Contacts of the helix formed by residues 482 - 496 (chain D) in PDB entry 6X34
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 GLY 482 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D ASP* 5.9 9.2 - - - -
479D GLN* 3.5 10.7 + - - -
480D GLU 3.8 0.8 - - - -
481D GLU* 1.3 78.2 - - - +
483D MET* 1.3 61.0 + - - +
484D LEU* 3.3 6.6 + - - -
485D SER* 4.0 8.7 + - - -
486D LEU* 3.9 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 483 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404D ILE* 4.8 9.0 - - - +
407D THR* 3.7 20.2 - - + +
408D ALA* 5.2 6.3 - - + +
411D TYR* 3.7 30.7 - - + -
478D PHE* 3.5 63.3 - - + +
481D GLU* 3.2 13.8 - - + +
482D GLY* 1.3 76.6 - - - +
484D LEU* 1.3 64.3 + - + +
486D LEU* 3.1 24.3 - - + +
487D VAL* 2.9 33.4 + - + +
525D ILE* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 484 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478D PHE* 4.3 10.5 - - + +
479D GLN* 3.6 45.1 - - + +
482D GLY* 3.3 2.2 - - - -
483D MET* 1.3 79.6 - - + +
485D SER* 1.3 61.4 + - - +
487D VAL* 3.1 12.8 - - + +
488D LEU* 2.9 36.5 + - + +
529D LEU* 6.3 2.7 - - + -
530D ILE* 4.7 9.9 - - + -
536D ASN* 4.1 32.3 - - + +
539D LEU* 4.6 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 485 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482D GLY* 4.0 9.2 + - - -
483D MET 3.4 0.2 - - - -
484D LEU* 1.3 77.6 - - - +
486D LEU* 1.3 57.2 + - - +
488D LEU* 3.3 17.6 + - - +
489D ASN* 2.9 29.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
408D ALA* 4.4 14.1 - - + +
411D TYR* 3.5 44.4 - - + -
412D ASN* 3.9 17.9 - - - +
415D ILE* 3.5 28.3 - - + -
482D GLY 3.9 4.4 + - - +
483D MET* 3.1 31.5 + - + +
484D LEU 3.1 0.2 - - - -
485D SER* 1.3 78.1 - - - +
487D VAL* 1.3 57.1 + - - +
489D ASN* 3.1 8.5 + - - +
490D CYS* 3.0 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 487 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411D TYR* 3.7 36.1 - - + +
478D PHE* 6.2 0.7 - - + -
483D MET* 2.9 20.3 + - + +
484D LEU* 3.1 21.5 - - + +
486D LEU* 1.3 72.1 - - - +
488D LEU* 1.3 69.0 + - + +
490D CYS* 3.5 9.9 - - - +
491D ILE* 2.9 32.9 + - + +
522D LEU* 4.8 11.7 - - + -
525D ILE* 6.3 4.9 - - + -
526D LEU* 4.8 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 488 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484D LEU* 2.9 30.2 + - + +
485D SER* 3.6 19.3 - - - +
486D LEU 3.2 0.2 - - - -
487D VAL* 1.3 80.5 - - + +
489D ASN* 1.3 55.8 + - - +
491D ILE* 3.1 12.1 - - + +
492D ASP* 2.9 30.4 + - - +
526D LEU* 4.1 24.5 - - + -
539D LEU* 6.1 4.0 - - + -
540D PHE* 4.2 27.1 - - + -
546D TRP* 5.1 7.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 489 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415D ILE* 3.5 33.8 - - + +
485D SER 2.9 14.2 + - - +
486D LEU* 3.4 9.9 - - - +
488D LEU* 1.3 75.6 - - - +
490D CYS* 1.3 57.9 + - - +
492D ASP* 3.8 5.4 - - - +
493D ARG* 2.9 57.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 490 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411D TYR* 4.6 18.8 - - - -
414D PHE* 4.6 22.4 - - + -
415D ILE* 3.8 24.0 - - - -
486D LEU* 3.0 38.2 + - - -
487D VAL* 3.5 11.2 - - - +
488D LEU 3.3 0.2 - - - -
489D ASN* 1.3 79.2 - - - +
491D ILE* 1.3 57.4 + - - +
493D ARG* 3.3 4.5 + - - +
494D LEU* 2.9 29.6 + - - +
522D LEU* 4.7 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 491 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487D VAL* 2.9 16.1 + - + +
488D LEU* 3.1 25.4 - - + +
490D CYS* 1.3 76.4 - - - +
492D ASP* 1.3 56.9 + - - +
494D LEU* 3.7 6.4 - - + +
495D ASN* 2.9 32.6 + - - +
522D LEU* 3.7 39.5 - - + +
523D TYR* 4.4 22.2 + - + -
526D LEU* 3.7 27.1 - - + -
546D TRP* 3.5 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 492 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488D LEU 2.9 19.4 + - - +
489D ASN* 3.8 6.5 - - - +
491D ILE* 1.3 78.7 - - - +
493D ARG* 1.3 61.3 + - + +
495D ASN* 3.2 4.8 + - - +
496D VAL* 2.9 30.3 + - - +
546D TRP* 4.7 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 493 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415D ILE* 5.2 6.9 + - + +
418D LEU* 4.7 20.5 - - + +
419D ASP* 4.1 28.7 - - - +
422D SER* 4.9 11.6 + - - -
489D ASN* 2.9 45.7 + - - +
490D CYS* 3.9 5.2 - - - +
492D ASP* 1.3 77.7 - - + +
494D LEU* 1.3 59.8 + - - +
496D VAL* 3.2 27.4 - - - +
497D TYR* 4.3 7.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 494 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D PHE* 4.4 22.7 - - + -
418D LEU* 6.3 2.9 - - + -
490D CYS 2.9 16.4 + - - +
491D ILE* 3.8 6.7 - - - +
493D ARG* 1.3 81.2 - - - +
495D ASN* 1.3 58.4 + - - +
496D VAL 3.4 0.2 - - - -
497D TYR* 4.0 11.8 + - + +
503D PHE* 4.6 17.3 - - + -
515D TRP* 3.4 48.2 + - + +
518D ILE* 3.6 31.6 - - + -
519D VAL* 3.7 20.0 - - + -
522D LEU* 5.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 495 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491D ILE 2.9 17.6 + - - +
492D ASP* 3.2 5.1 + - - +
494D LEU* 1.3 73.6 - - - +
496D VAL* 1.3 60.6 + - - +
497D TYR 2.9 18.7 - - - +
515D TRP* 5.1 7.5 - - - -
519D VAL* 6.3 0.6 - - - +
523D TYR* 3.3 25.4 + - - +
546D TRP* 5.8 6.5 + - + +
550D LYS* 4.7 17.7 + - - +
553D ARG* 2.9 54.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 496 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422D SER* 5.7 5.2 - - - -
492D ASP 2.9 13.7 + - - +
493D ARG* 3.2 26.9 - - - +
495D ASN* 1.3 77.2 - - - +
497D TYR* 1.3 78.8 + - + +
498D THR 4.2 0.2 + - - -
553D ARG* 5.3 0.3 + - - -
----------------------------------------------------------
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