Contacts of the strand formed by residues 403 - 409 (chain F) in PDB entry 1ZMD
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 MET 403 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221F GLU* 3.7 33.7 - - + +
222F ILE* 4.1 23.7 - - + +
225F ASN* 3.7 23.8 - - + +
385F LYS* 4.0 28.9 - - + -
386F PHE 3.3 19.3 - - - +
387F PRO* 4.0 3.6 - - + -
388F PHE* 3.8 5.6 - - - -
402F GLY* 1.3 79.0 - - - +
404F VAL* 1.3 64.8 + - - +
405F LYS* 4.7 7.6 - - + -
419F HIS 4.0 1.0 - - - +
420F ILE* 3.7 1.2 - - - -
421F LEU* 2.7 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 404 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385F LYS* 3.5 4.2 - - - +
386F PHE 3.0 28.9 + - - +
388F PHE* 3.7 26.9 - - + -
403F MET* 1.3 74.8 - - - +
405F LYS* 1.3 61.7 + - - +
406F ILE* 4.3 7.9 - - + -
419F HIS 3.5 8.1 - - - +
420F ILE* 4.1 9.4 - - + -
428F MET* 4.1 10.8 - - - -
458F ALA* 3.9 24.0 - - + +
459F PHE* 4.0 30.3 - - + +
462F ALA* 3.6 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 405 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219F ASP* 2.8 37.6 + - - -
221F GLU* 2.8 28.7 + - - +
222F ILE* 4.4 10.5 - - + -
371F GLU* 2.8 24.9 + - - +
383F VAL* 3.8 28.5 - - + -
384F GLY 3.5 2.9 - - - +
385F LYS* 4.0 10.1 - - + +
403F MET* 4.1 8.0 - - - -
404F VAL* 1.3 73.9 - - - +
406F ILE* 1.3 68.0 + - - +
407F LEU* 4.1 11.4 - - + -
418F ALA* 3.5 3.3 - - - -
419F HIS* 2.7 50.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 406 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382F LYS 3.8 0.5 - - - +
383F VAL* 3.4 5.9 - - - +
384F GLY 2.8 30.7 + - - +
404F VAL* 4.3 2.9 - - + -
405F LYS* 1.3 76.0 - - - +
407F LEU* 1.3 71.5 + - - +
408F GLY 4.2 0.2 + - - -
415F VAL* 4.2 6.3 - - + -
417F GLY 3.6 3.1 - - - +
418F ALA* 3.6 30.3 - - + -
442F CYS* 3.8 20.6 - - - -
459F PHE* 3.7 11.2 - - + -
462F ALA* 3.8 28.0 - - + +
463F ASN* 3.4 43.3 - - - +
466F ALA* 4.0 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219F ASP* 5.0 0.2 - - - +
369F LYS 3.3 25.8 - - - +
370F SER 3.7 2.2 - - - -
371F GLU* 3.6 37.5 - - + +
374F LEU* 3.8 22.2 - - + -
381F TYR* 4.2 4.5 - - + -
382F LYS 3.4 3.6 - - - +
383F VAL* 3.7 25.1 - - + -
405F LYS* 4.1 11.4 - - + -
406F ILE* 1.3 83.5 - - - +
408F GLY* 1.3 52.0 + - - +
415F VAL* 3.6 2.3 - - - +
416F LEU* 2.7 33.1 + - - -
417F GLY 2.9 18.3 + - - +
419F HIS* 3.9 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 408 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381F TYR* 3.1 2.6 - - - -
382F LYS* 2.7 46.7 + - - +
406F ILE* 4.1 1.8 - - - +
407F LEU* 1.3 74.6 - - - +
409F GLN* 1.3 65.3 + - - -
413F ASP 5.0 0.2 - - - -
414F ARG 3.2 9.9 - - - -
416F LEU* 3.9 4.3 - - - -
442F CYS* 4.1 17.5 - - - -
466F ALA* 5.2 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 409 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379F ILE* 4.4 8.3 - - - +
380F GLU* 2.9 21.3 - - - +
382F LYS* 4.0 1.9 - - - -
408F GLY* 1.3 69.8 - - - -
410F LYS* 1.3 68.8 + - - +
411F SER* 3.3 13.4 + - - +
412F THR* 2.9 37.3 - - + +
413F ASP* 3.0 23.2 + - - -
414F ARG* 2.8 17.1 + - + +
416F LEU* 3.3 22.3 - - + +
2021F SO4 2.8 33.6 + - - -
----------------------------------------------------------
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