Contacts of the helix formed by residues 478 - 495 (chain A) in PDB entry 2QCU
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 ASN 478 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A TRP 3.5 3.5 + - - +
477A LEU* 1.3 75.3 - - - +
479A ALA* 1.3 59.1 + - - +
480A ASP* 3.1 14.5 - - - +
481A GLN* 2.8 52.0 + - - +
482A GLN* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A ASN* 1.3 74.8 - - - +
480A ASP* 1.3 59.6 + - - +
482A GLN* 3.3 8.8 + - - +
483A SER* 2.9 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 480 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A ASN* 3.1 10.0 - - - +
479A ALA* 1.3 77.4 - - - +
481A GLN* 1.3 62.0 + - + +
483A SER* 3.2 10.3 + - - -
484A ARG* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A PHE* 3.4 26.9 + - - +
443A GLY* 3.9 13.8 - - - -
476A TRP 4.3 2.3 - - - +
477A LEU* 3.5 16.9 - - + +
478A ASN* 2.8 50.5 + - - +
480A ASP* 1.3 73.8 - - + +
482A GLN* 1.3 58.2 + - - +
484A ARG* 3.3 8.6 + - - +
485A VAL* 3.1 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A ALA* 4.2 4.7 - - + +
464A ASP* 4.8 7.3 + - - -
467A LEU* 3.8 25.1 - - + +
468A TRP* 4.0 18.4 + - - +
474A GLY* 3.4 20.1 - - - +
477A LEU* 3.0 29.2 - - + +
478A ASN 2.9 19.8 + - - +
479A ALA* 3.7 6.7 - - - +
481A GLN* 1.3 75.2 - - - +
483A SER* 1.3 63.2 + - - +
485A VAL* 3.3 4.7 + - - +
486A SER* 3.1 24.0 + - - -
802A SO4 4.6 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A ALA 2.9 15.0 + - - -
480A ASP* 3.2 16.8 + - - -
481A GLN 3.3 0.2 - - - -
482A GLN* 1.3 77.9 - - - +
484A ARG* 1.3 54.6 + - - +
486A SER* 3.1 9.7 + - - -
487A GLN* 2.9 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A GLU* 2.9 41.7 + - - +
442A PHE* 3.8 12.3 - - + -
480A ASP 3.0 14.0 + - - +
481A GLN* 3.3 11.4 + - - +
483A SER* 1.3 71.9 + - - +
485A VAL* 1.3 67.1 + - - +
487A GLN* 2.8 51.5 + - - +
488A TRP* 2.9 43.8 + - - +
491A GLU* 3.9 10.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A PHE* 3.9 34.1 - - + -
446A PHE* 4.3 7.0 - - + -
451A LEU* 4.0 24.6 - - + +
463A ALA* 3.8 20.0 - - + +
466A ALA* 5.0 0.2 - - + -
467A LEU* 4.3 13.5 - - + -
477A LEU* 4.0 14.8 - - + -
481A GLN 3.1 14.7 + - - +
482A GLN 3.5 8.5 - - - +
484A ARG* 1.3 75.4 - - - +
486A SER* 1.3 63.5 + - - +
488A TRP* 3.3 2.9 + - - +
489A LEU* 3.0 26.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A ALA* 3.2 25.9 + - - +
482A GLN 3.1 10.2 + - - -
483A SER* 3.1 12.9 + - - -
485A VAL* 1.3 74.3 - - - +
487A GLN* 1.3 63.8 + - - +
489A LEU* 3.1 9.7 + - - +
490A VAL* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A SER 2.9 15.2 + - - +
484A ARG* 2.8 34.0 + - - +
486A SER* 1.3 76.9 - - - +
488A TRP* 1.3 61.7 + - - +
489A LEU 3.3 0.2 + - - -
490A VAL* 3.3 9.3 + - + +
491A GLU* 2.8 49.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A GLU* 4.1 3.1 - - - -
442A PHE* 3.7 25.1 - + + -
448A GLU* 3.3 42.5 + - + +
451A LEU* 3.3 31.6 - - + -
452A LYS* 3.7 27.8 - - + -
455A VAL* 4.3 0.4 - - + -
484A ARG* 2.9 42.0 + - - +
485A VAL 3.7 3.6 - - - +
487A GLN* 1.3 71.8 - - - +
489A LEU* 1.3 68.5 + - + +
491A GLU* 3.2 11.7 + - + +
492A TYR* 2.8 70.1 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A LEU* 4.0 13.2 - - + -
455A VAL* 3.2 34.8 - - + -
460A VAL* 4.0 12.3 - - + -
461A ARG 4.3 10.3 - - - +
462A ARG* 3.4 12.3 - - - +
463A ALA* 3.4 37.5 - - + +
485A VAL* 3.0 25.0 + - + +
486A SER* 3.1 8.0 + - - +
488A TRP* 1.3 82.0 - - + +
490A VAL* 1.3 61.4 + - - +
492A TYR* 4.7 0.2 - - - -
493A THR* 2.6 42.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A SER* 3.0 22.3 + - - +
487A GLN* 3.5 10.3 - - + +
489A LEU* 1.3 73.8 - - + +
491A GLU* 1.3 60.8 + - + +
493A THR* 3.7 4.1 + - - -
494A GLN* 2.8 58.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ARG* 4.2 11.3 + - - -
487A GLN* 2.8 48.6 + - + +
488A TRP* 3.5 12.5 - - + +
490A VAL* 1.3 82.3 - - + +
492A TYR* 1.3 60.9 + - - +
494A GLN* 3.4 6.3 + - - +
495A GLN 3.0 9.2 + - - +
496A ARG* 2.7 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A LYS* 3.3 28.5 - - + -
455A VAL* 3.6 31.6 - - + -
456A ASP* 2.7 35.8 + - - -
488A TRP* 2.8 53.8 + + + +
489A LEU* 4.2 1.8 - - - +
491A GLU* 1.3 74.9 - - - +
493A THR* 1.3 58.5 + - + +
495A GLN 3.1 14.4 - - - +
496A ARG* 3.3 37.9 - - - +
497A LEU* 3.0 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A VAL* 3.9 35.0 - - + -
460A VAL 4.7 5.2 - - - +
461A ARG* 4.8 23.0 + - - +
462A ARG* 5.6 2.3 + - - -
489A LEU* 2.6 36.1 + - + +
490A VAL* 3.7 4.0 + - - -
492A TYR* 1.3 73.2 - - + +
494A GLN* 1.3 64.8 + - - +
497A LEU* 6.2 0.2 - - - -
498A SER* 3.4 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A VAL* 2.8 40.3 + - + +
491A GLU* 4.0 4.2 - - - +
492A TYR 3.3 0.4 - - - -
493A THR* 1.3 80.5 - - - +
495A GLN* 1.3 84.8 + - - +
498A SER* 4.0 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A GLU 3.0 17.6 + - - +
492A TYR 3.1 3.0 - - - +
493A THR 4.5 0.2 - - - -
494A GLN* 1.3 92.9 + - + +
496A ARG* 1.3 78.9 + - - +
497A LEU 3.1 1.1 - - - +
498A SER* 2.9 23.6 - - - +
499A LEU 4.0 16.8 + - - +
500A ALA* 5.1 4.6 - - - +
----------------------------------------------------------
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