Contacts of the strand formed by residues 541 - 551 (chain O) in PDB entry 2O93
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 ARG 541 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463O ALA* 2.6 49.5 + - + +
471O HIS* 3.2 13.3 + - - -
538O LYS 5.8 1.6 - - - +
539O ASN* 3.7 5.8 + - - +
540O THR* 1.3 78.3 - - - +
542O VAL* 1.3 71.0 + - - +
566O PRO* 3.4 30.3 - - - +
567O ILE 3.5 7.5 - - - +
568O GLU* 3.0 26.6 + - - +
577O LEU* 6.5 0.7 - - - -
579O MET* 5.5 9.1 - - - +
669O GLN* 3.5 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 542 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460O ILE* 3.6 17.0 - - + -
461O GLY 3.2 9.2 - - - +
463O ALA* 4.0 3.8 - - - -
471O HIS* 3.2 24.2 - - + -
474O TYR* 3.3 25.4 - - + -
518O ILE* 4.5 11.0 - - + -
541O ARG* 1.3 85.0 - - - +
543O ARG* 1.3 66.8 + - - +
566O PRO* 3.5 1.2 - - - +
567O ILE* 2.6 47.5 + - + +
569O CYS* 3.5 25.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 543 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460O ILE* 3.8 6.6 - - - +
461O GLY 2.8 35.6 + - - +
462O THR* 2.8 27.2 + - - +
463O ALA* 3.6 15.6 - - + +
464O ASP* 4.6 6.3 + - - +
466O ARG 5.1 1.6 + - - -
468O LEU* 2.9 33.7 - - + +
542O VAL* 1.3 79.3 - - - +
544O LEU* 1.3 63.4 + - - +
545O VAL* 3.3 2.1 + - + +
563O ALA* 4.3 12.6 - - + +
564O SER* 2.8 18.8 + - - +
565O ASN 2.9 27.1 - - - +
566O PRO* 3.6 10.5 - - + -
567O ILE* 5.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 544 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416O PRO* 3.6 38.6 - - + -
433O VAL* 4.1 25.1 - - + -
441O PRO* 4.5 13.5 - - + -
458O ILE* 4.9 12.6 - - + -
460O ILE* 3.8 22.4 - - + -
513O ILE* 5.7 2.7 - - + -
516O ALA* 5.3 7.6 - - + -
518O ILE* 5.5 2.2 - - + -
543O ARG* 1.3 70.3 - - - +
545O VAL* 1.3 59.9 - - - +
546O PHE* 3.9 22.8 - - + -
563O ALA* 2.9 5.4 - - - +
564O SER* 2.8 40.5 + - - +
567O ILE* 4.2 7.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 545 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458O ILE* 3.3 11.0 - - - +
459O PHE* 3.1 71.0 + - + +
461O GLY* 3.4 19.3 - - - +
468O LEU* 4.4 8.5 - - + -
543O ARG 3.3 17.3 - - - +
544O LEU* 1.3 74.7 - - - +
546O PHE* 1.3 65.9 + - - +
561O GLN* 4.0 24.0 - - + +
563O ALA* 4.1 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 546 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410O LEU* 4.4 7.2 - - + -
412O ILE* 3.4 33.0 - - + -
416O PRO* 6.4 0.2 - - + -
441O PRO* 5.5 3.1 - - + -
443O VAL* 3.3 28.0 - - + -
456O LEU* 3.9 14.8 - - + -
457O GLN 3.7 4.3 - - - -
458O ILE* 3.6 39.9 - - + -
513O ILE* 3.9 13.7 - - + -
544O LEU* 3.9 38.4 - - + -
545O VAL* 1.3 75.6 - - - +
547O ARG* 1.3 63.2 + - - +
561O GLN* 2.9 31.1 - - - +
562O THR 3.1 16.6 + - - +
564O SER* 4.9 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 547 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395O VAL* 2.8 31.7 + - - +
396O PRO 3.2 7.9 + - - -
397O LEU* 2.7 52.1 + - - +
399O TRP 4.1 6.7 + - - -
401O LEU* 4.7 12.4 - - + +
410O LEU* 4.1 1.3 - - - +
456O LEU* 3.9 3.6 - - - +
457O GLN* 3.2 55.3 + - + +
459O PHE* 4.0 11.6 - - + -
546O PHE* 1.3 78.9 - - - +
548O VAL* 1.3 59.9 + - - +
549O HIS* 5.1 7.1 - - + -
559O SER* 6.3 0.7 - - - -
560O LEU 2.9 18.8 - - - +
561O GLN* 2.4 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 548 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410O LEU* 4.1 14.1 - - + -
445O LEU* 3.5 43.5 - - + -
454O LEU* 4.0 14.6 - - + -
455O GLY 2.9 26.2 - - - +
456O LEU* 4.4 4.7 - - + -
457O GLN* 5.8 0.2 - - - -
503O LEU* 4.1 11.2 - - + -
547O ARG* 1.3 72.7 - - - +
549O HIS* 1.3 76.6 + - - +
550O ILE* 3.6 7.2 + - + +
559O SER* 4.0 1.8 - - - -
560O LEU* 3.3 20.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 549 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393O SER* 2.7 38.1 + - - -
394O SER* 4.0 2.8 - - - -
395O VAL* 3.6 30.6 + - + -
401O LEU* 6.4 0.7 - - + -
454O LEU* 3.6 14.9 - - - +
455O GLY 4.5 2.7 + - - +
457O GLN* 3.7 28.1 + - - +
547O ARG* 4.2 8.4 + - + -
548O VAL* 1.3 83.4 - - - +
550O ILE* 1.3 63.3 + - - +
551O PRO* 4.1 2.0 - - - +
557O ILE* 4.5 12.5 - - + +
558O VAL 4.2 2.8 + - - -
559O SER* 3.5 18.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 550 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408O TYR* 3.5 52.5 - - + +
445O LEU* 3.4 35.4 - - + -
448O TYR* 3.8 23.6 - - + -
454O LEU* 4.0 10.1 - - + -
548O VAL* 3.6 11.8 + - + +
549O HIS* 1.3 79.2 - - - +
551O PRO* 1.3 69.7 - - + +
552O GLU 3.7 1.1 + - - -
557O ILE* 3.4 7.5 - - - -
558O VAL* 3.0 37.8 + - + +
560O LEU* 4.6 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 551 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408O TYR* 5.6 0.2 + - - -
448O TYR* 4.8 9.7 - - + +
450O GLU* 5.1 7.1 - - - +
452O LYS* 6.3 2.5 - - + -
454O LEU* 3.9 20.9 - - + -
549O HIS 4.1 2.2 - - - +
550O ILE* 1.3 91.6 - - + +
552O GLU* 1.3 64.8 + - - +
553O SER 3.9 1.0 + - - -
556O ARG 4.3 3.8 - - - +
557O ILE* 4.8 9.9 - - + -
----------------------------------------------------------
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