Contacts of the strand formed by residues 486 - 501 (chain X) in PDB entry 3Q0F
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 TYR 486 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C C 3.6 7.3 + - - -
7C T 2.9 28.0 + - - -
375X GLU* 3.1 8.7 - - - +
376X PHE* 2.9 48.6 + - + +
377X GLN 3.9 12.8 - - - -
378X TYR 4.2 7.6 - - - -
379X ARG* 3.4 39.9 - - + +
382X LEU* 4.7 4.7 - - + -
411X VAL* 4.0 12.8 - - + -
413X SER* 4.1 14.8 + - - -
469X ILE* 3.7 24.9 - - + -
470X ARG 3.2 4.3 - - - -
471X GLY* 3.9 11.0 - - - -
472X ILE* 3.9 1.0 - - - +
484X LYS 3.7 0.8 - - - -
485X ASN* 1.3 94.2 - - + +
487X VAL* 1.3 64.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 487 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373X GLY* 3.7 32.5 - - - +
374X ASP 3.5 2.7 - - - +
375X GLU* 3.9 12.1 - - + +
376X PHE* 5.0 0.2 - - - -
469X ILE* 3.2 8.4 - - - -
470X ARG* 2.8 34.7 + - + +
472X ILE* 3.4 38.4 - - + -
486X TYR* 1.3 75.6 - - - +
488X TYR* 1.3 67.8 + - - +
489X ASP* 3.4 1.6 + - - +
522X LEU* 4.6 21.1 - - + -
523X PRO* 5.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 488 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366X THR* 4.7 9.6 + - + +
367X VAL 5.9 1.1 - - - -
370X VAL* 4.0 28.7 - - + -
371X GLU 3.4 22.9 - - - +
372X VAL* 3.7 16.7 - - + -
373X GLY* 2.9 29.1 + - - -
374X ASP 3.0 15.5 + - - +
376X PHE* 4.3 13.2 - - + -
387X ILE* 4.5 13.7 - - + -
467X ARG* 3.9 26.8 - - + +
468X VAL 3.7 8.1 - - - -
469X ILE* 4.5 6.1 - - + -
487X VAL* 1.3 73.8 - - - +
489X ASP* 1.3 59.7 + - - +
490X GLY* 3.5 30.2 - - - -
491X LEU* 3.2 28.9 - - - +
522X LEU* 4.1 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 489 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372X VAL* 4.4 1.1 - - - -
468X VAL* 2.8 26.1 + - + +
470X ARG* 2.8 31.6 + - + -
487X VAL 3.4 1.3 + - - +
488X TYR* 1.3 73.0 - - - +
490X GLY* 1.3 61.2 + - - +
492X TYR* 2.5 29.5 + - - -
515X ARG* 3.0 34.7 + - - -
522X LEU* 3.5 25.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 490 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372X VAL* 3.6 10.9 - - - +
467X ARG* 3.7 1.0 - - - -
468X VAL 3.2 24.3 + - - -
488X TYR* 3.5 31.1 + - - -
489X ASP* 1.3 79.9 - - - +
491X LEU* 1.3 59.8 + - - -
492X TYR* 4.0 2.6 - - - -
519X GLN* 3.4 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 491 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365X GLY* 3.8 16.2 - - - -
366X THR* 3.7 26.0 - - - +
465X PRO* 4.3 15.9 - - + -
466X VAL 3.4 3.6 - - - +
467X ARG* 3.7 24.9 - - + +
488X TYR* 3.2 22.2 - - - +
490X GLY* 1.3 71.7 - - - -
492X TYR* 1.3 66.8 - - - +
515X ARG* 3.7 0.3 - - - -
516X ILE* 3.0 28.3 + - + +
519X GLN* 2.8 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 492 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423X SER 4.7 3.3 + - - -
424X ASP 3.7 8.5 - - - -
426X LEU* 4.2 16.4 - - + -
465X PRO* 3.5 5.5 - - - +
466X VAL* 2.8 36.5 + - - +
468X VAL* 3.5 28.0 - - + -
470X ARG* 3.1 14.5 + - - -
489X ASP* 2.5 44.3 + - - -
490X GLY 4.0 1.1 - - - -
