Contacts of the helix formed by residues 469 - 485 (chain C) in PDB entry 1RQQ
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 CYS 469 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C SER 4.5 2.9 - - - -
463C LEU* 3.7 26.9 - - + -
464C ASN 4.0 23.6 - - - +
467C GLY* 3.0 15.4 - - - +
468C GLN* 1.3 80.2 - - - +
470C HIS* 1.3 62.6 + - - +
471C VAL 3.4 2.7 - - - -
472C GLN* 3.2 14.7 + - - +
473C HIS* 2.9 44.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 470 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C LEU* 4.2 31.7 + - + +
407C TYR* 4.3 13.0 + - - -
468C GLN* 3.4 4.4 - - - +
469C CYS* 1.3 77.7 - - - +
471C VAL* 1.3 64.3 + - + +
473C HIS* 2.9 16.6 + - - +
474C LEU* 2.9 64.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 471 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1159A GLU* 3.2 40.6 + - + +
1160A THR* 4.0 17.3 - - + -
469C CYS 3.4 0.6 - - - -
470C HIS* 1.3 82.1 - - + +
472C GLN* 1.3 62.7 + - - +
474C LEU* 3.1 17.0 + - + +
475C TRP 2.9 18.0 + - - -
450D PHE* 3.6 21.1 - - + -
457D LYS* 3.9 15.5 - - + -
458D HIS 4.7 1.6 - - - +
459D LEU* 3.6 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 472 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C LEU* 4.5 13.3 - - - +
462C SER* 3.8 15.1 + - - +
463C LEU* 3.0 31.8 - - + +
468C GLN 5.4 1.2 + - - +
469C CYS* 3.2 19.1 + - - +
470C HIS 3.2 0.6 - - - -
471C VAL* 1.3 78.7 - - - +
473C HIS* 1.3 63.9 + - - +
475C TRP* 3.1 3.6 + - + +
476C PHE* 3.0 53.1 + - + -
459D LEU* 3.7 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 473 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C LEU 4.9 5.7 + - - -
403C GLU* 4.7 2.8 - - - -
404C LEU* 3.9 42.2 + - + +
407C TYR* 3.7 35.5 + + + +
409C TRP* 3.5 15.7 - + + -
463C LEU* 4.1 17.2 - - + +
464C ASN 5.1 5.4 + - - -
469C CYS* 2.9 42.7 + - + +
470C HIS* 2.9 17.4 + - - +
472C GLN* 1.3 77.2 - - - +
474C LEU* 1.3 60.3 + - - +
476C PHE* 3.3 1.3 + + - -
477C GLN* 2.9 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 474 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1162A PTR 5.6 2.0 - - - +
407C TYR* 4.4 9.9 - - + +
470C HIS* 2.9 55.3 + - + +
471C VAL* 3.1 17.9 + - + +
473C HIS* 1.3 77.7 - - - +
475C TRP* 1.3 62.6 + - - +
477C GLN* 3.1 6.8 + - + +
478C SER* 2.9 21.5 + - - -
450D PHE* 4.2 6.7 - - + -
452D PHE* 3.6 39.6 - - + -
457D LYS* 4.2 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 475 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C VAL 2.9 8.4 + - - +
472C GLN* 3.1 7.8 + - + +
474C LEU* 1.3 75.4 - - - +
476C PHE* 1.3 89.4 + + - +
478C SER* 2.8 33.9 + - - -
479C VAL* 3.1 26.1 + - + +
432D GLY 4.3 4.9 - - - -
434D PHE* 3.7 44.2 - + + -
448D LEU* 3.7 25.7 - - + +
450D PHE* 3.7 35.8 - + + -
459D LEU* 4.0 12.8 - - + -
475D TRP* 3.9 16.1 - - - +
476D PHE* 4.2 18.6 - + - -
479D VAL* 3.9 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 476 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C TRP* 3.9 28.9 - + + -
434C PHE* 3.8 15.5 - + + -
436C ILE* 3.5 30.3 - - + -
448C LEU* 4.2 12.3 - - + -
461C LEU* 4.3 21.3 - - + -
463C LEU* 4.6 7.6 - - + -
472C GLN* 3.0 49.1 + - + -
473C HIS 3.9 0.2 - - - +
475C TRP* 1.3 97.0 - + - +
477C GLN* 1.3 57.1 + - - +
479C VAL* 3.3 5.3 + - - +
480C PHE* 2.9 28.6 + - - +
