Contacts of the strand formed by residues 434 - 441 (chain B) in PDB entry 2ZZ0
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 ARG 434 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B CYS* 3.0 8.3 - - - -
428B ASN* 3.0 30.0 + - + -
431B ASP* 2.9 56.8 + - + +
432B ASN* 3.4 18.3 + - - -
433B GLU* 1.3 71.0 - - - +
435B VAL* 1.3 69.4 + - - +
436B VAL* 3.3 10.8 + - + +
459B GLY* 3.5 41.3 + - - -
460B LEU 3.7 5.4 - - - +
461B THR* 4.4 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ILE* 3.9 37.7 - - + -
426B ILE 3.5 3.6 - - - +
427B CYS* 4.4 3.8 - - - -
433B GLU 4.5 0.2 - - - +
434B ARG* 1.3 75.6 - - - +
436B VAL* 1.3 60.4 + - - +
437B GLY 3.5 8.7 - - - +
438B PHE* 5.4 2.5 - - + -
456B LEU* 3.4 33.2 - - + +
460B LEU* 2.9 50.3 + - + +
461B THR 3.8 11.7 - - - +
462B LYS* 4.0 4.9 - - - +
465B LEU* 5.4 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B ASN* 4.6 3.3 - - - +
384B GLY* 3.5 5.4 - - - -
385B LEU* 2.8 55.8 + - + +
390B ALA* 4.4 2.2 - - + -
394B PHE* 4.6 12.6 - - + -
399B ILE* 5.3 2.0 - - + -
426B ILE* 2.8 37.4 + - + +
427B CYS* 4.5 4.3 - - - +
428B ASN* 3.9 18.6 - - + +
434B ARG* 3.8 18.8 - - + +
435B VAL* 1.3 75.3 - - - +
437B GLY* 1.3 51.9 + - - +
456B LEU* 4.4 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B CYS 3.6 4.9 - - - -
385B LEU 3.4 19.7 - - - -
425B ILE* 3.1 8.8 - - - +
426B ILE* 2.9 32.7 + - - -
435B VAL* 3.5 5.4 - - - +
436B VAL* 1.3 84.8 - - - +
438B PHE* 1.3 60.1 + - - +
439B HIS* 4.0 4.7 - - - -
456B LEU* 5.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ALA* 3.3 2.9 - - - -
383B CYS* 2.7 42.7 + - + +
424B LYS 3.9 2.9 - - - -
425B ILE* 4.3 12.1 - - + -
435B VAL* 5.4 2.7 - - + -
437B GLY* 1.3 73.3 - - - +
439B HIS* 1.3 65.0 + - - +
440B VAL* 3.7 20.4 - - + -
448B VAL* 4.4 3.4 - - + -
449B THR* 3.8 20.4 - - + -
452B PHE* 3.0 58.8 - + + -
456B LEU* 4.8 12.1 - - + -
460B LEU* 6.2 0.9 - - + -
479B PHE* 3.3 46.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ASP* 4.0 8.3 + - + +
232B MET* 2.9 30.1 - - + +
380B TYR* 2.7 27.3 + - + -
381B GLY 3.7 4.3 - - - -
382B ALA* 3.9 7.9 - - + +
383B CYS 5.1 0.2 - - - -
384B GLY 4.8 4.7 - - - -
385B LEU 2.9 29.1 + - - -
386B SER* 3.8 15.8 - - - -
423B ALA* 3.6 0.9 - - - -
424B LYS* 2.9 53.5 + - + +
426B ILE* 4.2 10.5 - - + +
437B GLY 4.0 3.1 - - - -
438B PHE* 1.3 90.5 + - - +
440B VAL* 1.3 59.3 + - - +
479B PHE* 3.6 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B MET* 4.5 0.4 - - - -
380B TYR* 3.2 6.5 - - - -
381B GLY* 2.8 39.4 + - - +
406B PHE* 4.2 14.4 - - + -
422B TYR 3.6 8.3 - - - +
438B PHE* 3.7 7.4 - - + -
439B HIS* 1.3 76.2 - - - +
441B LEU* 1.3 70.1 + - - +
442B GLY* 3.9 3.1 + - - +
443B PRO 6.2 0.4 - - - +
445B ALA* 4.1 12.5 - - + +
448B VAL* 4.4 14.6 - - + -
449B THR* 3.4 26.7 - - - +
479B PHE* 3.6 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B MET* 4.4 12.3 - - - +
235B LYS* 3.7 40.6 - - + +
236B ILE* 3.9 20.2 - - + +
239B HIS* 5.9 0.7 - - + -
378B LEU* 3.5 34.1 - - + +
379B GLU 3.2 17.0 - - - +
380B TYR* 4.0 7.4 - - + -
406B PHE* 3.6 2.3 - - - -
420B LYS 3.9 12.3 - - - +
421B CYS* 3.2 6.9 - - - +
422B TYR* 2.8 39.4 + - + +
440B VAL* 1.3 74.1 - - - +
442B GLY* 1.3 55.6 + - - +
----------------------------------------------------------
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