Contacts of the helix formed by residues 188 - 199 (chain A) in PDB entry 3S3J
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 188 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A GLU 3.2 0.8 + - - -
187A ASP* 1.3 76.0 + - - +
189A ILE* 1.3 63.6 + - - +
190A LEU 3.4 2.0 - - - -
191A ASP* 3.4 17.1 + - - +
192A ILE* 3.1 31.4 + - - +
262A ARG* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLY 3.7 14.8 - - - +
184A GLN* 3.8 25.4 - - - +
186A GLU* 2.9 26.9 + - + +
187A ASP 4.3 2.0 - - - +
188A GLY* 1.3 78.0 - - - +
190A LEU* 1.3 64.0 + - - +
192A ILE* 3.2 11.7 + - + +
193A CYS* 3.0 34.8 + - - -
258A VAL* 4.1 31.6 - - + +
261A LEU* 4.1 28.7 - - + -
262A ARG* 4.6 4.5 - - - +
286A THR* 4.4 3.6 - - + -
290A CYS* 4.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.2 21.0 - - + +
32A VAL* 4.1 24.5 - - + -
136A ILE* 3.8 36.1 - - + -
138A LEU* 4.1 20.0 - - + -
184A GLN 4.8 0.6 + - - -
186A GLU 4.6 1.0 + - - -
188A GLY 3.4 0.6 - - - -
189A ILE* 1.3 76.8 - - - +
191A ASP* 1.3 66.4 + - - +
193A CYS* 3.0 10.6 + - + -
194A LEU* 3.0 19.7 + - + +
290A CYS* 3.6 28.5 - - - +
291A LEU* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE* 4.3 17.8 - - - +
188A GLY* 3.4 16.4 + - - +
190A LEU* 1.3 78.0 - - - +
192A ILE* 1.3 64.7 + - + +
194A LEU* 3.1 11.6 + - - +
195A ILE* 3.0 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLY* 3.1 21.5 + - - +
189A ILE* 3.2 14.1 + - + +
191A ASP* 1.3 78.3 - - + +
193A CYS* 1.3 57.4 + - - +
195A ILE* 3.4 10.1 + - + +
196A LEU* 2.9 26.3 + - + +
261A LEU* 4.0 36.6 - - + +
262A ARG* 4.2 20.6 - - + -
264A TRP* 3.8 26.8 - - + -
265A LYS* 4.0 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ILE* 3.0 27.2 + - - -
190A LEU* 3.0 8.7 + - - +
192A ILE* 1.3 77.5 - - - +
194A LEU* 1.3 63.5 + - - +
196A LEU* 3.1 17.2 + - - +
197A LEU* 3.1 19.8 + - - +
261A LEU* 5.0 2.9 - - - -
287A VAL* 3.8 44.8 - - + +
290A CYS* 3.9 17.7 - - - -
291A LEU* 4.3 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 5.5 1.6 - - + -
113A GLY* 4.3 20.2 - - - -
114A LEU* 4.6 14.1 - - + +
136A ILE* 3.7 37.5 - - + -
138A LEU* 5.7 0.4 - - + -
190A LEU* 3.0 22.5 + - + +
191A ASP* 3.5 14.4 - - - +
193A CYS* 1.3 73.6 - - - +
195A ILE* 1.3 60.7 + - + +
197A LEU* 3.2 17.7 + - + +
198A ASP* 2.9 37.9 + - - +
214A ARG* 4.5 5.3 + - - +
291A LEU* 4.4 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ASP* 3.0 23.0 + - + +
192A ILE* 3.5 12.3 - - + +
194A LEU* 1.3 74.1 - - + +
196A LEU* 1.3 64.8 + - - +
198A ASP* 2.9 20.1 + - + +
199A VAL* 2.9 22.3 + - + +
264A TRP* 4.3 5.8 - - + -
265A LYS* 4.5 23.1 - - + -
269A CYS* 4.0 26.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ILE* 2.9 14.8 + - + +
193A CYS* 3.1 11.8 + - - +
195A ILE* 1.3 76.1 - - - +
197A LEU* 1.3 79.5 + - + +
199A VAL* 3.5 10.8 + - - +
200A ASN* 3.5 9.0 + - - +
223A VAL* 4.9 0.7 - - + +
224A VAL* 4.6 15.0 - - + +
227A MET* 3.5 36.8 - - + +
228A VAL* 5.2 4.9 - - + +
236A VAL* 3.8 28.3 - - + -
261A LEU* 5.4 3.4 - - + -
264A TRP* 3.8 17.7 - - + -
287A VAL* 4.6 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 4.4 12.8 - - + -
193A CYS 3.1 13.4 + - - +
194A LEU* 3.2 17.0 + - + +
196A LEU* 1.3 89.6 - - + +
198A ASP* 1.3 58.6 + - - +
199A VAL 3.1 0.2 - - - -
200A ASN* 2.7 37.2 + - - +
203A PHE* 3.9 1.0 - - - +
214A ARG* 3.4 44.7 + - + +
220A VAL* 4.6 9.6 - - + -
223A VAL* 4.2 15.5 - - + -
224A VAL* 4.4 14.8 - - + -
287A VAL* 5.8 0.2 - - + -
291A LEU* 4.2 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 2.9 24.1 + - - +
195A ILE* 2.9 12.1 + - + +
197A LEU* 1.3 75.2 - - - +
199A VAL* 1.3 61.7 + - + +
200A ASN 3.5 0.2 - - - -
203A PHE* 3.0 45.5 - - + -
204A LEU* 5.1 1.7 - - - +
211A CYS* 4.9 1.0 - - - -
214A ARG* 2.7 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ILE* 2.9 31.1 + - + +
196A LEU* 3.6 6.7 - - - +
197A LEU 3.1 0.2 - - - -
198A ASP* 1.3 81.9 - - + +
200A ASN* 1.3 66.9 + - - +
201A PRO* 3.7 1.6 - - - +
204A LEU* 4.3 16.3 - - - +
227A MET* 3.5 26.2 - - + +
234A GLN* 4.0 31.2 - - + +
264A TRP* 4.2 13.7 - - + -
269A CYS* 4.8 6.3 - - - -
----------------------------------------------------------
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