Contacts of the helix formed by residues 546 - 555 (chain A) in PDB entry 3MXN
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 VAL 546 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A PHE* 1.3 75.3 - - - +
547A ASP* 1.3 67.4 - - - +
548A GLU* 3.7 18.8 - - + +
549A ILE* 3.0 38.5 + - + +
550A LEU* 3.4 8.0 + - - +
604A MET* 3.8 28.0 - - + +
605A VAL 3.1 24.3 + - - +
606A LEU* 3.7 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ILE* 3.6 34.8 - - + +
528A TRP* 3.0 42.2 + - - +
545A PHE 3.6 2.0 + - - -
546A VAL* 1.3 71.9 - - - +
548A GLU* 1.3 69.7 + - - +
550A LEU* 3.1 3.8 + - - +
551A THR* 2.9 45.3 + - - -
557A SER* 5.7 1.4 - - - -
558A VAL* 5.2 1.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
546A VAL* 3.7 22.8 - - + +
547A ASP* 1.3 86.8 + - - +
549A ILE* 1.3 62.3 + - + +
551A THR* 3.6 7.0 + - - -
552A SER* 3.1 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A PHE* 4.3 14.6 - - + -
546A VAL* 3.0 32.8 + - + +
548A GLU* 1.3 76.7 - - + +
550A LEU* 1.3 66.1 + - + +
552A SER* 3.2 7.0 + - - -
553A LEU* 3.0 35.3 + - + +
605A VAL* 3.7 32.5 - - + +
606A LEU 4.6 2.0 - - - +
607A ALA* 3.9 13.9 - - - +
608A LEU* 3.7 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A LEU* 4.2 7.2 - - + -
528A TRP* 3.6 28.9 - - + +
529A SER* 3.7 36.6 - - - -
530A ILE* 3.9 23.3 - - + +
545A PHE* 4.1 21.5 - - + +
546A VAL 3.4 5.1 + - - +
547A ASP 3.1 3.2 + - - +
549A ILE* 1.3 79.6 - - + +
551A THR* 1.3 55.9 + - - +
553A LEU* 3.2 9.1 + - + +
554A ILE* 2.9 38.3 + - + +
581A CYS* 4.4 19.3 - - - -
585A LEU* 4.5 9.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
528A TRP* 3.4 8.9 - - - -
547A ASP* 2.9 35.8 + - - -
548A GLU* 3.9 7.6 - - - -
550A LEU* 1.3 76.5 - - - +
552A SER* 1.3 57.3 + - - +
555A GLY* 2.8 30.7 + - - -
556A PHE 3.6 9.4 + - - +
557A SER* 3.8 31.8 - - - +
560A GLU* 5.2 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A GLU 3.1 18.1 + - - -
549A ILE* 3.2 7.6 + - - -
551A THR* 1.3 78.1 - - - +
553A LEU* 1.3 67.1 + - - +
555A GLY* 3.8 7.2 + - - -
580A LYS* 4.3 5.7 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
549A ILE* 3.0 36.3 + - + +
550A LEU* 3.2 6.5 + - + +
552A SER* 1.3 82.5 - - - +
554A ILE* 1.3 60.6 + - - +
577A GLY 4.0 1.6 - - - +
580A LYS* 2.9 33.8 + - - +
581A CYS* 3.9 19.0 + - - -
584A ASP* 3.6 28.3 - - + +
585A LEU* 3.8 30.3 - - + -
588A LEU* 6.0 3.8 - - + -
608A LEU* 5.0 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A LEU* 4.0 19.7 - - + -
528A TRP* 3.6 34.5 - - + +
550A LEU* 2.9 24.4 + - + +
553A LEU* 1.3 76.9 - - - +
555A GLY* 1.3 59.2 + - - +
556A PHE* 3.9 18.7 - - + +
574A PHE* 3.8 31.0 - - + +
577A GLY* 3.1 35.3 - - - +
578A LEU* 4.1 4.5 - - + +
580A LYS* 5.3 1.3 - - - +
581A CYS* 3.6 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A THR* 2.8 18.8 + - - -
552A SER* 3.8 6.0 + - - -
553A LEU 3.4 2.4 - - - -
554A ILE* 1.3 72.3 - - - +
556A PHE* 1.3 70.8 + - - +
560A GLU* 4.1 5.1 - - - +
----------------------------------------------------------
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