Contacts of the strand formed by residues 449 - 454 (chain E) in PDB entry 1FZB
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 LYS 449 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254E ASN* 6.0 0.4 - - - +
255E ARG* 3.5 4.9 - - - +
256E GLN* 3.7 31.9 - - + +
313E GLU 4.4 0.2 - - - -
314E MET* 2.9 5.9 - - - +
315E GLU* 2.7 72.1 + - + +
321E LYS* 4.3 18.7 - - - +
447E MET* 3.9 3.1 - - - +
448E ARG* 1.3 93.1 - - - +
450E MET* 1.3 60.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 450 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253E GLN* 3.7 7.3 + - - +
254E ASN 3.6 0.7 - - - -
255E ARG* 2.7 44.6 + - + +
312E ILE* 3.9 17.5 - - - -
313E GLU 3.2 6.3 - - - -
314E MET* 3.8 41.7 - - + -
412E PRO* 3.8 33.0 - - + -
435E VAL* 3.9 27.6 - - + -
436E VAL 4.2 17.5 - - - +
437E TRP* 4.3 4.9 - - + -
447E MET* 4.2 9.4 - - + -
449E LYS* 1.3 74.7 - - - +
451E SER* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 451 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251E VAL* 5.5 1.1 - - - -
253E GLN* 3.5 13.0 - - - +
254E ASN* 4.0 13.2 - - - -
311E LEU 4.4 0.7 - - - -
312E ILE* 3.1 11.1 - - - +
313E GLU* 2.7 60.3 + - - +
321E LYS* 5.0 4.2 + - - -
450E MET* 1.3 77.2 - - - +
452E MET* 1.3 64.8 + - - +
453E LYS* 4.2 14.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 452 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251E VAL* 3.7 1.4 - - - +
252E ILE* 2.6 45.7 + - + -
253E GLN* 3.0 32.9 + - + +
293E TRP* 3.4 37.2 - - + -
310E LEU* 4.1 16.6 - - + -
311E LEU 3.6 3.8 - - - -
312E ILE* 4.2 21.8 - - + -
329E PHE* 6.1 2.9 - - - -
402E TRP* 4.1 27.8 - - + -
403E TRP* 5.1 4.9 - - + -
412E PRO* 4.8 8.1 - - + -
450E MET* 5.7 0.2 - - + -
451E SER* 1.3 78.5 - - - +
453E LYS* 1.3 56.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 453 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241E ASP* 3.0 26.8 + - - +
244E THR* 5.1 0.7 - - - +
249E TRP* 3.8 29.1 - - + -
250E THR 3.2 13.2 - - - +
251E VAL* 3.8 20.5 - - - +
252E ILE 3.9 0.7 - - - +
310E LEU* 3.3 4.1 - - - +
311E LEU* 2.8 52.3 + - + +
313E GLU* 3.3 30.7 + - - +
451E SER* 4.2 17.2 + - - -
452E MET* 1.3 73.7 - - - +
454E ILE* 1.3 65.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 454 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249E TRP* 3.1 8.5 - - - -
250E THR* 2.9 44.0 + - - +
252E ILE* 3.8 17.9 - - + -
299E ILE* 5.1 0.9 - - - +
302E LEU* 3.6 41.7 - - + -
303E THR* 4.5 11.2 - - + +
308E THR* 4.8 9.2 - - + -
309E GLU 3.2 11.2 - - - +
310E LEU* 4.3 5.8 - - + -
329E PHE* 3.9 31.6 - - + -
453E LYS* 1.3 79.2 - - - +
455E ARG* 1.3 69.7 + - - +
----------------------------------------------------------
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