Contacts of the helix formed by residues 526 - 533 (chain C) in PDB entry 1XMI
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 LEU 526 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C ILE* 5.4 2.2 - - + -
506C ILE* 4.1 15.5 - - + -
521C ILE* 2.7 18.4 + - + +
524C CYS* 3.9 12.6 - - + +
525C GLN* 1.3 71.4 - - - +
527C GLU* 1.3 65.0 + - - +
528C GLU 3.3 2.9 - - - -
529C ASP* 3.2 25.9 + - + +
530C ILE* 3.0 39.5 + - + +
552C GLN* 4.5 4.3 - - + +
555C ARG* 3.7 35.9 - - + +
556C ILE* 3.8 25.6 - - + -
559C ALA* 3.7 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 527 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A LYS* 4.7 5.6 + - - -
518C ARG* 5.6 2.3 - - - +
521C ILE* 3.6 21.0 + - + +
522C LYS* 3.4 52.0 + - + +
525C GLN* 3.5 2.3 - - - -
526C LEU* 1.3 77.9 - - - +
528C GLU* 1.3 64.4 + - + +
530C ILE* 3.7 4.9 + - - +
531C SER* 3.1 25.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 528 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525C GLN 5.0 3.7 + - - +
526C LEU 3.3 0.6 - - - -
527C GLU* 1.3 78.8 - - + +
529C ASP* 1.3 58.0 + - - +
531C SER* 2.8 22.7 + - - -
532C LYS* 2.8 26.4 + - - +
667C ARG* 6.4 1.1 - - - +
671C LEU* 3.8 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 529 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C ILE* 5.7 2.2 - - + -
525C GLN 3.2 23.4 - - - +
526C LEU* 3.2 22.7 + - + +
528C GLU* 1.3 78.5 - - - +
530C ILE* 1.3 65.2 + - + +
532C LYS* 3.1 16.2 + - - +
533C PHE* 3.1 26.6 + - + -
552C GLN* 3.0 32.7 + - + +
555C ARG* 3.5 21.1 + - - -
667C ARG* 4.7 8.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 530 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C ILE* 4.3 25.6 - - + -
517C TYR* 4.2 3.8 - - - +
521C ILE* 4.0 27.4 - - + -
526C LEU* 3.0 38.1 + - + +
527C GLU* 4.1 4.0 - - - +
529C ASP* 1.3 75.5 - - + +
531C SER* 1.3 64.1 + - - +
533C PHE* 3.3 13.5 + - - +
536C LYS* 3.1 31.2 - - + -
537C ASP* 3.4 48.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 531 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527C GLU 3.1 14.2 + - - -
528C GLU* 2.8 26.2 + - - -
530C ILE* 1.3 80.7 - - - +
532C LYS* 1.3 59.4 + - - +
533C PHE 3.3 8.0 - - - +
536C LYS* 5.0 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 532 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528C GLU 2.8 19.7 + - - +
529C ASP* 3.1 8.9 + - - +
531C SER* 1.3 78.4 + - - +
533C PHE* 1.3 63.5 + - + +
534C ALA 3.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 533 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C ILE* 3.7 24.5 - - + -
529C ASP* 3.1 28.9 + - + -
530C ILE 3.4 8.1 - - - +
531C SER 3.2 12.6 - - - +
532C LYS* 1.3 80.2 - - + +
534C ALA* 1.3 65.7 + - - +
535C GLU 3.4 0.4 - - - +
536C LYS* 3.1 25.6 + - - +
539C ILE* 3.7 42.8 - - + -
541C LEU* 5.9 0.9 - - + -
547C THR* 5.5 10.1 - - + -
548C LEU* 4.3 19.1 - - + -
552C GLN* 4.3 16.8 - - - -
----------------------------------------------------------
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