Contacts of the strand formed by residues 190 - 197 (chain C) in PDB entry 3O4O
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 GLY 190 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C LYS* 4.6 3.8 - - - -
188C ASP 3.7 0.2 + - - -
189C ALA* 1.3 76.3 - - - +
191C TYR* 1.3 69.2 + - - -
192C TYR* 3.6 9.4 - - - -
212C GLU* 3.5 4.9 - - - -
213C LEU* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 191 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C LEU* 5.3 9.2 - - + -
121C PRO* 3.7 32.9 + - + +
124C SER* 3.0 27.7 + - - -
158C LYS* 4.2 6.9 - - - +
159C ASP* 3.8 34.1 + - - +
190C GLY* 1.3 75.0 - - - -
192C TYR* 1.3 67.7 + - - +
193C ARG* 5.7 0.4 - - + -
210C SER* 4.9 8.3 - - - +
211C ILE 3.3 5.2 - - - -
212C GLU* 3.3 42.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 192 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C LEU* 3.9 13.9 - - + -
156C TRP* 4.4 9.0 - + + -
157C TYR 3.6 11.4 - - - +
158C LYS* 3.1 37.5 - - + -
159C ASP 5.2 0.2 - - - +
163C LEU* 5.1 2.0 - - + -
170C PHE* 3.2 35.7 - + - -
179C LEU* 4.3 20.9 - - + -
188C ASP 2.8 28.7 + - - -
190C GLY 3.6 14.4 - - - -
191C TYR* 1.3 77.9 - - - +
193C ARG* 1.3 73.8 + - - +
210C SER* 3.7 6.8 + - - -
211C ILE* 2.6 41.5 + - + +
213C LEU* 3.9 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 193 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 4.3 15.2 - - - +
115C ASN* 4.7 5.7 + - - -
120C LEU* 3.0 43.9 - - + +
155C GLN 3.6 1.6 - - - +
156C TRP* 3.3 32.5 - - - -
157C TYR* 3.1 29.2 + - + +
159C ASP 6.0 1.8 - - - +
160C SER* 5.5 6.5 - - - +
191C TYR* 5.7 0.4 - - + -
192C TYR* 1.3 89.0 - - - +
194C CYS* 1.3 65.1 + - - +
195C VAL* 4.4 7.1 - - + +
208C THR* 2.9 34.3 + - + +
209C ARG 3.3 7.0 - - - +
210C SER* 4.2 5.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 194 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C CYS* 1.7 96.9 - - - -
140C PRO* 4.5 1.6 - - - -
154C ILE* 4.1 6.7 - - + -
156C TRP* 3.2 30.8 - - - -
193C ARG* 1.3 72.9 - - - +
195C VAL* 1.3 66.4 + - - +
196C LEU 4.2 0.4 - - - -
207C ILE 4.3 0.7 - - - -
208C THR* 3.2 2.9 - - - +
209C ARG* 2.9 33.9 + - + -
211C ILE* 4.5 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C LYS 3.7 1.6 - - - +
154C ILE* 3.5 15.9 - - - +
155C GLN* 3.5 35.9 + - - +
157C TYR* 3.5 33.0 - - + -
193C ARG* 4.2 4.5 - - + +
194C CYS* 1.3 83.1 - - - +
196C LEU* 1.3 60.5 + - - +
197C THR* 3.5 4.1 + - + +
206C ASN* 3.9 32.5 - - + +
207C ILE 3.6 6.5 - - - +
208C THR* 4.1 15.0 - - + +
338C NAG 4.7 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C LEU* 3.7 35.8 - - + +
145C PHE* 4.4 20.0 - - + +
146C THR* 4.2 16.2 - - - +
152C VAL* 4.9 9.0 - - + -
153C LYS* 4.3 22.2 - - + +
154C ILE* 4.3 12.6 - - + +
194C CYS* 4.2 0.4 - - - +
195C VAL* 1.3 71.6 - - - +
197C THR* 1.3 86.1 + - - +
198C PHE* 4.6 4.5 - - + +
205C TYR 3.4 3.1 - - - +
206C ASN* 4.5 0.4 - - - -
207C ILE* 2.7 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 197 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C LYS* 3.4 27.1 + - - +
155C GLN* 4.6 18.8 + - - +
195C VAL* 3.5 5.8 + - + +
196C LEU* 1.3 85.0 - - - +
198C PHE* 1.3 64.0 + - - +
199C ALA* 5.3 0.5 - - - +
204C GLN* 4.9 13.9 - - + -
205C TYR 3.3 4.7 - - - +
206C ASN* 3.4 22.7 - - - +
338C NAG 5.4 0.7 - - - -
----------------------------------------------------------
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