Contacts of the helix formed by residues 469 - 485 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462D SER 4.6 2.5 - - - -
463D LEU* 4.2 11.4 - - + -
464D ASN 3.9 35.2 - - - +
467D GLY* 3.1 12.4 - - - +
468D GLN* 1.3 80.2 - - - +
470D HIS* 1.3 64.5 + - - +
471D VAL 3.4 2.2 - - - -
472D GLN* 3.3 22.1 + - - +
473D HIS* 3.0 42.6 + - + +
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Residues in contact with HIS 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402D LEU* 4.5 21.8 + - + +
407D TYR* 4.2 13.6 + - - -
468D GLN* 3.4 4.0 - - - +
469D CYS* 1.3 77.5 - - - +
471D VAL* 1.3 65.5 + - + +
473D HIS* 2.9 15.7 + - - +
474D LEU* 2.9 61.5 + - + +
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Residues in contact with VAL 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1159B GLU* 4.0 31.6 - - + +
1160B THR* 4.5 13.0 - - + -
450C PHE* 3.6 21.3 - - + -
457C LYS* 4.0 12.8 - - + -
458C HIS 4.7 0.9 - - - +
459C LEU* 3.2 25.4 - - + -
468D GLN 4.9 2.0 + - - +
469D CYS 3.4 0.6 - - - -
470D HIS* 1.3 79.5 - - + +
472D GLN* 1.3 64.7 + - - +
474D LEU* 3.1 17.1 + - + +
475D TRP* 2.9 18.5 + - - +
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Residues in contact with GLN 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459C LEU* 3.7 28.8 - - + +
461D LEU* 4.7 10.7 - - - +
462D SER 3.8 16.1 + - - +
463D LEU* 3.1 28.2 - - + +
468D GLN 5.4 1.0 + - - +
469D CYS* 3.3 22.5 + - - +
470D HIS 3.2 0.2 - - - -
471D VAL* 1.3 78.2 - - - +
473D HIS* 1.3 64.0 + - - +
475D TRP* 3.1 5.2 + - + +
476D PHE* 3.1 51.3 + - + -
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Residues in contact with HIS 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402D LEU 4.1 9.6 + - - -
403D GLU* 4.9 0.7 - - - -
404D LEU* 3.9 48.9 - - + +
407D TYR* 3.6 32.7 + + + +
409D TRP* 3.5 15.2 - + - -
463D LEU* 4.5 10.1 - - + +
464D ASN 5.2 4.4 + - - -
469D CYS* 3.0 42.8 + - + +
470D HIS* 2.9 18.9 + - - +
472D GLN* 1.3 77.5 - - - +
474D LEU* 1.3 59.9 + - - +
476D PHE* 3.3 1.4 + - - -
477D GLN* 2.9 24.2 + - - +
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Residues in contact with LEU 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1162B PTR 5.9 0.7 - - - +
450C PHE* 4.1 6.5 - - + -
452C PHE* 3.6 49.7 - - + -
457C LYS* 4.2 20.0 - - + +
407D TYR* 4.7 7.0 - - + +
470D HIS* 2.9 52.2 + - + +
471D VAL* 3.3 14.8 - - + +
473D HIS* 1.3 78.1 - - - +
475D TRP* 1.3 64.5 + - - +
477D GLN* 3.1 7.2 + - + +
478D SER* 2.9 24.1 + - - -
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Residues in contact with TRP 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432C GLY 4.2 6.5 - - - -
434C PHE* 3.8 33.2 - + + -
448C LEU* 3.6 21.1 - - + +
450C PHE* 3.5 35.4 - + + -
459C LEU* 3.9 12.3 - - + -
475C TRP* 3.9 9.8 - - - +
476C PHE* 4.0 22.8 - + - -
479C VAL* 3.7 28.9 - - + -
471D VAL 2.9 8.9 + - - +
472D GLN* 3.3 7.9 - - + +
474D LEU* 1.3 76.5 - - - +
476D PHE* 1.3 93.7 + + - +
478D SER* 2.5 32.3 + - - -
479D VAL* 3.2 20.3 + - + +
482D MET* 5.5 0.2 - - + -
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Residues in contact with PHE 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C TRP* 4.2 22.7 - + - -
409D TRP* 3.8 38.5 + + + -
434D PHE* 3.7 16.1 - + + -
436D ILE* 4.5 7.6 - - + -
448D LEU* 4.5 9.9 - - + -
461D LEU* 4.3 27.4 - - + -
463D LEU* 4.3 10.1 - - + -
472D GLN* 3.1 45.7 + - + -
473D HIS* 3.9 0.4 - - - +
475D TRP* 1.3 99.6 - + - +
477D GLN* 1.3 62.7 + - - +
479D VAL* 3.3 2.8 + - - +
480D PHE* 2.9 24.1 + - - +
