Contacts of the helix formed by residues 525 - 539 (chain N) in PDB entry 5GJQ
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 525 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494N TYR* 6.2 1.8 - - - -
520N MET* 4.3 16.8 - - + -
523N SER 4.3 1.3 - - - -
524N LYS* 1.3 83.0 - - - +
526N ALA* 1.3 63.8 + - - +
527N GLN* 4.1 11.4 - - + +
528N ALA* 3.7 29.5 - - - +
529N ILE* 3.3 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 526 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525N ASN* 1.3 71.1 - - - +
527N GLN* 1.3 55.7 + - + +
529N ILE* 3.0 20.9 - - + +
530N GLU* 2.6 41.8 + - + +
559N ARG* 4.8 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 527 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525N ASN* 3.1 11.3 - - + -
526N ALA* 1.3 74.6 - - + +
528N ALA* 1.3 56.1 + - - +
530N GLU* 2.9 11.5 + - - +
531N ASP* 2.6 44.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 528 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494N TYR* 3.4 45.2 - - + -
520N MET* 5.7 4.3 - - + -
525N ASN* 3.6 23.4 + - - +
527N GLN* 1.3 76.6 - - - +
529N ILE* 1.3 52.8 + - + +
531N ASP* 3.0 1.9 + - - -
532N MET* 2.3 45.9 + - + +
555N VAL* 5.7 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 529 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525N ASN 3.3 9.3 + - - +
526N ALA* 3.0 26.2 + - + +
527N GLN 3.1 0.6 - - - -
528N ALA* 1.3 76.6 - - - +
530N GLU* 1.3 56.0 + - + +
532N MET* 4.2 6.7 - - - +
533N VAL* 2.4 38.9 + - + +
552N ILE* 4.8 3.3 - - + +
555N VAL* 4.0 17.7 - - + +
556N MET* 3.9 14.1 - - + -
559N ARG* 3.2 32.1 - - - +
563N ALA* 6.3 0.4 - - - -
566N LEU* 3.5 40.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 530 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526N ALA* 2.6 25.7 + - + +
527N GLN* 3.2 10.1 - - - +
529N ILE* 1.3 73.6 - - + +
531N ASP* 1.3 55.6 + - - +
533N VAL* 3.5 5.6 - - - +
534N GLY* 2.3 39.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 531 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494N TYR* 2.5 27.6 + - - +
498N LYS* 2.8 21.3 + - - -
527N GLN* 2.6 26.0 + - - +
528N ALA* 3.0 9.5 + - - +
530N GLU* 1.3 70.5 - - - +
532N MET* 1.3 51.7 + - - +
534N GLY* 2.9 2.6 + - - -
535N TYR* 2.3 56.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 532 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494N TYR* 3.4 39.0 - - + +
498N LYS* 5.1 0.4 - - + -
501N LEU* 4.0 10.8 - - + -
512N ALA 6.1 0.2 - - - -
513N GLY* 5.2 5.2 - - - +
516N LEU* 4.8 13.5 - - + -
517N GLY 6.0 0.7 - - - -
528N ALA* 2.3 39.8 + - + +
529N ILE* 3.5 4.5 - - + +
531N ASP* 1.3 66.1 - - - +
533N VAL* 1.3 52.9 + - - +
535N TYR* 2.9 21.2 + - + +
536N ALA* 2.3 40.3 + - - +
548N LEU* 3.6 32.5 - - + +
551N GLY* 5.5 3.1 - - - -
552N ILE* 3.8 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 533 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529N ILE* 2.4 29.3 + - + +
530N GLU* 3.5 4.7 - - - +
532N MET* 1.3 71.4 - - - +
534N GLY* 1.3 65.0 + - - +
536N ALA* 3.0 10.0 - - - +
537N GLN* 3.0 34.5 + - - +
552N ILE* 4.5 5.3 - - + +
566N LEU* 3.9 28.7 - - + -
569N SER* 5.5 5.4 - - - -
578N LEU* 5.1 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 534 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530N GLU 2.3 26.7 + - - -
531N ASP* 3.2 2.0 - - - -
533N VAL* 1.3 64.7 - - - +
535N TYR* 1.3 55.1 + - - -
537N GLN* 2.7 10.2 + - - +
538N GLU* 2.3 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 535 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498N LYS* 3.4 33.6 + - + +
501N LEU* 3.5 27.6 - - + -
502N TYR* 3.4 34.9 - + + +
531N ASP* 2.3 61.9 + - + +
532N MET* 3.4 9.0 - - + +
534N GLY* 1.3 64.2 - - - -
536N ALA* 1.3 57.0 + - - +
538N GLU* 3.6 21.0 + - - -
539N THR* 2.2 66.8 + - + +
548N LEU* 3.6 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 536 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532N MET 2.3 27.6 + - - +
533N VAL* 3.0 15.3 - - - +
535N TYR* 1.3 71.9 - - - +
537N GLN* 1.3 62.9 + - + +
539N THR 3.2 6.2 - - - +
545N LEU* 3.1 27.1 - - + +
548N LEU* 3.3 19.4 - - + +
552N ILE* 6.5 0.2 - - + -
578N LEU* 3.6 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 537 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533N VAL* 3.6 19.8 - - - +
534N GLY* 2.7 10.9 + - - +
536N ALA* 1.3 78.5 - - - +
538N GLU* 1.3 63.7 + - - +
539N THR 4.2 0.9 - - - +
540N GLN* 4.9 4.3 - - - +
573N ASP* 5.9 1.8 - - - +
578N LEU* 4.3 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 538 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502N TYR* 4.1 18.9 - - - -
531N ASP 4.9 0.2 - - - +
534N GLY* 2.3 32.8 + - - +
535N TYR* 3.6 31.9 + - - -
537N GLN* 1.3 73.6 - - - +
539N THR* 1.3 68.9 + - + +
540N GLN* 3.4 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 539 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501N LEU* 5.4 1.1 - - + -
502N TYR* 5.0 4.3 - - + -
504N ASP* 4.1 21.3 - - - +
535N TYR* 2.2 78.6 + - + +
536N ALA 3.2 13.5 + - - +
537N GLN 4.2 1.0 - - - +
538N GLU* 1.3 76.5 - - + +
540N GLN* 1.3 64.1 + - - +
541N HIS* 3.6 4.2 + - - +
544N ILE* 4.1 18.9 - - + +
545N LEU* 4.0 7.3 - - - +
548N LEU* 3.7 11.8 - - - +
----------------------------------------------------------
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