Contacts of the strand formed by residues 338 - 341 (chain E) in PDB entry 4RYD
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 ALA 338 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316E SER 3.6 2.8 + - - -
317E ILE* 3.4 13.1 - - + +
318E SER 2.9 23.0 + - - -
336E THR* 3.6 4.6 - - - +
337E LEU* 1.3 80.2 - - - +
339E THR* 1.3 65.8 + - - +
397E VAL* 3.5 13.0 - - + -
401E SER* 3.7 4.5 - - - +
424E TYR 3.4 9.2 - - - -
426E TYR 4.3 0.2 - - - +
427E GLY 3.5 8.3 - - - +
429E LEU* 3.5 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 339 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317E ILE* 4.1 0.9 - - - -
318E SER* 3.2 16.3 - - - +
319E SER 3.4 25.4 - - - +
320E ALA* 3.7 13.5 - - + +
338E ALA* 1.3 76.1 + - - +
340E THR* 1.3 75.1 + - - +
406E LEU* 4.7 1.1 - - + -
424E TYR* 2.8 44.1 + - + +
427E GLY 2.7 18.7 + - - -
428E LEU* 3.4 7.4 - - + -
429E LEU* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 340 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E LEU* 4.0 14.6 - - + -
317E ILE* 4.0 2.4 - - + +
318E SER 3.1 3.6 + - - -
319E SER* 3.3 14.0 - - - -
320E ALA 3.3 1.4 + - - -
339E THR* 1.3 83.1 - - - +
341E TYR* 1.3 65.1 + - - +
370E SER* 2.8 54.1 + - - +
373E LEU* 4.1 12.3 - - + +
374E ALA* 3.9 11.4 - - + +
377E ILE* 5.1 0.2 - - + -
428E LEU* 4.1 2.5 - - - -
429E LEU* 3.4 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 341 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E TRP* 3.6 29.6 - + + -
123E TYR* 3.9 20.0 - - + -
130E ARG* 3.6 29.2 - - + +
131E ASP* 3.6 20.9 - - - -
132E LEU* 4.0 15.0 - - + +
320E ALA* 3.4 18.6 - - + -
321E THR 3.3 27.1 - - - -
322E GLN 4.2 5.9 + - - -
324E GLY* 4.9 2.7 - - - -
340E THR* 1.3 78.4 - - - +
342E SER* 1.3 60.9 + - - +
351E ILE* 4.0 2.7 - - - +
369E ALA 4.5 0.2 - - - +
370E SER* 3.5 4.7 + - - -
373E LEU* 3.4 20.7 - - + +
405E HIS* 5.0 3.8 - - - +
406E LEU* 4.6 6.4 - - + +
428E LEU* 3.2 32.9 - - + +
----------------------------------------------------------
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