Contacts of the helix formed by residues 506 - 517 (chain B) in PDB entry 1ASZ
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 PRO 506 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ALA* 4.0 20.4 - - + -
279B PRO* 5.9 0.9 - - + +
505B ASP* 1.3 91.6 - - + +
507B GLY* 1.3 63.5 + - - +
508B LEU 2.8 8.0 + - - -
509B LYS* 3.3 13.8 + - + +
510B ASP* 3.9 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 507 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ALA* 3.8 11.9 - - - +
279B PRO 3.7 22.4 + - - -
280B SER* 5.0 5.3 - - - -
304B PHE* 4.0 12.0 - - - -
505B ASP* 2.9 14.3 + - - -
506B PRO* 1.3 77.4 - - - +
508B LEU* 1.3 70.4 + - - +
510B ASP* 6.4 0.2 - - - -
511B TYR* 4.9 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 508 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B SER* 5.3 0.2 - - - -
281B GLU* 3.9 20.0 - - + +
304B PHE* 3.5 35.9 - - + -
455B PHE* 3.7 17.5 - - + -
496B MET* 3.2 31.0 - - + -
501B LEU* 3.7 17.5 - - + -
502B SER 4.2 2.7 - - - +
503B PRO* 4.5 1.8 - - + -
505B ASP* 3.2 21.7 + - - +
506B PRO 2.8 2.0 + - - -
507B GLY* 1.3 78.4 - - - +
509B LYS* 1.3 56.8 + - - +
510B ASP 3.5 1.6 - - - -
511B TYR* 3.5 10.8 + - + +
512B CYS* 2.8 37.2 + - - +
676S A 4.1 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 509 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B PRO 4.0 10.0 + - - +
504B GLU* 3.1 42.0 + - - +
505B ASP 2.8 20.6 + - - +
506B PRO* 3.3 8.0 + - + +
508B LEU* 1.3 74.5 - - - +
510B ASP* 1.3 64.0 + - - +
512B CYS* 2.7 22.9 + - - +
513B ASP* 2.9 49.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 510 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A ARG* 3.2 47.6 + - - +
557A PRO* 4.5 15.6 - - + +
308B GLN* 4.0 7.0 - - - +
506B PRO* 3.9 13.3 + - - +
507B GLY 6.4 0.2 - - - -
508B LEU 3.5 0.2 - - - -
509B LYS* 1.3 87.2 - - - +
511B TYR* 1.3 63.8 + - - +
512B CYS 3.1 1.0 + - - -
513B ASP* 3.4 7.3 + - - +
514B GLY* 3.2 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 511 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B PHE* 3.4 59.8 - + + -
307B GLN* 2.8 34.9 + - + -
308B GLN* 3.6 23.8 + - - +
455B PHE* 3.7 26.0 - + - -
456B TYR* 3.8 18.4 - - - +
486B ILE 5.3 0.2 + - - -
492B LEU* 4.4 11.9 - - + +
496B MET* 5.5 0.7 - - - -
507B GLY 4.9 1.5 + - - +
508B LEU* 3.5 17.8 + - + +
509B LYS 3.3 0.6 - - - -
510B ASP* 1.3 77.9 - - - +
512B CYS* 1.3 63.8 + - + +
514B GLY 3.8 0.7 + - - -
515B PHE* 3.3 38.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 512 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B HIS* 3.0 48.9 + - - -
492B LEU* 4.6 12.8 - - - -
493B GLN* 4.2 17.9 - - - -
496B MET* 4.7 2.0 - - - -
503B PRO* 4.2 19.7 - - + +
508B LEU 2.8 19.7 + - - +
509B LYS 2.7 8.0 + - - +
511B TYR* 1.3 80.2 - - + +
513B ASP* 1.3 58.8 + - - +
514B GLY 3.0 1.8 - - - -
515B PHE* 2.8 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 513 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B HIS* 4.5 4.3 - - - -
503B PRO 5.3 0.3 - - - +
509B LYS* 2.9 54.8 + - - +
510B ASP* 3.9 6.4 + - - +
512B CYS* 1.3 74.8 - - - +
514B GLY* 1.3 59.1 + - - +
516B SER* 2.6 41.9 + - - +
517B TYR* 3.4 26.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 514 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A VAL* 5.4 2.7 - - - -
308B GLN* 3.7 24.2 - - - -
311B VAL* 3.7 20.2 - - - +
510B ASP 3.2 11.1 + - - -
511B TYR 4.1 0.2 - - - -
512B CYS 3.0 2.0 - - - -
513B ASP* 1.3 78.1 - - - +
515B PHE* 1.3 60.0 + - - +
517B TYR* 3.1 30.4 + - - +
518B GLY 4.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 515 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLN* 3.7 29.2 - - + -
308B GLN* 4.7 2.9 - - - -
311B VAL* 4.5 9.9 - - + -
486B ILE 3.7 6.3 - - - -
487B HIS* 3.1 45.5 - - + +
489B HIS* 4.2 17.8 + - + +
492B LEU* 3.9 15.0 - - + -
511B TYR* 3.3 49.4 - + - -
512B CYS* 2.8 12.8 + - - +
514B GLY* 1.3 76.4 - - - +
516B SER* 1.3 60.3 + - - +
517B TYR 3.0 2.1 + - - -
518B GLY* 3.1 14.6 + - - -
519B CYS* 4.3 13.1 + - + -
522B HIS* 4.0 14.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 516 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLU 4.7 2.6 - - - +
200A THR* 3.7 2.6 - - - +
201A PRO* 3.4 28.6 - - - +
489B HIS* 4.0 30.9 + - - -
512B CYS 3.6 1.2 + - - -
513B ASP* 2.6 27.8 + - - +
515B PHE* 1.3 72.5 - - - +
517B TYR* 1.3 69.0 + - - -
518B GLY 3.2 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 517 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ARG* 3.4 7.1 + - - -
163A GLU* 3.9 2.4 - - - +
200A THR* 3.5 19.9 + - - +
201A PRO* 5.7 1.3 - - + -
204A LEU* 4.3 25.4 - - + -
205A PRO* 4.7 6.8 - - + +
234A TYR* 4.1 23.6 - + + -
236A VAL* 5.1 10.8 - - + -
237A ILE* 3.9 29.6 - - + -
240A ARG* 3.4 23.2 + - - +
311B VAL* 4.7 5.2 - - + -
513B ASP* 3.8 27.0 + - + +
514B GLY* 3.5 20.4 - - - +
515B PHE 3.0 1.6 - - - -
516B SER* 1.3 92.9 - - - +
518B GLY* 1.3 62.1 + - - +
----------------------------------------------------------
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