 33.2 + - - +
524B CYS* 2.0 49.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 465 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B GLU 3.4 1.6 - - - +
445B VAL* 3.2 3.6 - - - -
446B TYR* 3.1 40.7 + - + +
448B PHE* 5.0 9.1 - - + -
463B ALA 4.3 0.2 - - - -
464B CYS* 1.3 70.7 - - - +
466B ILE* 1.3 87.7 + - - +
467B GLN* 3.9 29.6 - - + +
504B PHE* 4.4 11.0 - - + -
505B VAL 3.8 5.2 - - - +
506B PHE* 3.1 38.8 - - + -
450D THR* 5.1 7.0 - - - +
461D THR* 4.3 14.8 - - + -
463D ALA* 4.5 11.2 - - + -
508D ARG* 4.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 466 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B PRO* 3.6 31.2 - - + -
444B GLU 3.2 6.7 - - - +
445B VAL* 4.2 13.0 - - + -
464B CYS* 4.3 13.2 - - - +
465B LEU* 1.3 81.2 - - - +
467B GLN* 1.3 61.4 + - - +
469B PHE* 3.3 5.2 - - + -
474B ILE* 3.6 14.4 - - + -
476B VAL* 3.5 37.9 - - + -
504B PHE* 3.2 2.4 - - - -
505B VAL* 2.9 40.7 + - + +
507B SER* 6.2 0.2 - - - -
524B CYS* 4.6 0.7 - - - -
525B ARG 4.5 2.2 - - - +
526B ALA* 3.7 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 467 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B PRO* 3.7 0.5 - - - +
444B GLU* 2.8 47.6 + - + +
446B TYR* 4.1 13.3 + - + -
465B LEU* 3.9 11.3 - - + +
466B ILE* 1.3 74.6 - - - +
468B ASN* 1.3 95.4 + - - +
469B PHE* 3.2 6.8 + - - -
503B PHE 3.3 7.6 - - - -
504B PHE* 3.7 14.4 - - + -
450D THR* 5.8 0.2 - - - +
461D THR* 3.0 32.8 + - - +
508D ARG* 2.9 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 468 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B ALA* 4.0 8.8 - - - +
442B ALA 2.8 16.5 - - - +
444B GLU* 2.6 42.0 + - - +
467B GLN* 1.3 98.7 - - - +
469B PHE* 1.3 56.8 + - - +
470B MET* 5.9 0.2 - - - -
498B THR* 4.2 9.1 + - - -
500B GLY* 5.4 7.1 - - - +
502B GLY* 4.3 12.5 - - - -
503B PHE 2.9 9.5 + - - +
508D ARG* 4.1 14.6 + - - -
510D GLU* 4.5 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 469 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B ALA 3.0 12.8 - - - +
442B ALA 3.8 5.4 - - - +
443B PRO* 3.8 9.2 - - + -
466B ILE* 3.3 22.0 - - + -
467B GLN* 3.5 11.2 - - - -
468B ASN* 1.3 77.7 - - - +
470B MET* 1.3 69.2 + - - +
471B PRO 3.4 12.8 - - - -
472B GLU 4.0 8.7 - - - -
474B ILE* 3.8 36.8 - - + -
495B PRO* 4.9 3.1 - - + -
502B GLY* 3.4 1.6 - - - -
503B PHE* 2.8 73.2 + - + -
504B PHE* 3.6 4.5 - - - -
505B VAL* 4.4 7.2 - - + -
528B HIS* 3.2 31.2 - + + +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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