Contacts of the helix formed by residues 540 - 552 (chain A) in PDB entry 1O95
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 PHE 540 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG* 3.7 18.8 - - - +
427A HIS* 6.4 0.2 - - - -
431A VAL* 3.8 28.3 - - + -
434A LEU* 4.2 7.2 - - + -
437A LEU* 4.4 4.0 - - + -
440A TRP* 4.3 16.4 - + + -
491A TRP* 6.0 1.3 - + - -
539A TYR* 1.3 119.1 - + + +
541A MET* 1.3 98.5 + - + +
542A ALA 3.7 0.4 - - - -
543A PRO* 3.6 2.9 - - - +
544A SER* 2.8 38.5 + - - -
568A MET* 4.0 15.9 - - - -
573A GLU* 4.8 2.0 - - - +
681A ILE* 5.7 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 541 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A VAL* 4.2 11.2 - - + -
434A LEU* 4.4 6.3 - - - -
491A TRP* 3.8 47.1 - - + +
517A PRO* 4.1 15.0 - - + -
521A MET* 4.0 22.9 - - + +
537A ASP* 4.2 3.1 + - - +
539A TYR 3.1 4.0 + - - -
540A PHE* 1.3 101.7 - - + +
542A ALA* 1.3 71.9 + - - +
544A SER* 2.9 11.6 + - - -
545A LEU* 3.0 30.1 + - + +
641A VAL* 3.8 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 542 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A ILE* 4.1 7.4 - - + +
535A ASN* 3.6 37.5 - - + +
537A ASP* 5.0 0.6 + - - +
539A TYR 4.4 2.4 + - - +
541A MET* 1.3 75.5 - - - +
543A PRO* 1.3 64.2 - - + +
545A LEU* 2.6 30.2 + - - +
546A ALA* 2.9 12.3 + - - +
558A ILE* 5.1 4.3 - - + -
564A LEU* 4.0 6.7 - - + -
641A VAL* 3.3 18.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A TYR 3.6 15.0 - - - +
540A PHE* 3.6 13.2 - - - +
542A ALA* 1.3 96.1 - - + +
544A SER* 1.3 63.3 + - - +
546A ALA* 3.6 10.3 + - + +
547A GLU* 3.0 16.1 + - - -
558A ILE* 5.4 1.1 - - + -
564A LEU* 3.8 19.9 - - + -
565A ALA* 4.4 7.0 - - + -
568A MET* 4.2 11.4 - - - -
577A MET* 3.5 34.2 - - + +
578A MET* 5.5 1.1 - - + -
581A LEU* 4.0 11.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG* 2.7 35.1 + - - +
434A LEU* 4.4 23.8 - - - -
435A PRO* 4.5 3.9 - - - +
437A LEU* 4.5 0.5 - - - +
540A PHE* 2.8 28.7 + - - -
541A MET 2.9 6.0 + - - -
542A ALA 2.7 0.4 + - - -
543A PRO* 1.3 79.1 - - - +
545A LEU* 1.3 55.9 + - - +
547A GLU* 2.8 32.6 + - - +
548A LYS* 3.0 9.5 + - - +
577A MET* 4.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A LEU* 4.0 23.3 - - + -
517A PRO* 4.4 15.3 - - + -
520A VAL* 3.7 36.8 - - + -
521A MET* 4.8 3.8 - - + -
533A ILE* 3.8 11.9 - - + -
541A MET* 3.0 24.3 + - - +
542A ALA* 2.6 14.2 + - - +
544A SER* 1.3 67.4 - - - +
546A ALA* 1.3 68.1 + - - +
548A LYS* 3.0 6.1 + - + +
549A LEU* 2.8 30.8 + - + +
639A VAL* 3.5 28.9 - - + -
641A VAL* 4.7 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A ILE* 3.5 14.6 - - + +
542A ALA 2.9 9.2 + - - +
543A PRO* 3.6 11.0 - - + +
545A LEU* 1.3 80.6 - - - +
547A GLU* 1.3 62.6 + - - +
549A LEU* 3.2 1.8 + - - +
550A ALA* 3.0 25.9 + - - +
556A VAL* 4.3 6.9 - - + +
558A ILE* 3.6 31.9 - - + -
581A LEU* 4.4 4.5 - - + -
586A VAL* 4.1 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG* 3.6 22.5 + - - +
273A PHE* 5.9 0.6 - - - -
435A PRO* 3.6 31.3 - - + +
543A PRO 3.0 12.6 + - - +
544A SER* 2.8 17.8 + - - +
546A ALA* 1.3 70.6 - - - +
548A LYS* 1.3 54.8 + - - +
550A ALA* 4.7 0.4 - - - -
551A THR* 3.1 30.7 + - - +
577A MET* 3.8 5.5 - - + +
580A ARG* 2.9 42.7 + - + -
581A LEU* 4.5 5.1 - - + +
584A LEU* 3.7 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ALA 4.7 11.7 + - - -
434A LEU* 4.4 14.1 - - + +
435A PRO* 3.6 26.9 - - + +
520A VAL* 4.3 33.4 - - + -
521A MET* 4.9 9.1 + - - +
523A GLY* 6.2 1.6 - - - -
544A SER 3.0 6.6 + - - +
545A LEU* 3.0 9.8 + - + +
547A GLU* 1.3 75.0 - - - +
549A LEU* 1.3 66.7 + - + +
551A THR* 3.1 6.9 + - - -
552A ALA* 2.8 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A VAL* 4.8 16.8 - - + -
527A ILE* 4.7 15.7 - - + -
531A VAL* 4.2 13.0 - - + -
533A ILE* 4.4 10.5 - - + -
545A LEU* 2.8 27.7 + - + +
546A ALA* 3.9 2.5 - - - +
548A LYS* 1.3 77.1 - - + +
550A ALA* 1.3 60.2 + - - +
552A ALA* 2.9 13.9 + - + +
553A GLY 2.9 21.5 + - - -
554A HIS* 3.1 34.0 + - + +
556A VAL* 4.3 11.4 - - + -
639A VAL* 3.6 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A ALA 3.0 16.4 + - - +
547A GLU 3.8 4.5 - - - +
549A LEU* 1.3 75.9 - - - +
551A THR* 1.3 55.4 - - - +
553A GLY* 2.4 28.2 + - - -
554A HIS 4.1 11.7 - - - +
556A VAL* 4.1 7.2 - - + +
584A LEU* 4.1 19.7 - - + +
586A VAL* 4.0 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A PRO* 6.3 0.9 - - - -
547A GLU* 3.1 11.9 + - - +
548A LYS* 3.1 7.8 + - - -
550A ALA* 1.3 77.3 - - - +
552A ALA* 1.3 55.1 + - - +
553A GLY 3.2 3.5 + - - -
584A LEU* 3.1 32.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A LYS* 2.8 13.8 + - + +
549A LEU* 2.9 20.8 + - + +
551A THR* 1.3 76.8 - - - +
553A GLY* 1.3 59.1 + - - +
554A HIS* 3.3 16.4 + - + +
----------------------------------------------------------
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