475D TRP* 4.0 24.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 477 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C TYR* 3.4 23.0 - - + -
408C PRO* 4.0 7.0 - - - +
409C TRP* 2.9 34.0 + - - +
473C HIS 2.9 17.7 + - - +
474C LEU* 3.1 10.5 + - + +
476C PHE* 1.3 76.6 - - - +
478C SER* 1.3 51.9 + - - +
480C PHE* 3.2 17.7 + - - +
481C ASP* 2.7 69.4 + - - +
484C ARG* 4.9 2.6 - - - +
452D PHE* 4.4 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 478 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C LEU 2.9 12.1 + - - -
475C TRP* 2.8 30.7 + - - -
477C GLN* 1.3 78.9 - - - +
479C VAL* 1.3 61.1 + - - +
481C ASP* 3.2 14.4 + - - +
482C MET* 3.1 34.4 + - - +
431D HIS* 3.9 22.4 + - - -
432D GLY* 4.3 11.2 - - - -
450D PHE* 4.7 2.0 - - - -
451D ASN 5.1 2.0 - - - -
452D PHE* 4.1 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 479 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C PHE* 3.6 21.8 - - + -
475C TRP* 3.1 45.1 + - + +
476C PHE* 3.7 7.9 - - - +
477C GLN 3.2 0.2 - - - -
478C SER* 1.3 80.6 + - - +
480C PHE* 1.3 65.7 + - - +
482C MET* 3.0 13.4 + - + +
483C LEU* 3.0 24.5 + - + +
475D TRP* 3.7 18.4 - - + -
479D VAL* 3.8 24.2 - - + -
482D MET* 4.5 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 480 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C PRO* 3.6 35.2 - - + -
409C TRP* 3.5 30.1 - + + -
434C PHE* 4.0 4.9 - + + -
476C PHE 2.9 15.0 + - - +
477C GLN* 3.3 26.5 - - - +
479C VAL* 1.3 77.7 - - - +
481C ASP* 1.3 57.7 + - - +
483C LEU* 3.1 20.3 + - + +
484C ARG* 2.9 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 481 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C GLN* 2.7 50.4 + - - +
478C SER* 3.3 11.6 + - - +
479C VAL 3.1 0.2 - - - -
480C PHE* 1.3 75.2 - - - +
482C MET* 1.3 60.5 + - + +
484C ARG* 2.8 63.2 + - - +
485C HIS* 3.6 5.4 + - - +
431D HIS* 3.2 28.5 + - + +
452D PHE* 4.8 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 482 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C TRP* 5.1 0.2 - - + -
478C SER* 3.1 24.3 + - - +
479C VAL* 3.0 23.2 + - + +
481C ASP* 1.3 76.4 - - + +
483C LEU* 1.3 65.8 + - - +
485C HIS* 3.2 11.3 + - - +
486C PHE* 3.3 17.7 - - - -
431D HIS* 5.0 6.3 - - + +
432D GLY* 3.7 29.6 - - - +
479D VAL* 4.1 19.5 - - + +
482D MET* 4.5 16.6 - - + +
483D LEU* 3.5 38.4 - - - -
486D PHE* 4.5 19.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 483 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C HIS 5.0 2.5 - - - +
432C GLY* 3.8 16.2 - - - +
433C LEU* 3.9 13.7 - - + +
434C PHE* 3.5 41.5 - - + +
479C VAL* 3.0 16.0 + - + +
480C PHE* 3.1 17.5 + - + +
482C MET* 1.3 73.1 - - - +
484C ARG* 1.3 54.6 - - - +
485C HIS 2.6 16.8 + - - -
486C PHE* 2.9 25.9 + - + +
482D MET* 3.1 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 484 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C GLN* 4.9 2.6 - - - +
480C PHE* 2.9 29.7 + - + +
481C ASP* 2.8 60.2 + - - +
483C LEU* 1.3 73.7 - - - +
485C HIS* 1.3 57.4 + - + +
486C PHE 3.2 11.0 + - - +
431D HIS* 5.9 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 485 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C ASP 4.1 6.7 - - - +
482C MET 3.2 11.2 + - - +
483C LEU 2.6 6.3 + - - -
484C ARG* 1.3 76.7 - - + +
486C PHE* 1.3 69.0 + - - +
486D PHE* 4.1 20.4 - - + -
----------------------------------------------------------
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