Contacts of the helix formed by residues 197 - 214 (chain C) in PDB entry 1J1J
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 197 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C LYS 3.8 2.7 + - - -
194C ARG 3.0 11.7 + - - -
195C TYR 2.8 2.0 + - - -
196C ASP* 1.3 75.7 - - - +
198C LEU* 1.3 63.9 + - - +
199C LYS 3.2 2.5 - - - -
200C TYR* 3.2 29.0 + - - +
201C ASP* 3.4 13.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C LEU* 4.1 17.3 - - + +
148C ALA* 3.4 33.7 - - + -
174C ILE* 4.4 11.9 - - + +
177C LEU* 4.3 5.2 - - + -
178C ASP* 3.8 36.6 - - + +
181C PHE* 4.0 22.7 - - + -
194C ARG 3.7 2.0 + - - -
195C TYR* 2.7 30.8 + - + +
197C GLY* 1.3 70.6 - - - +
199C LYS* 1.3 57.8 + - - +
201C ASP* 3.1 6.7 + - + +
202C VAL* 2.8 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 199 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C ASP* 3.6 29.6 - - - +
182C ARG* 5.1 4.7 - - - +
195C TYR* 3.6 40.7 + - - -
196C ASP* 4.0 22.0 + - - +
198C LEU* 1.3 76.5 - - - +
200C TYR* 1.3 65.3 + - + +
202C VAL* 3.2 8.9 + - - +
203C LYS* 3.0 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 200 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C ASP 4.0 18.2 - - - -
197C GLY* 3.2 15.1 + - - +
198C LEU 3.1 0.2 - - - -
199C LYS* 1.3 81.9 - - + +
201C ASP* 1.3 61.2 + - - +
203C LYS* 3.2 11.1 + - + +
204C LYS* 2.8 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 201 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LYS* 6.1 1.2 - - - -
145C LEU 4.8 0.9 - - - +
148C ALA* 4.1 10.3 - - + +
149C SER* 3.1 35.0 + - - -
152C SER* 3.0 25.9 + - - +
174C ILE* 4.7 2.9 - - + -
197C GLY 3.4 14.8 + - - +
198C LEU* 3.1 15.7 + - + +
200C TYR* 1.3 78.0 - - - +
202C VAL* 1.3 57.5 + - - +
204C LYS* 3.5 4.9 - - - +
205C VAL* 2.8 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ILE* 3.6 25.8 - - + +
175C ASN* 3.6 14.6 - - - +
178C ASP* 4.0 21.8 - - + +
198C LEU* 2.8 31.5 + - + +
199C LYS* 3.4 9.9 - - + +
200C TYR 3.2 0.2 - - - -
201C ASP* 1.3 77.1 - - - +
203C LYS* 1.3 57.8 + - + +
205C VAL* 3.9 1.8 - - - +
206C GLU* 3.0 38.6 + - - +
153D ARG* 3.4 33.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 203 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C LYS* 3.0 25.1 + - + +
200C TYR* 3.7 11.2 - - + +
202C VAL* 1.3 75.7 - - + +
204C LYS* 1.3 66.8 + - - +
206C GLU* 3.2 8.8 + - - +
207C GLU* 2.9 38.7 + - - +
149D SER* 4.4 9.6 + - - -
150D GLU* 5.6 0.6 + - - +
152D SER* 5.2 0.2 + - - -
153D ARG* 3.1 49.6 - - + +
204D LYS* 4.0 16.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 204 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LYS* 6.2 4.0 - - + -
203B LYS* 3.1 48.2 - - - +
152C SER* 4.2 20.4 - - - +
156C VAL* 3.9 10.1 - - + -
200C TYR 2.8 17.4 + - - +
201C ASP* 3.5 9.9 - - - +
203C LYS* 1.3 77.7 - - - +
205C VAL* 1.3 62.6 + - - +
207C GLU* 3.2 29.4 + - - +
208C VAL* 3.3 15.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 205 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C LEU 4.5 0.2 - - - +
152C SER* 3.5 34.3 - - - +
155C SER* 4.5 5.8 - - - +
167C PRO 4.4 3.6 - - - +
170C ILE* 3.9 11.0 - - + +
171C SER* 3.3 39.0 - - - +
174C ILE* 4.1 18.4 - - + -
201C ASP 2.8 20.3 + - - +
202C VAL* 4.0 3.6 - - - +
204C LYS* 1.3 74.8 - - - +
206C GLU* 1.3 65.3 + - - +
208C VAL* 3.2 16.2 + - - +
209C VAL* 3.4 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 206 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C SER* 4.0 18.6 - - - +
