Contacts of the strand formed by residues 226 - 231 (chain T) in PDB entry 1VYH
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 CYS 226 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189T HIS 5.5 0.4 - - - +
217T LYS* 3.4 37.7 - - - +
218T MET 3.7 2.2 - - - -
219T TRP* 3.5 27.4 - - + -
224T GLY 3.8 0.6 + - - -
225T TYR* 1.3 76.7 - - - +
227T VAL* 1.3 61.9 + - - +
228T LYS 3.9 7.0 - - - -
229T THR* 3.6 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 227 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206T HIS* 5.1 10.3 - - + +
218T MET* 2.8 24.0 + - + +
219T TRP 4.2 0.7 - - - -
220T GLU* 3.6 23.3 - - + +
225T TYR* 3.6 16.6 - - + +
226T CYS* 1.3 80.1 - - - +
228T LYS* 1.3 73.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 228 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216T ILE 3.9 0.6 - - - +
217T LYS* 3.4 1.2 - - - -
218T MET* 2.9 56.8 + - + +
226T CYS* 3.9 2.5 - - - -
227T VAL* 1.3 89.7 - - + +
229T THR* 1.3 67.0 + - - +
230T PHE* 4.5 13.7 - - + -
263T VAL* 3.7 21.7 + - - +
264T ALA* 3.7 24.6 + - - +
266T LYS* 4.7 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 229 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215T THR* 3.2 35.9 - - + +
216T ILE 3.3 2.2 - - - -
217T LYS* 3.3 19.8 + - + +
226T CYS* 3.6 10.2 - - - -
228T LYS* 1.3 78.3 + - - +
230T PHE* 1.3 66.0 + - - +
231T THR* 3.6 8.2 + - - +
266T LYS* 5.6 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 230 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208T VAL* 5.5 0.9 - - + -
214T LYS 4.2 0.5 - - - +
215T THR* 4.1 5.8 - - - -
216T ILE* 2.7 75.8 + - + +
218T MET* 4.3 22.9 - - + -
228T LYS* 4.5 17.7 - - + -
229T THR* 1.3 73.6 - - - +
231T THR* 1.3 62.9 + - - +
232T GLY 3.7 1.7 + - - -
249T ILE* 5.3 9.0 - - + -
261T TRP* 3.6 44.8 - + + -
262T VAL 4.2 7.2 - - - -
263T VAL* 4.2 22.2 - - + -
266T LYS* 3.5 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 231 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214T LYS 4.9 2.9 - - - -
215T THR* 5.8 1.8 - - - -
229T THR* 3.6 10.0 + - - +
230T PHE* 1.3 71.2 - - - +
232T GLY* 1.3 63.9 + - - +
259T ARG* 5.5 0.2 + - - -
261T TRP* 3.0 15.8 - - - -
----------------------------------------------------------
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