Contacts of the strand formed by residues 326 - 329 (chain G) in PDB entry 5TWV
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 TYR 326 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E ALA* 3.5 29.4 + - + +
34E ARG 3.4 31.0 - - - -
35E PHE* 4.6 13.2 - + + -
43E ASN 5.3 0.4 + - - -
44E VAL* 3.6 13.1 - - + +
45E ALA* 3.6 16.9 + - - -
232E PRO* 5.7 2.2 - - + -
233E LEU* 4.4 28.3 - - + +
319G VAL* 4.0 26.7 - - + -
320G ALA 3.6 2.9 - - - -
321G GLU* 3.6 32.8 + - + +
322G GLU 6.2 0.2 - - - -
325G ARG* 1.3 79.7 - - - +
327G SER* 1.3 62.2 + - - +
328G VAL* 5.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 327 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E ALA* 3.4 20.8 + - - +
46E HIS 5.0 0.3 - - - -
47E LYS* 4.5 11.1 - - - +
318G ILE 3.3 2.4 - - - +
319G VAL* 3.5 2.3 - - - -
320G ALA* 2.8 47.9 + - - +
322G GLU* 3.5 26.8 + - - -
325G ARG 3.7 2.0 + - - -
326G TYR* 1.3 73.0 - - - +
328G VAL* 1.3 65.1 + - - +
329G ASP 4.2 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 328 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E VAL* 4.2 10.8 - - + -
45E ALA 3.0 15.2 + - - +
46E HIS* 3.8 22.0 - - + +
47E LYS* 3.1 23.8 + - - +
253G ALA* 4.2 8.5 - - + -
254G PRO* 4.0 20.0 - - + -
318G ILE* 3.5 19.7 - - + -
319G VAL* 4.1 22.2 - - + -
326G TYR 5.0 2.2 - - - +
327G SER* 1.3 78.4 + - - +
329G ASP* 1.3 62.0 + - - +
330G TYR* 3.7 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 329 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E LYS* 3.6 10.0 - - + +
48E ASN* 3.6 10.6 - - - +
215F VAL* 3.3 32.2 - - - +
216F ARG* 5.4 3.1 - - - +
318G ILE* 3.0 35.4 + - - +
327G SER 4.2 0.6 - - - -
328G VAL* 1.3 70.3 - - - +
330G TYR* 1.3 60.7 + - - +
331G SER* 2.6 25.3 + - - -
332G LYS* 3.4 38.9 + - + +
----------------------------------------------------------
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