Contacts of the helix formed by residues 482 - 495 (chain A) in PDB entry 1Q2L
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 482 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LYS 3.2 6.8 + - - -
481A ILE* 1.3 79.6 - - - +
483A ALA* 1.3 59.2 + - - +
484A GLN* 3.5 13.5 + - - +
485A THR* 3.0 28.3 + - - -
486A PHE* 3.1 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A SER* 1.3 72.3 - - - +
484A GLN* 1.3 61.7 + - - +
486A PHE* 3.3 11.8 + - - +
487A ALA* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A SER* 3.2 10.6 + - - +
483A ALA* 1.3 79.5 - - - +
485A THR* 1.3 58.4 + - - +
487A ALA* 3.3 7.1 + - - +
488A ASP* 2.9 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ILE* 5.1 5.4 - - + -
366A ASP* 5.2 2.7 - - - +
481A ILE* 3.7 15.5 - - + -
482A SER* 3.0 23.3 + - - -
483A ALA 3.2 0.2 - - - -
484A GLN* 1.3 77.1 + - - +
486A PHE* 1.3 65.1 + - - +
488A ASP* 3.2 7.3 + - + +
489A TRP* 3.0 57.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A GLY* 4.5 6.5 - - - -
451A PRO* 3.6 39.0 - - + -
452A GLN* 3.7 42.0 - - + +
480A LYS* 6.5 0.4 - - - -
481A ILE* 3.2 47.1 - - + -
482A SER 3.1 22.2 + - - -
483A ALA* 3.3 10.1 + - - +
485A THR* 1.3 76.7 - - - +
487A ALA* 1.3 60.9 + - - +
489A TRP* 3.4 8.8 + + - +
490A GLN* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ALA 2.9 18.0 + - - +
484A GLN* 3.3 9.6 - - - +
486A PHE* 1.3 77.5 - - - +
488A ASP* 1.3 62.2 + - - +
490A GLN* 3.3 1.8 + - - -
491A LYS* 3.0 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ASP* 3.9 18.5 - - - +
484A GLN* 2.9 15.1 + - + +
485A THR* 3.2 10.3 + - + +
487A ALA* 1.3 76.3 - - - +
489A TRP* 1.3 59.7 + - + +
491A LYS* 3.2 7.4 + - - +
492A LYS* 2.9 65.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ILE* 4.4 7.4 - - + -
366A ASP* 3.1 43.8 + - - +
369A VAL* 3.6 20.8 - - + +
370A ALA* 3.6 14.2 - - - +
373A PHE* 5.8 2.9 - - + +
451A PRO* 4.2 25.8 - - + -
456A ILE* 3.6 33.2 - - + -
458A TYR* 3.6 20.9 - - - -
481A ILE* 3.7 29.2 - - + -
485A THR* 3.0 34.4 + - + +
486A PHE* 3.8 11.7 - + - +
488A ASP* 1.3 84.7 - - - +
490A GLN* 1.3 58.9 + - - +
492A LYS* 3.5 1.1 + - + -
493A ALA* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A PHE* 5.5 3.3 - - - +
377A ASN* 3.4 25.5 + - - +
451A PRO* 6.0 1.6 - - - +
486A PHE 3.1 17.2 + - - +
487A ALA* 3.3 0.4 + - - -
489A TRP* 1.3 75.5 - - - +
491A LYS* 1.3 80.0 + - - +
493A ALA* 3.8 13.3 - - - +
494A ALA* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A ALA* 3.0 40.6 + - + +
488A ASP* 3.7 7.4 - - - +
490A GLN* 1.3 95.0 - - - +
492A LYS* 1.3 65.0 + - + +
494A ALA* 3.3 15.2 + - - +
495A ASP* 3.5 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ASP* 4.0 26.0 - - + +
367A GLN* 3.3 29.2 + - - +
370A ALA* 3.6 15.5 - - + -
488A ASP* 2.9 53.2 + - - +
489A TRP* 5.2 0.4 - - - -
491A LYS* 1.3 76.4 - - + +
493A ALA* 1.3 63.3 + - - +
495A ASP* 3.1 17.1 + - - +
496A ILE* 3.2 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ALA* 3.5 26.4 - - - +
373A PHE* 4.9 2.7 - - + -
374A SER* 3.3 28.3 + - - +
377A ASN* 4.5 1.8 - - - +
489A TRP 2.9 19.3 + - - +
490A GLN* 3.5 22.2 - - - +
491A LYS 3.2 0.2 - - - -
492A LYS* 1.3 74.7 - - - +
494A ALA* 1.3 65.4 + - - +
496A ILE* 3.1 12.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
490A GLN* 3.0 20.8 + - - +
491A LYS* 3.6 11.7 - - - +
492A LYS 3.3 0.2 - - - -
493A ALA* 1.3 77.4 - - - +
495A ASP* 1.3 65.5 + - - +
496A ILE 3.4 3.8 + - - +
497A ALA* 5.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A TRP* 5.9 0.3 - - - -
491A LYS 3.5 12.3 + - - +
492A LYS* 3.1 12.2 + - - +
493A ALA 3.1 1.0 - - - -
494A ALA* 1.3 81.4 - - - +
496A ILE* 1.3 61.8 + - + +
497A ALA* 3.8 3.4 + - - +
----------------------------------------------------------
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