Contacts of the helix formed by residues 184 - 189 (chain C) in PDB entry 3VI4
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 184 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C ALA 4.8 1.2 - - - +
160C GLY 4.7 0.5 - - - +
163C TYR* 3.1 37.4 - - - +
164C CYS* 3.2 5.5 + - - -
165C GLN* 5.2 1.3 - - - -
182C GLY 3.0 1.8 + - - -
183C PRO* 1.3 79.7 - - - +
185C SER* 1.3 68.5 + - - +
186C TYR 3.5 0.9 + - - -
187C PHE 4.1 1.7 + - - -
188C TRP* 3.3 28.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C GLY 3.8 6.3 - - - -
161C GLN* 3.7 4.3 - - - +
164C CYS* 3.3 25.8 - - - +
182C GLY 3.5 3.2 + - - -
183C PRO 3.6 0.6 - - - -
184C GLY* 1.3 76.6 - - - +
186C TYR* 1.3 72.3 + - - +
188C TRP 3.1 1.0 + - - -
189C GLN 3.0 24.8 + - - -
190C GLY* 3.1 5.2 + - - -
191C GLN* 3.0 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 186 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C PHE* 5.9 1.8 - + + -
158C ALA 3.7 2.2 - - - -
159C ALA 3.6 10.3 - - - -
160C GLY* 2.8 30.9 + - - -
161C GLN* 3.0 27.6 + - + -
184C GLY 3.5 0.6 + - - -
185C SER* 1.3 74.1 - - - +
187C PHE* 1.3 74.6 + - - +
188C TRP 3.1 0.5 + - - -
189C GLN* 3.2 32.3 + - - +
190C GLY 4.8 6.1 - - - -
191C GLN* 3.2 33.9 + - + -
218C GLN* 5.1 1.4 + - - -
219C THR* 4.4 2.2 + - - -
220C ARG 4.5 1.3 - - - -
221C GLN* 3.1 68.3 + - + +
5001G ARG* 3.8 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C TRP* 3.6 30.1 - + - -
158C ALA* 2.9 28.9 + - + -
159C ALA* 3.6 22.4 - - + -
184C GLY 4.1 0.8 + - - -
186C TYR* 1.3 74.7 - - - +
188C TRP* 1.3 88.1 + + + +
189C GLN 3.1 0.3 + - - -
227C ASP* 3.3 18.7 - - + +
228C ASP* 3.0 23.5 + - - +
225D LEU* 4.7 4.5 - - + -
226D ASP* 5.8 0.2 - - - -
227D SER 5.8 0.2 - - - -
5001G ARG* 3.3 49.4 - - + -
5002G GLY* 3.8 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 188 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C ALA* 4.3 6.3 - - + -
163C TYR* 3.8 27.2 + + + -
165C GLN* 4.7 4.0 - - - +
183C PRO 3.5 6.0 - - - +
184C GLY* 3.3 24.6 + - - -
185C SER 3.1 7.6 + - - -
187C PHE* 1.3 111.9 - + + +
189C GLN* 1.3 56.1 + - - +
190C GLY 3.1 0.9 - - - -
228C ASP* 3.5 18.8 - - - +
229C SER 2.7 27.4 + - - -
230C TYR* 3.0 36.1 + + + -
174D PRO* 3.4 29.7 - - + +
175D TYR* 6.1 0.8 - - - -
225D LEU* 3.8 19.1 - - + -
226D ASP* 3.6 41.8 + - + -
227D SER 5.3 0.2 - - - -
270D LEU* 4.1 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 189 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C SER 3.0 3.7 + - - +
186C TYR* 3.2 21.7 + - + +
187C PHE 3.1 4.9 + - - -
188C TRP* 1.3 77.9 - - - +
190C GLY* 1.3 62.2 + - - +
220C ARG 4.5 2.6 + - - -
221C GLN* 3.9 6.5 - - - +
222C ALA* 2.9 47.4 + - - +
223C SER 3.5 6.2 - - - +
226C TYR* 3.4 32.2 - - + +
227C ASP* 3.3 6.7 - - - +
229C SER* 3.8 7.3 - - - +
230C TYR 3.6 1.7 + - - -
231C LEU* 3.0 23.1 + - - +
252C VAL* 4.8 0.2 - - - +
5001G ARG* 3.1 25.1 + - - -
2N NAG 5.2 2.8 + - - +
----------------------------------------------------------
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