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Residues in contact with GLN 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452C PHE* 4.6 12.1 - - + -
407D TYR* 3.3 21.3 - - + -
408D PRO* 4.1 7.2 - - - +
409D TRP* 3.1 26.6 + - - +
473D HIS 2.9 17.2 + - - +
474D LEU* 3.1 9.8 + - + +
476D PHE* 1.3 75.8 - - - +
478D SER* 1.3 53.9 + - - +
480D PHE* 3.2 26.3 + - - +
481D ASP* 2.7 68.7 + - - +
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Residues in contact with SER 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C HIS* 3.9 23.6 + - - -
432C GLY* 4.4 14.4 - - - -
450C PHE* 4.5 1.9 - - - -
451C ASN 5.0 1.8 - - - -
452C PHE* 4.3 6.0 - - - -
474D LEU 2.9 11.7 + - - -
475D TRP* 2.5 37.7 + - - -
477D GLN* 1.3 74.9 - - - +
479D VAL* 1.3 63.4 + - - +
481D ASP* 3.2 12.7 + - - +
482D MET* 3.1 27.6 + - - +
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Residues in contact with VAL 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C TRP* 3.9 9.2 - - + -
479C VAL* 3.8 28.0 - - + -
482C MET* 4.1 15.4 - - + +
434D PHE* 3.6 21.1 - - + -
475D TRP* 3.2 49.6 + - + +
476D PHE* 3.8 6.3 - - - +
477D GLN 3.2 0.2 - - - -
478D SER* 1.3 73.8 + - - +
480D PHE* 1.3 66.6 + - - +
482D MET* 3.0 12.9 + - + +
483D LEU* 3.0 20.5 + - + +
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Residues in contact with PHE 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408D PRO* 3.4 35.4 - - + -
409D TRP* 3.6 29.2 - + + -
434D PHE* 3.9 10.9 - + + -
476D PHE 2.9 14.2 + - - +
477D GLN* 3.3 31.2 - - - +
479D VAL* 1.3 78.8 - - - +
481D ASP* 1.3 57.0 + - - +
483D LEU* 3.2 17.1 + - + +
484D ARG* 2.9 51.3 + - + +
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Residues in contact with ASP 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431C HIS* 3.3 28.8 + - + +
452C PHE* 4.9 1.6 - - - -
477D GLN* 2.7 46.8 + - - +
478D SER* 3.3 11.9 - - - +
479D VAL 3.1 0.2 - - - -
480D PHE* 1.3 79.3 - - - +
482D MET* 1.3 62.0 + - - +
483D LEU 3.3 0.3 + - - -
484D ARG* 3.4 18.9 + - - +
485D HIS* 3.6 28.7 + - + +
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Residues in contact with MET 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431C HIS* 5.2 6.7 - - + +
432C GLY* 3.5 39.9 - - - +
479C VAL* 4.5 11.2 - - + +
482C MET* 4.5 17.7 - - + +
483C LEU* 3.1 41.1 - - + -
486C PHE* 4.4 24.0 - - + -
475D TRP* 5.5 0.2 - - + -
478D SER* 3.1 26.2 + - - +
479D VAL* 3.0 16.1 + - + +
481D ASP* 1.3 75.9 - - + +
483D LEU* 1.3 64.3 + - - +
485D HIS* 3.2 12.7 + - - +
486D PHE* 3.3 17.7 - - - -
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Residues in contact with LEU 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482C MET* 3.5 25.8 - - - -
431D HIS 4.8 3.6 - - - +
432D GLY* 4.0 1.6 - - - +
433D LEU* 3.7 49.4 - - + +
434D PHE* 3.9 24.2 - - + +
479D VAL 3.0 12.6 + - - +
480D PHE* 3.3 18.4 - - + +
481D ASP 3.2 0.2 - - - -
482D MET* 1.3 73.2 - - - +
484D ARG* 1.3 54.7 + - - +
485D HIS 2.6 17.4 + - - -
486D PHE* 2.9 28.7 + - + +
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Residues in contact with ARG 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480D PHE* 2.9 35.8 + - + +
481D ASP* 3.4 16.9 + - - +
483D LEU* 1.3 77.0 - - - +
485D HIS* 1.3 67.7 + - + +
486D PHE 3.2 9.8 + - - +
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Residues in contact with HIS 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C PHE* 4.1 28.5 - + + -
481D ASP* 3.6 21.9 + - + +
482D MET* 3.2 9.1 + - - +
483D LEU 2.6 5.9 + - - -
484D ARG* 1.3 89.0 - - + +
486D PHE* 1.3 70.6 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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