Contacts of the strand formed by residues 390 - 395 (chain A) in PDB entry 1YI1
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 390 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU* 3.2 53.1 + - + +
298A GLU* 4.2 14.5 + - - +
299A SER* 4.2 9.1 - - - +
365A ASP* 2.9 23.9 + - - +
366A LEU* 3.3 20.9 - - + +
367A LEU 2.7 31.4 + - - -
389A ALA* 1.3 70.2 - - - +
391A ILE* 1.3 55.3 + - - +
392A VAL* 5.7 0.4 - - + -
408A HIS* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A LEU* 3.6 23.6 - - + +
369A ALA* 4.9 0.2 - - + -
374A PHE* 3.9 24.2 - - + -
386A ALA* 4.4 16.2 - - + +
389A ALA 3.6 13.7 - - - +
390A LYS* 1.3 73.0 - - - +
392A VAL* 1.3 68.1 + - - +
393A HIS* 4.6 1.1 - - + +
405A LYS* 3.9 38.6 - - + +
406A THR 4.4 6.3 - - - +
407A PRO* 3.4 15.1 - - + +
408A HIS* 2.8 44.8 + - + +
409A VAL 3.2 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ILE* 3.8 34.5 - - + -
295A LEU* 3.9 28.9 - - + -
366A LEU* 4.1 9.2 - - + -
367A LEU 2.9 6.5 + - - +
368A LEU* 3.7 24.3 - - + -
369A ALA* 2.8 28.6 + - - +
370A PHE* 4.4 10.4 - - + -
390A LYS* 5.3 0.9 - - + -
391A ILE* 1.3 74.6 - - - +
393A HIS* 1.3 62.5 + - - +
394A ILE* 4.2 4.9 + - + -
409A VAL* 3.1 17.5 - - + +
411A VAL* 5.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ALA* 3.4 13.2 - - + -
372A VAL* 3.3 24.2 + - + -
373A ARG* 5.3 0.9 - - - -
374A PHE* 3.6 34.7 - + + -
391A ILE* 4.0 2.9 - - + -
392A VAL* 1.3 74.9 - - - +
394A ILE* 1.3 72.1 + - - +
395A ASP* 3.6 11.6 + - + +
400A GLU* 3.6 26.0 + - + -
401A ILE* 3.9 20.9 - - + +
402A GLY 4.5 1.0 + - - -
405A LYS 5.3 1.2 + - - -
407A PRO* 3.8 23.8 - - + +
409A VAL 3.0 8.9 + - - -
410A SER* 3.4 5.4 - - - -
411A VAL 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ILE* 4.1 15.9 - - + -
369A ALA 3.3 7.6 + - - +
370A PHE* 3.6 38.4 - - + -
371A GLY 3.4 23.9 + - - -
392A VAL* 4.6 3.6 - - + -
393A HIS* 1.3 73.5 - - - +
395A ASP* 1.3 62.4 + - - +
411A VAL* 3.2 32.3 - - + +
413A GLY 3.9 15.3 - - - +
415A VAL* 4.0 21.1 - - + -
418A ALA* 3.5 27.4 - - + -
422A MET* 4.3 2.9 - - + -
701A FAD 4.0 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A VAL 3.0 19.2 + - - +
393A HIS* 3.6 14.9 + - + +
394A ILE* 1.3 75.0 - - - +
396A ILE* 1.3 62.6 + - - +
397A ASP* 2.8 28.7 + - - +
400A GLU* 3.9 9.6 - - - +
401A ILE* 4.0 17.1 - - + +
411A VAL 3.1 5.9 + - - -
412A CYS* 3.2 11.4 - - - -
413A GLY 2.9 21.5 + - - -
701A FAD 2.7 48.4 + - - -
----------------------------------------------------------
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