Contacts of the helix formed by residues 383 - 390 (chain B) in PDB entry 6ZGI
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 SER 383 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B VAL* 1.3 87.0 - - - +
384B PRO* 1.3 72.9 - - - +
385B THR* 4.1 4.3 - - - -
386B LYS* 3.1 31.7 + - - +
387B LEU* 3.8 2.3 + - - +
983C ARG 3.3 5.2 + - - -
984C LEU* 3.8 1.9 - - - +
985C ASP* 3.2 35.9 + - - -
988C GLU* 3.2 20.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A GLY 3.7 23.6 - - - +
414A GLN* 4.9 8.5 - - - +
415A THR* 4.0 26.0 + - + +
365B TYR* 4.1 9.9 + - - -
377B PHE* 4.6 9.2 - - + -
379B CYS* 4.9 11.6 - - + +
382B VAL 4.0 5.4 - - - +
383B SER* 1.3 83.8 - - - +
385B THR* 1.3 60.7 + - - +
386B LYS 3.3 0.8 + - - -
387B LEU* 3.6 31.7 + - + +
388B ASN 5.3 0.2 + - - -
985C ASP* 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A GLY* 4.3 17.9 + - - +
414A GLN 4.0 22.0 - - - +
415A THR* 5.0 3.6 - - - +
420A ASP* 6.2 0.2 - - - +
424A LYS* 4.5 11.0 - - - +
383B SER* 4.1 3.5 - - - -
384B PRO* 1.3 76.7 - - - +
386B LYS* 1.3 65.5 + - - +
387B LEU 3.5 0.8 + - - -
388B ASN* 4.8 4.8 + - - +
389B ASP* 4.4 7.1 - - - +
985C ASP* 4.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B SER* 3.1 28.6 + - - +
385B THR* 1.3 85.9 - - - +
387B LEU* 1.3 65.2 + - - +
388B ASN 3.1 3.4 - - - -
389B ASP* 3.0 29.7 + - - +
390B LEU* 3.6 18.5 - - + +
981C LEU 3.6 14.7 + - - -
982C SER* 4.4 4.1 - - - +
983C ARG* 3.8 37.2 - - - +
984C LEU 3.9 14.8 + - - +
985C ASP* 4.2 4.9 - - + +
986C PRO* 6.2 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A THR* 5.5 0.7 - - + -
365B TYR* 4.3 24.7 - - + +
377B PHE* 4.4 21.1 - - + -
379B CYS* 4.5 4.7 - - - -
382B VAL* 4.3 26.7 - - + -
383B SER 3.8 5.3 + - - +
384B PRO* 3.6 26.4 + - + +
385B THR 3.5 1.4 - - - -
386B LYS* 1.3 78.1 - - - +
388B ASN* 1.3 61.9 + - - +
389B ASP 3.3 0.9 + - - -
390B LEU* 3.6 7.0 + - - +
392B PHE* 3.6 43.6 - - + -
432B CYS* 4.9 5.2 - - - -
515B PHE* 4.7 7.4 - - + -
526B GLY* 5.0 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A ASN* 5.8 3.8 - - - +
363B ALA 4.8 0.3 - - - +
365B TYR* 3.4 32.3 + - - -
384B PRO 5.3 0.2 + - - -
385B THR 4.8 5.0 + - - +
386B LYS 3.1 1.2 + - - -
387B LEU* 1.3 76.9 - - - +
389B ASP* 1.3 69.3 + - - +
390B LEU 3.5 1.3 + - - -
526B GLY 4.4 8.3 - - - +
527B PRO* 3.7 42.2 + - - +
528B LYS* 4.3 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B PHE* 3.9 10.1 - - - -
385B THR 4.4 10.9 - - - +
386B LYS* 3.0 23.7 + - - +
388B ASN* 1.3 84.5 - - - +
390B LEU* 1.3 63.3 + - + +
528B LYS* 3.6 33.6 + - + +
542B ASN* 4.2 7.7 + - - +
545B GLY* 3.4 19.9 - - - +
547B THR* 6.0 1.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B PHE* 4.5 6.3 - - - -
382B VAL* 3.9 28.0 - - + -
386B LYS* 3.6 20.9 - - + +
387B LEU* 3.6 1.6 + - - +
388B ASN 3.5 1.2 - - - -
389B ASP* 1.3 82.3 - - + +
391B CYS* 1.3 59.8 - - - +
392B PHE* 3.7 25.2 - - + -
517B LEU* 3.9 18.6 - - + -
518B LEU* 4.5 19.5 - - + -
525B CYS* 3.8 1.0 - - - -
526B GLY* 3.2 23.9 + - - -
545B GLY* 4.0 22.9 - - - +
982C SER* 5.0 1.1 - - - -
983C ARG* 4.3 21.8 - - + +
----------------------------------------------------------
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