491X LEU* 1.3 79.9 - - - +
493X LEU* 1.3 65.0 + - - +
513X LEU* 4.1 25.1 - - + -
514X ARG 3.3 13.5 - - - +
515X ARG* 3.3 43.0 - - + -
516X ILE* 4.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 493 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463X LYS* 3.7 26.5 - - + +
464X ASN 3.6 25.1 - - - +
465X PRO* 3.8 4.5 - - + -
492X TYR* 1.3 78.4 - - - +
494X VAL* 1.3 64.4 + - - +
495X GLU* 3.3 10.4 + - + +
513X LEU* 3.2 5.2 - - - -
514X ARG* 2.9 32.9 + - + +
516X ILE* 3.8 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 494 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456X LEU* 3.7 33.4 - - + +
459X SER* 4.0 20.5 + - - +
460X ILE* 3.3 49.3 - - + +
463X LYS* 6.0 0.4 - - - +
464X ASN 4.9 1.6 + - - -
466X VAL* 4.2 7.4 - - + -
493X LEU* 1.3 71.9 - - - +
495X GLU* 1.3 61.9 + - - +
496X GLU 4.1 13.2 - - - +
511X PHE* 4.4 16.8 - - + -
512X LYS 3.8 6.1 - - - +
513X LEU* 3.9 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 495 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460X ILE* 3.8 11.8 - - - +
493X LEU* 4.0 15.3 - - + +
494X VAL* 1.3 73.5 - - - +
496X GLU* 1.3 65.8 + - + +
512X LYS* 2.8 45.6 + - - +
514X ARG* 3.2 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 496 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460X ILE* 3.7 13.9 - - - -
494X VAL* 3.5 4.9 - - - +
495X GLU* 1.3 82.9 - - + +
497X TYR* 1.3 72.5 - - - +
498X TRP* 4.1 17.6 - - + +
511X PHE* 3.5 2.4 - - - -
512X LYS* 2.9 62.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 497 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449X LEU* 4.1 9.2 - - + +
457X LYS* 2.9 47.4 + - + +
460X ILE* 3.8 16.8 - - + -
496X GLU* 1.3 82.2 - - - +
498X TRP* 1.3 82.1 + - - +
499X GLU* 5.2 3.4 - - - -
509X PHE* 4.2 26.2 - + - -
510X LYS 3.1 14.6 - - - +
511X PHE* 3.4 28.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 498 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427X ILE* 4.0 29.2 - - + -
496X GLU* 4.1 20.2 - - - +
497X TYR* 1.3 95.4 - - - +
499X GLU* 1.3 77.2 + - - +
500X GLU* 3.4 25.2 + - + +
509X PHE* 3.5 4.0 - - - -
510X LYS* 2.9 56.3 + - + +
512X LYS* 4.0 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 499 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497X TYR* 5.2 3.9 - - + -
498X TRP* 1.3 86.3 - - - +
500X GLU* 1.3 63.9 + - - +
507X LEU* 3.5 41.2 - - + +
508X VAL 3.2 8.7 - - - +
509X PHE* 3.8 18.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 500 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498X TRP* 3.4 33.3 + - + +
499X GLU* 1.3 74.0 - - - +
501X THR* 1.3 69.4 + - - +
502X GLY 4.2 0.2 - - - -
507X LEU* 3.4 8.1 - - - +
508X VAL* 2.7 40.4 + - + +
510X LYS* 3.5 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 501 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500X GLU* 1.3 82.5 + - - +
502X GLY* 1.3 77.3 + - - +
505X GLY* 3.6 27.1 - - - +
506X LYS 3.5 3.1 - - - +
507X LEU* 4.2 11.4 - - - +
----------------------------------------------------------
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