Contacts of the strand formed by residues 411 - 415 (chain K) in PDB entry 4ZZ7
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 GLY 411 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251K ASN* 2.8 48.0 + - - +
252K HIS 3.7 0.5 + - - -
281K MET* 3.5 10.5 - - - -
409K GLY 3.9 0.4 - - - -
410K ASN* 1.3 83.2 - - - +
412K THR* 1.3 62.0 + - - -
431K VAL* 3.8 3.6 - - - +
433K MET 3.3 8.1 - - - -
441K PRO* 5.0 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 412 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251K ASN* 5.1 0.9 - - - -
252K HIS 2.7 23.6 + - - -
283K LEU* 5.8 1.3 - - - -
403K ILE* 3.9 11.5 - - - +
411K GLY* 1.3 75.5 - - - -
413K CYS* 1.3 56.8 + - - +
425K PHE* 3.4 32.0 - - + -
429K ILE* 4.0 5.4 - - + -
431K VAL* 3.5 31.4 - - + -
433K MET 3.0 7.5 + - - -
434K VAL* 3.5 10.7 - - + -
435K GLY 2.7 29.8 + - - -
439K PRO 5.4 0.7 - - - -
441K PRO* 3.4 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 413 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252K HIS 3.0 4.6 + - - +
253K ALA* 3.2 6.2 - - + -
254K ILE 2.9 23.9 + - - -
283K LEU* 4.1 11.4 - - + -
412K THR* 1.3 81.1 + - - +
414K ILE* 1.3 69.8 + - - +
415K PHE* 3.8 22.9 - - - -
425K PHE* 3.7 8.9 - - - -
435K GLY 3.4 6.3 - - - -
438K ILE 3.3 44.0 - - - +
439K PRO* 3.7 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 414 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254K ILE* 3.6 14.6 - - + +
256K MET* 4.0 17.5 - - + -
396K MET* 3.6 31.0 - - + -
413K CYS* 1.3 77.7 - - - +
415K PHE* 1.3 67.9 + - - +
416K THR* 3.6 24.2 + - + +
421K ALA* 4.2 3.8 - - + +
422K ALA* 4.7 0.9 - - - -
425K PHE* 3.2 38.4 - - + -
435K GLY 3.3 2.4 + - - +
436K ILE* 3.6 21.9 - - + -
437K ASN* 2.9 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 415 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253K ALA* 3.8 24.0 - - + -
254K ILE 3.0 15.4 + - - +
255K VAL* 4.1 17.0 - - + -
256K MET* 3.3 24.8 + - - +
259K ALA* 3.4 19.6 - - + +
260K ASP 5.5 0.7 - - - +
263K ASN* 4.8 2.7 - - - -
264K ALA* 4.0 31.9 - - + -
267K GLN* 3.8 24.2 - - + -
268K LEU* 4.2 16.2 - - + -
413K CYS* 3.8 19.5 - - - -
414K ILE* 1.3 71.6 - - - +
416K THR* 1.3 62.1 + - - +
437K ASN* 3.4 20.6 - - + +
439K PRO* 4.2 17.0 - - + -
----------------------------------------------------------
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