Contacts of the strand formed by residues 211 - 216 (chain C) in PDB entry 1ZSV
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 211 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C THR* 3.7 15.7 - - + +
146C MET* 3.7 27.1 - - + -
170C VAL* 3.7 31.8 - - + +
203C LEU* 2.7 47.0 + - + +
206C ALA* 3.7 11.8 - - - +
207C SER* 3.6 20.9 - - - -
210C GLY* 1.3 73.0 - - - -
212C ASP* 1.3 64.1 + - - +
213C CYS 4.2 6.3 - - - +
226C VAL* 5.2 6.3 - - + -
229C GLN* 3.0 31.6 + - + -
230C MET* 3.5 22.6 - - - +
231C LYS* 2.8 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C GLY 4.6 1.2 - - - +
143C GLU* 3.3 30.8 - - + -
144C THR* 2.8 32.2 + - - +
210C GLY 4.3 0.2 + - - -
211C TYR* 1.3 72.3 - - - +
213C CYS* 1.3 65.1 + - - +
230C MET* 3.7 0.8 - - - +
231C LYS* 3.3 39.7 + - - +
234C GLY* 3.3 7.6 - - - -
235C ARG* 3.1 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C CYS* 3.9 19.7 - - - -
139C VAL* 3.4 26.2 - - + -
143C GLU* 4.5 2.5 - - - -
144C THR 3.4 2.6 + - - +
145C VAL* 3.4 13.7 - - + -
146C MET* 2.9 25.5 + - - +
211C TYR* 4.2 2.1 - - - +
212C ASP* 1.3 82.5 - - - +
214C TYR* 1.3 60.9 + - - +
230C MET* 4.1 3.1 - - - -
235C ARG* 3.1 46.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C CYS* 3.9 3.6 - - - -
146C MET* 3.4 32.8 - - + -
148C ASN* 2.6 37.6 + - - -
213C CYS* 1.3 75.1 - - - +
215C PHE* 1.3 72.2 + - - +
216C ASP* 3.7 14.4 + - + -
222C PHE* 3.6 4.9 - + - -
223C SER* 2.9 35.8 + - - -
226C VAL* 3.6 26.9 - - + -
227C ILE* 5.3 1.1 - - + -
230C MET* 3.8 19.3 - - + -
235C ARG 2.9 8.1 + - - +
236C ILE* 3.4 28.5 - - + +
237C ALA 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C THR 4.0 6.7 - - - -
129C ALA 4.0 1.8 - - - -
132C GLY* 3.8 12.6 - - - -
133C LEU* 3.7 28.3 - - + -
137C CYS* 4.6 5.6 - - - -
145C VAL* 4.8 3.8 - - + +
146C MET 2.9 14.5 + - - +
147C VAL* 3.7 6.1 - - + +
148C ASN* 3.3 25.8 + - - +
154C VAL* 3.7 27.6 - - + -
158C VAL* 3.6 42.6 - - + -
214C TYR* 1.3 74.7 - - - +
216C ASP* 1.3 57.2 + - - +
217C ASN* 3.8 13.9 - - - -
237C ALA* 3.8 9.2 - - + -
239C CYS* 3.7 26.2 - - + -
270C PHE* 4.0 4.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ASN* 3.1 12.0 + - - +
214C TYR* 3.5 19.3 - - + -
215C PHE* 1.3 71.5 - - - +
217C ASN* 1.3 60.4 + - - +
218C VAL 3.0 7.6 + - - -
219C GLY* 2.9 30.0 + - - -
223C SER* 2.7 25.2 + - - -
236C ILE* 4.3 7.7 - - + +
237C ALA 3.0 14.9 + - - +
238C ILE* 4.6 12.0 - - - +
239C CYS* 2.9 32.7 + - - +
240C GLY 3.1 8.9 + - - +
----------------------------------------------------------
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