Contacts of the helix formed by residues 485 - 497 (chain D) in PDB entry 1B6C
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 ALA 485 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D ALA* 4.1 5.7 - - - +
313D LEU* 4.2 8.1 - - + -
314D ALA* 3.7 31.2 - - - +
317D HIS* 4.1 15.8 + - + +
401D ILE* 3.5 24.3 - - + +
404D MET* 5.3 2.5 - - - -
484D THR* 1.3 73.6 + - - +
486D LEU* 1.3 56.2 - - - +
488D ILE* 3.3 8.6 + - - +
489D LYS* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 486 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D ALA* 4.0 7.9 - - + +
318D MET* 4.2 26.5 - - + -
484D THR* 3.1 10.9 - - + +
485D ALA* 1.3 77.5 - - - +
487D ARG* 1.3 61.4 + - - +
489D LYS* 2.9 23.5 + - + +
490D LYS* 2.8 62.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 487 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483D LEU* 4.1 21.5 - - + -
484D THR* 2.9 30.2 - - + +
486D LEU* 1.3 76.0 - - - +
488D ILE* 1.3 62.1 + - - +
490D LYS* 3.0 39.8 + - - +
491D THR* 2.8 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 488 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D ALA* 3.9 9.2 - - + -
401D ILE* 4.4 8.7 - - + -
404D MET* 4.4 15.0 - - - -
408D PHE* 3.6 27.1 - - + -
470D ILE* 3.9 11.4 - - + -
474D CYS* 3.6 31.0 - - - -
483D LEU* 3.8 22.7 - - + -
484D THR 3.0 17.0 + - - +
485D ALA* 3.7 7.4 - - - +
487D ARG* 1.3 75.1 - - - +
489D LYS* 1.3 62.4 + - - +
491D THR* 4.1 6.9 - - - +
492D LEU* 3.0 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 489 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D LEU* 4.1 7.5 - - + +
310D ALA* 4.1 10.3 - - + +
311D SER* 3.4 35.9 - - - +
314D ALA* 4.8 4.5 - - + -
485D ALA 2.9 13.2 + - - +
486D LEU* 2.9 31.6 + - + +
488D ILE* 1.3 77.6 - - - +
490D LYS* 1.3 62.6 + - - +
492D LEU* 3.6 3.8 - - - +
493D SER* 2.9 50.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 490 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484D THR* 5.9 0.2 - - - -
486D LEU* 2.8 50.6 + - + +
487D ARG* 3.0 45.6 + - - +
489D LYS* 1.3 80.8 - - - +
491D THR* 1.3 66.6 + - + +
492D LEU 3.0 1.8 - - - -
493D SER* 2.8 18.4 + - - -
494D GLN* 3.0 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 491 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466D VAL* 3.9 20.3 - - - +
470D ILE* 3.9 12.9 - - + +
483D LEU* 5.4 4.5 - - + -
487D ARG* 2.8 37.7 + - + +
488D ILE* 4.1 6.5 - - - -
490D LYS* 1.3 73.6 - - + +
492D LEU* 1.3 57.1 + - - +
494D GLN* 3.5 8.9 + - - +
495D LEU* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 492 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D ILE* 4.2 9.7 - - + +
306D ALA* 3.8 37.9 - - + +
307D LEU* 3.9 17.9 - - + +
310D ALA* 4.6 1.1 - - + -
408D PHE* 3.9 4.5 - - + -
466D VAL* 4.5 1.6 - - + -
467D MET* 4.2 13.0 - - - -
470D ILE* 3.4 24.2 - - + -
488D ILE* 3.0 36.5 + - + +
489D LYS* 3.6 4.7 - - - +
491D THR* 1.3 78.6 + - - +
493D SER* 1.3 58.3 + - - +
495D LEU* 3.5 21.0 + - + +
496D SER* 2.9 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 493 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D LEU* 4.3 10.4 - - - +
489D LYS* 2.9 37.5 + - - +
490D LYS* 2.8 12.4 + - - -
492D LEU* 1.3 74.9 - - - +
494D GLN* 1.3 65.2 + - - +
496D SER* 3.2 8.4 + - - -
497D GLN* 3.2 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 494 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490D LYS 3.0 10.8 + - - +
491D THR* 3.7 12.6 - - - +
493D SER* 1.3 76.3 - - - +
495D LEU* 1.3 64.7 + - - +
497D GLN* 3.1 18.7 + - - +
498D GLN* 3.1 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 495 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D ILE* 4.0 24.6 - - + +
462D GLU* 4.0 17.7 - - + +
463D ALA* 4.1 17.5 - - - +
466D VAL* 3.9 38.4 - - + -
467D MET* 5.3 2.7 - - + -
491D THR 3.1 17.8 + - - +
492D LEU* 3.6 16.2 - - + +
493D SER 3.3 0.2 - - - -
494D GLN* 1.3 76.9 - - - +
496D SER* 1.3 62.0 + - - +
498D GLN* 3.1 20.9 + - - +
499D GLU* 3.0 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 496 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D ILE* 3.9 23.4 - - - +
307D LEU* 4.3 13.7 - - - +
492D LEU 2.9 17.7 + - - -
493D SER* 3.2 9.8 + - - -
495D LEU* 1.3 76.8 - - - +
497D GLN* 1.3 62.1 + - - +
498D GLN 3.4 0.2 - - - -
499D GLU* 3.8 3.0 + - - +
500D GLY 3.5 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 497 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493D SER* 3.2 22.1 + - - +
494D GLN* 3.1 12.7 + - - +
496D SER* 1.3 75.7 - - - +
498D GLN* 1.3 59.4 + - + +
499D GLU 3.1 7.8 + - - -
500D GLY* 3.8 8.3 + - - +
----------------------------------------------------------
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