Contacts of the helix formed by residues 492 - 502 (chain A) in PDB entry 1LMU
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 THR 492 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A HIS 4.0 1.8 - - - +
491A PHE* 1.3 76.8 - - - +
493A ASP* 1.3 66.4 + - - +
494A ALA* 3.4 8.2 + - - +
495A THR* 2.8 26.0 + - + +
496A LEU* 2.9 23.9 + - - +
546A ARG* 3.7 26.2 - - + +
547A TYR* 3.8 28.5 - - + -
548A ILE* 3.9 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ALA* 3.9 16.2 - - + -
306A GLY* 4.5 6.3 - - - +
307A LEU 4.5 5.2 - - - +
308A SER* 4.0 24.9 + - - -
309A ALA 5.3 2.5 - - - +
492A THR* 1.3 75.4 - - - +
494A ALA* 1.3 62.8 + - - +
496A LEU* 4.1 1.5 - - - +
497A LEU* 3.2 23.4 + - - +
532A ILE* 5.4 7.1 - - + +
536A PHE* 5.3 2.4 - - - -
543A LYS* 3.0 35.3 + - - +
546A ARG 4.2 2.8 + - - -
548A ILE* 3.3 21.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ILE* 3.6 18.0 - - + +
302A ALA* 3.5 19.4 - - + +
303A LYS* 3.5 36.3 - - + +
492A THR* 3.1 7.2 + - - +
493A ASP* 1.3 80.7 - - - +
495A THR* 1.3 63.2 + - - +
497A LEU 3.4 0.2 + - - -
498A SER* 2.9 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ARG* 4.2 9.0 + - - +
490A HIS 4.6 0.7 - - - +
491A PHE* 2.9 27.5 - - + -
492A THR* 2.8 43.2 + - + +
494A ALA* 1.3 78.9 - - - +
496A LEU* 1.3 59.0 + - - +
498A SER* 2.6 25.2 + - - -
499A ALA* 2.9 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A VAL* 4.3 26.7 - - + +
205A LEU* 4.5 10.5 - - + -
206A VAL* 3.9 29.6 - - + -
491A PHE* 3.4 25.6 - - + -
492A THR 2.9 13.5 + - - +
493A ASP 4.1 2.7 - - - +
495A THR* 1.3 80.6 - - - +
497A LEU* 1.3 63.6 + - - +
499A ALA* 3.1 12.0 + - - +
500A MET* 3.1 18.2 + - + +
532A ILE* 4.3 22.4 - - + -
541A LEU* 4.7 5.6 - - + -
548A ILE* 4.0 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A SER* 3.8 19.3 - - - -
298A GLN* 3.7 21.8 - - + +
299A ILE* 2.9 32.8 - - + -
309A ALA* 4.3 9.4 - - + -
493A ASP 3.2 16.3 + - - +
494A ALA* 3.8 1.8 - - - +
496A LEU* 1.3 78.2 - - - +
498A SER* 1.3 64.1 + - - +
500A MET* 3.0 25.0 + - + +
501A THR* 2.9 18.5 + - - -
528A ARG* 4.0 22.7 - - + +
532A ILE* 4.0 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ILE* 3.9 15.7 - - - +
303A LYS* 6.4 0.2 - - - -
494A ALA 2.9 13.1 + - - -
495A THR* 2.6 29.9 + - - -
497A LEU* 1.3 76.6 - - - +
499A ALA* 1.3 52.3 + - - +
501A THR* 2.9 12.4 - - - +
502A GLY* 2.7 34.5 + - - +
505A ARG* 5.4 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU* 3.8 16.2 - - + -
491A PHE* 3.8 9.0 - - + -
495A THR 2.9 14.4 + - - +
496A LEU* 3.1 10.1 + - - +
498A SER* 1.3 78.1 + - - +
500A MET* 1.4 56.5 + - - +
502A GLY 3.0 3.0 - - - +
503A ILE* 3.0 33.1 + - - +
505A ARG* 6.2 0.9 - - - +
506A PHE* 3.3 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A VAL* 5.5 1.1 - - - -
202A VAL* 3.5 40.6 - - + -
205A LEU* 4.7 10.1 - - + -
496A LEU* 3.1 16.2 + - + +
497A LEU* 3.0 31.8 + - + +
499A ALA* 1.4 74.4 - - - +
501A THR* 1.3 66.5 + - - +
503A ILE* 3.7 5.5 + - - +
521A GLY* 3.7 1.0 - - - -
522A LEU* 3.1 36.9 + - + +
528A ARG* 3.9 26.9 - - + +
531A ILE* 5.2 3.8 - - - -
532A ILE* 3.5 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A SER* 4.0 14.8 + - - +
299A ILE* 4.9 4.5 - - + -
497A LEU* 2.9 21.1 + - + +
498A SER* 2.9 27.6 - - - +
500A MET* 1.3 79.4 - - - +
502A GLY* 1.4 71.9 + - - +
503A ILE 3.4 0.2 + - - -
517A ARG* 5.5 4.2 + - - -
520A ASP* 3.9 14.5 + - - -
521A GLY* 3.4 19.9 + - - -
528A ARG* 4.3 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A SER 2.7 18.8 + - - +
499A ALA* 3.0 9.0 - - - +
501A THR* 1.4 75.4 - - - +
503A ILE* 1.3 62.7 + - - -
504A ALA* 3.2 6.3 + - - -
505A ARG* 3.6 25.6 + - - +
506A PHE* 4.1 2.9 - - - -
517A ARG* 6.2 2.5 - - - -
----------------------------------------------------------
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