Contacts of the helix formed by residues 194 - 209 (chain J) in PDB entry 5A31
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 194 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192J LYS* 3.7 8.3 + - - +
193J LEU* 1.3 83.9 + - - +
195J ASN* 1.3 67.8 + - - +
196J GLU* 4.0 7.9 - - + +
197J GLU* 3.5 31.6 - - + +
198J GLN* 3.2 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 195 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192J LYS* 4.6 23.8 + - - +
194J CYS* 1.3 75.9 - - - +
196J GLU* 1.3 64.1 + - + +
198J GLN* 3.7 5.1 - - - +
199J GLU* 3.3 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 196 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194J CYS* 4.0 8.4 - - + +
195J ASN* 1.3 79.5 - - + +
197J GLU* 1.3 63.6 + - + +
199J GLU* 3.3 7.0 + - - +
200J LEU* 2.9 28.4 + - - +
225J ASN* 5.2 8.1 + - - -
2K ASN* 3.8 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 197 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162J TYR* 4.0 22.1 + - - +
193J LEU* 2.7 36.5 - - + +
194J CYS* 3.5 21.4 + - + +
195J ASN 3.4 0.4 - - - -
196J GLU* 1.3 84.4 - - + +
198J GLN* 1.3 64.9 + - - +
200J LEU* 3.6 15.7 - - + +
201J LEU* 3.1 33.1 + - + +
2K ASN* 4.5 19.4 - - + +
5K ARG* 4.7 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 198 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190J LEU* 2.4 48.1 + - - +
191J SER 3.2 21.0 - - - +
192J LYS* 3.3 29.3 - - + +
193J LEU* 3.7 4.3 + - - +
194J CYS 3.2 18.1 + - - +
195J ASN* 3.7 7.0 - - - +
196J GLU 3.3 0.2 - - - -
197J GLU* 1.3 77.0 - - - +
199J GLU* 1.3 63.8 + - + +
201J LEU* 3.5 1.6 + - - +
202J ARG* 3.2 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 199 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195J ASN 3.3 11.2 + - - +
196J GLU* 3.3 9.5 + - - +
198J GLN* 1.3 80.5 - - + +
200J LEU* 1.3 58.3 + - - +
202J ARG* 3.4 16.1 + - - +
203J PHE* 2.9 32.6 + - - +
224J VAL* 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196J GLU 2.9 17.0 + - - +
197J GLU* 3.6 16.8 - - + +
198J GLN 3.3 0.2 - - - -
199J GLU* 1.3 77.4 - - - +
201J LEU* 1.3 60.9 + - + +
203J PHE* 3.4 3.3 + - - +
204J LEU* 3.0 48.8 + - + +
224J VAL* 4.3 27.6 - - + -
227J LEU* 4.4 13.7 - - + -
6K LEU* 4.9 4.3 - - + -
25K TRP* 4.5 17.0 - - + -
28K LYS* 6.4 0.2 - - + -
32K LEU* 4.2 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161J VAL* 4.0 17.3 - - + -
162J TYR* 4.2 28.5 - - + +
190J LEU* 4.0 27.8 - - + -
193J LEU* 5.9 2.9 - - + -
197J GLU* 3.1 20.0 + - + +
200J LEU* 1.3 79.3 - - + +
202J ARG* 1.3 65.5 + - - +
204J LEU* 3.4 3.7 + - + +
205J PHE* 3.0 52.5 + - + -
25K TRP* 3.4 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 202 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185J LEU* 4.0 13.7 - - + -
190J LEU* 3.6 27.3 - - + +
198J GLN* 3.2 35.7 + - - +
199J GLU* 4.0 16.0 - - - +
201J LEU* 1.3 75.4 - - - +
203J PHE* 1.3 58.1 + - - +
206J GLU* 2.8 56.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 203 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199J GLU 2.9 18.9 + - - +
