Contacts of the helix formed by residues 542 - 555 (chain A) in PDB entry 3APO
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 SER 542 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ARG* 5.5 2.7 - - - +
489A GLU* 3.9 8.4 + - - -
540A HIS* 2.6 20.9 + - - -
541A HIS* 1.3 76.9 - - - +
543A ALA* 1.3 66.1 + - - +
544A GLU* 3.6 13.7 + - - +
545A GLN* 3.2 23.1 + - - +
546A ILE* 3.0 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A GLU* 3.0 42.5 + - - +
492A LYS* 3.9 19.7 - - + -
493A ALA* 4.2 6.7 - - + +
542A SER* 1.3 71.8 + - - +
544A GLU* 1.3 64.2 + - - +
546A ILE* 3.4 5.1 + - - +
547A LEU* 3.0 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ARG* 6.4 0.4 - - - +
542A SER* 3.2 11.1 + - - +
543A ALA* 1.3 76.5 - - - +
545A GLN* 1.3 74.0 + - - +
547A LEU* 3.3 12.4 + - + +
548A GLU* 3.0 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A TYR* 2.9 25.1 - - + +
539A GLY* 5.4 0.4 - - - -
540A HIS* 3.6 22.7 + - + +
542A SER* 3.2 24.3 + - - +
544A GLU* 1.3 93.9 + - - +
546A ILE* 1.3 64.3 + - - +
548A GLU* 3.4 26.5 + - - +
549A PHE* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A LEU* 4.2 17.7 - - + -
486A LEU* 3.7 29.4 - - + -
489A GLU* 4.4 9.9 - - + +
490A LEU* 4.4 12.3 - - + -
493A ALA* 4.3 10.1 - - + -
526A THR* 5.6 3.6 - - + -
537A TYR* 3.8 29.4 - - + -
542A SER 3.0 30.0 + - - +
543A ALA* 3.7 6.5 - - - +
545A GLN* 1.3 75.2 - - - +
547A LEU* 1.3 57.5 + - - +
549A PHE* 3.3 6.9 + - + +
550A ILE* 3.0 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A ALA* 3.8 34.8 - - + +
496A LEU* 3.9 31.4 - - + -
497A LEU* 3.9 24.5 - - + -
543A ALA* 3.0 31.9 + - + +
544A GLU* 3.4 8.3 - - + +
545A GLN 3.2 0.2 - - - -
546A ILE* 1.3 74.1 - - - +
548A GLU* 1.3 59.0 + - - +
550A ILE* 3.2 6.5 + - - +
551A GLU* 2.8 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A GLU* 3.0 28.4 + - + +
545A GLN* 3.4 33.8 + - - +
547A LEU* 1.3 75.7 - - - +
549A PHE* 1.3 57.5 + - - +
551A GLU* 3.4 6.4 + - - +
552A ASP* 3.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A LEU* 5.4 2.9 - - + -
528A VAL* 3.6 25.6 - - + -
535A HIS* 4.0 13.2 - - + -
536A GLU 3.9 16.2 - - - -
537A TYR* 3.5 51.6 - + + -
538A GLU 5.6 0.2 - - - -
545A GLN 3.1 13.7 + - - +
546A ILE* 3.5 8.7 - - + +
547A LEU 3.2 0.2 - - - -
548A GLU* 1.3 77.7 - - - +
550A ILE* 1.3 71.7 + - + +
552A ASP* 3.3 9.5 + - - +
553A LEU* 3.1 43.6 + - + +
603A ARG* 6.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A LEU* 3.7 13.2 - - + -
497A LEU* 3.5 34.1 - - + -
500A GLN* 4.1 18.8 - - - +
501A LEU* 4.0 21.3 - - + -
528A VAL* 4.3 12.3 - - + -
546A ILE* 3.0 34.5 + - + +
547A LEU* 3.2 7.4 + - - +
549A PHE* 1.3 83.8 - - + +
551A GLU* 1.3 65.7 + - - +
553A LEU* 3.1 11.3 + - + +
554A ARG* 3.0 21.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A GLN* 5.0 1.1 - - - +
547A LEU 2.8 19.6 + - - +
548A GLU* 3.7 8.1 - - - +
550A ILE* 1.3 73.7 - - - +
552A ASP* 1.3 58.2 + - - +
554A ARG* 3.4 31.6 + - - +
555A ASN* 2.5 58.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A GLU 3.0 17.3 + - - +
549A PHE* 3.6 10.4 - - - +
550A ILE 3.2 0.4 - - - -
551A GLU* 1.3 75.2 - - - +
553A LEU* 1.3 67.6 + - - +
555A ASN 4.2 8.3 - - - +
556A PRO* 3.2 28.2 - - - +
557A SER* 4.3 14.5 + - - -
603A ARG* 2.9 38.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A VAL* 3.8 36.6 - - + -
530A ASN* 5.3 10.2 + - + +
535A HIS* 3.5 41.5 - - + +
549A PHE* 3.1 37.6 + - + +
550A ILE* 3.1 11.0 + - + +
552A ASP* 1.3 80.7 - - - +
554A ARG* 1.3 61.2 + - - +
556A PRO* 3.5 16.4 - - - +
603A ARG* 6.1 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A GLN* 3.4 47.2 + - - +
550A ILE* 3.0 12.8 + - + +
551A GLU* 3.2 31.7 + - - +
553A LEU* 1.3 78.9 - - - +
555A ASN* 1.3 67.4 + - - +
556A PRO* 3.3 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A GLU* 2.5 41.1 + - - +
552A ASP* 3.2 14.7 - - - +
554A ARG* 1.3 81.0 + - - +
556A PRO* 1.3 69.9 - - - +
557A SER 3.8 0.2 + - - -
----------------------------------------------------------
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