Contacts of the strand formed by residues 486 - 494 (chain D) in PDB entry 1ZUM
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 THR 486 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D TYR* 3.8 12.8 - - + +
156D HIS* 3.4 38.2 + - + +
157D GLU 3.2 10.1 + - - +
159D VAL* 3.8 5.2 - - - -
185D THR* 3.8 18.2 - - - +
264D ARG* 3.2 18.0 + - - -
482D LEU 3.6 13.7 + - - -
483D GLN* 3.3 12.2 + - - +
484D ALA 3.4 0.8 - - - -
485D TYR* 1.3 82.4 + - - +
487D LYS* 1.3 68.9 + - - +
488D VAL* 4.5 5.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 487 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C GLN* 6.1 4.0 - - - +
467C GLY 5.0 6.1 - - - +
475C ARG* 4.5 15.9 - - - +
70D PHE* 6.1 2.2 - - - -
155D ARG 3.6 0.5 - - - +
157D GLU* 2.7 52.6 + - + +
158D PRO 3.6 18.7 + - - +
159D VAL* 4.0 23.4 + - + +
264D ARG* 4.5 7.6 - - - +
486D THR* 1.3 76.9 - - - +
488D VAL* 1.3 63.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 488 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C GLY* 3.9 7.8 - - - +
464C PRO* 4.6 6.1 - - + -
475C ARG* 3.5 39.4 + - + +
480C TYR* 3.4 37.9 - - + +
483C GLN* 5.8 0.2 - - - +
154D THR* 3.8 31.2 - - + -
155D ARG 3.5 4.0 - - - +
156D HIS* 3.9 10.5 - - + -
486D THR* 4.9 4.5 - - + +
487D LYS* 1.3 77.6 - - - +
489D LYS* 1.3 64.7 + - - +
490D THR* 4.2 4.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 489 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C SER 2.8 26.2 + - - +
444C GLN 2.9 18.8 + - - -
446C LEU 2.7 29.3 + - - -
447C GLN* 5.0 1.1 - - - +
448C ALA 3.5 22.7 - - - +
449C GLY 3.5 3.8 - - - -
451C VAL* 4.2 4.9 - - + -
153D TYR 3.8 0.2 - - - +
154D THR* 3.0 5.4 - - - -
155D ARG* 2.8 46.2 + - + +
157D GLU* 3.3 32.9 + - + +
487D LYS 4.0 0.4 + - - -
488D VAL* 1.3 74.9 - - - +
490D THR* 1.3 72.5 + - - +
491D VAL* 4.1 14.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 490 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C GLY 2.7 14.7 + - - -
450C THR* 3.1 11.9 - - + -
451C VAL 2.8 30.8 + - - -
463C SER* 4.2 10.8 - - - +
464C PRO* 3.0 44.2 + - + +
152D SER* 3.7 20.9 - - - +
153D TYR 3.3 7.2 - - - +
154D THR* 3.6 6.9 - - + +
488D VAL* 4.5 1.7 + - - +
489D LYS* 1.3 75.1 - - - +
491D VAL* 1.3 57.9 + - - +
492D THR* 3.7 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 491 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3116A EDO 4.2 7.0 - - - +
443C SER* 4.0 20.6 - - - -
451C VAL* 3.2 13.7 - - + +
453C VAL* 4.3 4.3 - - + -
151D PHE 3.7 1.2 - - - +
152D SER* 3.1 3.1 - - - -
153D TYR* 2.8 76.4 + - + +
155D ARG* 4.9 2.7 - - - +
489D LYS* 4.1 22.2 - - + +
490D THR* 1.3 76.8 - - - +
492D THR* 1.3 65.8 + - - +
493D VAL* 3.9 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 492 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C THR* 5.0 1.1 - - - +
451C VAL 2.9 8.5 + - - -
452C TRP* 3.2 25.7 + - + +
453C VAL 2.8 28.4 + - - -
455C CYS* 3.5 4.6 - - - -
458C VAL* 3.9 32.1 + - + +
463C SER* 4.4 1.9 + - - -
146D ILE* 4.6 5.2 - - + +
150D PHE* 4.1 17.7 - - + -
151D PHE 3.4 2.9 - - - -
152D SER* 2.8 26.7 + - - -
490D THR* 3.7 9.8 - - - +
491D VAL* 1.3 71.8 - - - +
493D VAL* 1.3 57.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 493 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B LEU* 4.2 7.6 - - + -
440B ASN* 3.8 22.2 - - - +
453C VAL* 3.6 31.4 - - + -
150D PHE* 3.1 6.4 - - - -
151D PHE* 2.8 51.2 + - + +
153D TYR* 4.5 9.9 - - + +
491D VAL* 3.9 18.8 - - + -
492D THR* 1.3 76.6 - - - +
494D LYS* 1.3 77.8 + - - +
495D VAL* 3.3 1.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 494 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B LEU* 4.8 2.4 - - - +
437B ASP* 4.0 14.5 - - - +
440B ASN* 4.8 0.7 + - - -
285C TRP* 3.7 38.1 - - + +
453C VAL 2.9 11.8 + - - +
454C ASN* 3.2 37.7 + - + +
455C CYS* 4.1 0.8 - - + -
149D ASP* 3.7 14.7 - - - +
150D PHE* 3.7 18.1 - - + -
493D VAL* 1.3 83.5 - - - +
495D VAL* 1.3 69.4 + - - +
496D PRO* 6.4 0.4 - - - -
----------------------------------------------------------
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