200J LEU* 3.5 3.6 - - + +
202J ARG* 1.3 76.7 - - - +
204J LEU* 1.3 89.0 + - + +
206J GLU* 3.4 7.8 + - + +
207J ASN* 3.2 30.1 + - + +
220J ILE* 5.0 13.9 - - + -
222J GLU* 3.2 40.6 - - + +
223J SER* 4.6 3.4 - - - -
224J VAL* 3.3 33.2 - - + -
227J LEU* 5.0 4.9 - - + -
228J GLU* 5.4 2.7 - - - -
233J VAL* 4.0 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200J LEU* 3.0 40.8 + - + +
201J LEU* 3.9 5.4 - - + +
203J PHE* 1.3 98.2 - - + +
205J PHE* 1.3 71.8 + - + +
207J ASN* 2.8 31.9 - - - +
208J LYS* 3.5 7.4 + - - +
227J LEU* 5.2 1.6 - - + -
233J VAL* 4.9 2.7 - - + -
24K PHE* 4.2 10.8 - - + -
25K TRP* 3.7 27.1 - - + -
28K LYS* 3.4 40.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 205 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157J LEU* 5.7 1.3 - - + -
161J VAL* 3.9 24.9 - - + -
162J TYR 4.8 2.9 - - - -
164J PHE* 4.0 34.5 - + + -
167J PHE* 4.0 37.9 - + + -
185J LEU* 3.4 30.3 - - + -
188J LEU* 4.8 13.7 - - + -
190J LEU* 5.7 0.2 - - + -
201J LEU* 3.0 50.2 + - + +
204J LEU* 1.3 84.2 - - + +
206J GLU* 1.3 67.9 + - - +
208J LYS* 3.2 5.2 + - + +
209J LEU* 3.1 25.1 + - - +
24K PHE* 5.0 3.1 - + - -
25K TRP* 5.2 2.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 206 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185J LEU* 2.7 32.7 - - - +
202J ARG* 2.8 47.0 + - - +
203J PHE* 3.5 9.0 - - + +
205J PHE* 1.3 77.2 - - - +
207J ASN* 1.3 62.5 + - - +
209J LEU* 3.4 30.8 + - + +
220J ILE* 6.5 0.9 - - + -
240J ARG* 4.1 7.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 207 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203J PHE* 3.2 17.1 + - + +
204J LEU* 2.8 24.7 + - - +
205J PHE 3.2 0.6 - - - -
206J GLU* 1.3 80.1 - - - +
208J LYS* 1.3 100.5 + - - +
209J LEU 3.6 0.2 + - - -
211J LYS* 2.9 33.3 + - - -
220J ILE* 4.6 13.9 - - + -
232J ASP 4.7 0.6 - - - -
233J VAL* 4.2 23.2 - - - +
236J SER* 3.3 28.8 + - - +
240J ARG* 3.7 7.7 + - - +
28K LYS* 5.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 208 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164J PHE* 3.7 35.7 - - + -
167J PHE* 4.2 14.8 - - + -
168J ASP* 4.6 8.7 - - - +
171J THR* 3.1 23.0 + - + -
204J LEU* 3.5 8.3 + - - +
205J PHE* 3.2 9.1 + - + +
207J ASN* 1.3 101.7 + - - +
209J LEU* 1.3 64.6 + - - +
210J LYS* 4.3 1.0 - - - -
211J LYS* 4.9 2.5 - - - +
232J ASP* 4.4 25.3 + - - +
235J VAL* 5.7 1.4 - - - +
236J SER* 5.3 3.1 - - - +
239J GLU* 4.9 11.4 - - - +
266J SER* 5.5 4.6 + - - -
24K PHE* 4.0 13.6 - - - -
28K LYS* 4.6 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167J PHE* 4.1 15.3 - - + -
181J GLU* 3.8 26.7 - - + +
182J LYS* 4.7 21.1 - - + +
185J LEU* 3.9 16.6 - - + -
205J PHE 3.1 19.6 + - - +
206J GLU* 3.4 35.0 + - + +
207J ASN 4.0 0.3 - - - +
208J LYS* 1.3 78.6 - - - +
210J LYS* 1.3 71.3 + - - +
211J LYS* 3.3 14.6 + - - +
240J ARG* 5.5 0.5 + - - -
----------------------------------------------------------
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