Contacts of the strand formed by residues 552 - 560 (chain B) in PDB entry 2O1S
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 ALA 552 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B LYS 3.3 3.2 + - - +
506B LEU* 3.3 23.5 - - + +
507B ALA 3.2 20.6 + - - -
550B HIS* 3.5 6.2 - - - +
551B GLU* 1.3 84.8 - - + +
553B LEU* 1.3 65.1 + - - +
580B VAL* 4.8 2.7 - - - -
581B PRO* 3.4 23.6 - - + +
618B TRP* 3.9 13.9 - - + -
619B LEU* 4.8 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B LEU* 4.9 1.6 - - - -
507B ALA* 3.4 31.4 - - + +
509B LEU* 4.0 12.8 - - + -
543B ILE* 4.4 9.9 - - + +
546B MSE 3.9 23.8 - - + +
547B ALA* 4.4 9.0 - - + -
550B HIS* 5.2 0.2 - - + -
552B ALA* 1.3 75.5 - - - +
554B VAL* 1.3 63.0 + - - +
569B VAL* 4.3 16.2 - - + -
573B LEU* 3.7 28.3 - - + -
580B VAL* 4.0 11.4 - - + -
581B PRO 2.9 7.6 + - - +
582B VAL* 3.1 14.2 - - + -
583B LEU 2.8 22.7 + - - -
618B TRP* 3.9 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 554 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B LEU* 5.2 9.2 - - + -
507B ALA 3.0 7.6 + - - +
508B ILE* 3.1 39.4 - - + +
509B LEU* 2.7 32.3 + - - +
553B LEU* 1.3 75.9 - - - +
555B THR* 1.3 62.6 + - - +
556B VAL* 4.6 4.9 - - + -
583B LEU* 3.4 23.1 - - + +
585B ILE* 3.8 26.2 - - + -
615B ILE* 4.1 17.5 - - + -
618B TRP* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 555 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B LEU* 3.4 15.9 - - + -
511B PHE* 4.4 4.0 - - + -
554B VAL* 1.3 76.5 - - - +
556B VAL* 1.3 60.6 + - - +
557B GLU* 4.9 1.9 + - - -
566B GLY* 3.4 27.1 - - - -
569B VAL* 3.8 26.5 - - + -
582B VAL* 4.0 12.1 - - + -
583B LEU 2.9 3.7 + - - +
584B ASN* 2.8 29.6 + - - +
585B ILE* 2.8 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 556 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B ILE* 4.1 21.3 - - + -
509B LEU 2.9 9.2 + - - +
510B ASN* 3.8 22.4 - - - +
511B PHE* 2.8 32.5 + - - +
514B LEU* 3.8 26.7 - - + -
518B ALA* 4.5 4.0 - - + -
554B VAL* 4.6 2.9 - - + -
555B THR* 1.3 79.2 - - - +
557B GLU* 1.3 66.8 + - - +
585B ILE* 3.6 18.2 - - + -
611B MSE 4.0 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 557 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B LEU* 4.0 6.4 - - + +
511B PHE* 3.6 22.7 - - + +
514B LEU* 4.0 10.5 - - - +
555B THR* 4.9 1.6 + - - -
556B VAL* 1.3 79.1 - - - +
558B GLU* 1.3 58.7 + - - +
559B ASN* 3.3 29.1 + - - +
560B ALA 4.1 8.9 - - - +
561B ILE* 4.8 4.9 - - - +
564B GLY* 3.4 7.5 - - - -
565B ALA* 2.9 26.4 + - + +
566B GLY* 2.9 28.1 + - - -
567B SER 4.5 0.5 + - - -
584B ASN* 5.6 2.8 - - - +
585B ILE 3.1 11.9 + - - +
586B GLY* 3.2 19.6 - - - -
606B LEU* 5.2 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 558 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B ALA 3.9 4.3 - - - +
422B GLY* 3.4 18.6 - - - -
423B ILE* 3.2 28.5 + - + +
433B GLY 4.4 0.2 - - - +
437B LEU* 5.3 1.4 - - - +
475B ARG* 3.4 23.7 + - - +
477B PRO* 4.5 2.9 - - - +
511B PHE 4.3 5.3 + - - -
512B GLY* 6.6 0.2 - - - -
513B THR* 4.8 9.0 + - - +
514B LEU* 3.8 30.9 - - + +
557B GLU* 1.3 70.6 - - - +
559B ASN* 1.3 58.1 + - - +
587B LEU* 4.2 11.6 - - + +
601B ARG* 2.9 47.3 + - - +
606B LEU* 4.4 2.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 559 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B ALA 2.9 18.4 + - - +
436B ASP 3.1 7.1 + - - -
437B LEU* 2.8 37.0 + - + +
438B SER* 2.9 27.7 + - - -
475B ARG* 3.4 12.4 + - - +
557B GLU* 3.3 21.5 + - + +
558B GLU* 1.3 78.4 - - - +
560B ALA* 1.3 87.6 + - - +
561B ILE 3.3 0.2 + - - -
564B GLY* 3.9 1.0 - - - -
586B GLY* 3.6 4.7 - - - -
587B LEU* 2.8 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 560 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A CYS* 4.4 6.5 - - + +
434B ALA* 2.7 19.5 + - + +
435B PHE* 3.9 23.3 - - + -
438B SER* 4.2 2.0 - - - +
557B GLU* 3.6 5.9 - - - +
559B ASN* 1.3 90.7 + - - +
561B ILE* 1.3 65.4 + - - +
562B MSE 3.5 14.8 + - + +
564B GLY* 3.7 3.8 + - - -
587B LEU* 3.7 13.4 - - + +
588B PRO 5.5 3.8 - - - +
----------------------------------------------------------
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