175C ASN* 3.3 15.9 + - - +
202C VAL* 3.0 27.9 + - - +
203C LYS* 3.2 8.0 + - - +
205C VAL* 1.3 76.3 - - + +
207C GLU* 1.3 59.2 + - + +
209C VAL* 3.4 6.1 + - - +
210C TYR* 3.0 26.9 + - - +
46D HIS* 4.2 5.5 - - - +
153D ARG* 2.8 48.4 + - - +
156D VAL* 4.2 6.9 - - + +
157D ASN* 3.3 32.7 + - - +
160D THR* 4.4 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LYS* 5.0 3.3 - - - +
203C LYS* 2.9 31.8 + - - +
204C LYS* 3.4 27.3 + - - +
205C VAL 3.1 0.2 - - - -
206C GLU* 1.3 75.8 - - - +
208C VAL* 1.3 64.8 + - - +
210C TYR* 3.2 11.7 - - + +
211C ASP* 3.0 29.0 + - - +
156D VAL* 4.5 17.7 - - + -
200D TYR* 5.4 3.1 + - - -
204D LYS* 4.6 14.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 208 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LYS* 4.2 5.6 - - - -
206B GLU* 4.7 3.6 - - - +
155C SER* 3.4 28.3 - - - +
156C VAL* 3.9 29.2 - - + -
159C VAL* 4.0 15.3 - - + -
167C PRO* 3.6 19.5 - - + -
204C LYS* 3.3 21.1 + - + +
205C VAL* 3.2 8.9 + - - +
207C GLU* 1.3 79.1 - - - +
209C VAL* 1.3 63.6 + - - +
211C ASP* 3.2 11.9 + - - +
212C LEU* 3.1 20.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C PRO* 3.6 31.2 - - + +
168C LEU* 3.4 31.2 - - + +
171C SER* 3.7 15.9 - - - +
205C VAL 3.5 13.9 - - - +
206C GLU* 3.7 6.7 - - - +
207C GLU 3.3 0.2 - - - -
208C VAL* 1.3 74.1 - - - +
210C TYR* 1.3 55.8 + - - +
212C LEU* 3.1 8.4 + - - +
213C SER* 2.7 36.4 + - - +
217C PHE* 4.9 1.8 - - + +
160D THR* 3.5 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 210 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C GLU 3.0 14.3 + - - +
207C GLU* 3.2 12.6 - - + +
209C VAL* 1.3 76.2 - - - +
211C ASP* 1.3 78.3 + - - +
213C SER* 3.0 4.0 + - - -
214C ILE* 3.0 37.4 + - + +
156D VAL* 3.4 40.4 - - + -
159D VAL* 3.6 35.2 - - + +
160D THR* 3.4 14.3 + - - +
208D VAL* 3.5 26.1 + - + +
211D ASP* 2.8 39.5 + - - +
212D LEU* 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LYS* 2.8 32.4 + - - -
206B GLU* 4.5 6.8 - - - +
207B GLU* 4.4 11.9 - - - +
210B TYR* 4.4 12.0 - - + -
207C GLU* 3.0 18.5 + - - +
208C VAL* 3.2 10.1 + - - +
210C TYR* 1.3 93.8 - - - +
212C LEU* 1.3 67.5 + - + +
214C ILE* 3.1 27.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLU* 5.2 1.1 - - - +
210B TYR* 4.4 20.2 - - + +
159C VAL* 3.5 33.7 - - + -
164C TYR* 3.4 36.3 - - + +
167C PRO* 3.7 28.9 - - + -
168C LEU* 4.1 5.6 - - + -
208C VAL* 3.1 13.2 + - + +
209C VAL* 3.1 8.1 + - - +
211C ASP* 1.3 83.1 - - + +
213C SER* 1.3 58.5 + - - +
214C ILE 3.0 8.8 + - - -
215C ARG* 3.4 26.0 + - - -
217C PHE* 3.7 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C VAL 2.7 18.7 + - - -
210C TYR* 3.0 11.3 + - - -
212C LEU* 1.3 69.0 - - - +
214C ILE* 1.3 52.7 + - - +
215C ARG 2.6 18.2 + - - -
216C GLY* 3.7 5.9 + - - -
217C PHE* 2.9 43.4 + - - +
159D VAL* 4.3 8.2 + - - +
160D THR* 3.2 30.7 + - - -
164D TYR* 4.5 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B TYR* 5.6 2.5 - - + -
210C TYR* 3.0 41.7 + - + +
211C ASP* 3.1 22.4 - - - +
212C LEU 3.0 1.4 - - - -
213C SER* 1.3 75.3 - - - +
215C ARG* 1.3 69.0 + - + +
159D VAL* 4.1 15.7 - - + -
164D TYR* 6.0 1.6 - - - -
211D ASP* 4.6 8.5 - - + +
212D LEU* 5.1 7.2 - - + -
215D ARG* 3.0 55.0 - - - +
217D PHE* 5.0 11.1 - - + -
----------------------------------------------------------
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