Contacts of the helix formed by residues 187 - 200 (chain A) in PDB entry 5J3V
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 SER 187 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TYR* 2.7 44.9 + - - -
185A HIS* 3.1 5.6 + - - -
186A SER* 1.3 79.8 + - - +
188A PRO* 1.3 69.7 - - - +
189A LYS* 3.2 13.5 + - - +
190A ILE* 3.2 11.1 + - - +
191A ARG* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A SER 3.5 4.7 - - - +
187A SER* 1.3 85.8 - - - +
189A LYS* 1.3 58.7 + - + +
190A ILE 3.2 0.2 - - - -
191A ARG* 3.3 31.3 - - + +
192A SER* 3.0 30.0 + - - -
226A ASP* 5.6 0.2 - - - +
228A GLU* 3.9 32.0 - - + +
231A VAL* 3.9 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TYR* 3.7 7.9 - - - +
146A GLU* 4.1 27.2 + - - +
187A SER* 3.1 11.8 + - - +
188A PRO* 1.3 79.8 - - - +
190A ILE* 1.3 61.5 + - - +
192A SER* 2.9 19.0 + - - +
193A HIS* 3.2 34.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TYR* 3.6 29.4 - - + +
145A CYS* 4.0 13.5 - - - -
146A GLU* 3.8 32.1 - - + -
149A PHE* 3.8 23.6 - - + -
182A PHE* 3.8 15.0 - - + -
185A HIS* 3.6 35.0 - - + +
187A SER* 3.2 7.9 + - - +
189A LYS* 1.3 79.6 - - - +
191A ARG* 1.3 64.3 + - - +
192A SER 3.3 0.2 - - - -
193A HIS* 3.2 7.2 + - + +
194A ALA* 3.0 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PHE 3.7 15.5 - - - +
183A PHE* 3.5 25.6 - - - +
184A LYS* 4.6 1.6 - - - +
185A HIS 3.2 25.3 + - - +
186A SER 3.5 10.5 + - - -
187A SER 3.1 13.3 + - - +
188A PRO* 3.3 37.4 - - + +
190A ILE* 1.3 76.7 - - - +
192A SER* 1.3 61.9 + - - +
194A ALA* 3.2 2.8 + - - +
195A VAL* 3.1 30.0 + - - +
223A LEU* 3.8 16.7 - - + +
226A ASP* 2.6 34.1 + - - -
231A VAL* 4.6 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLN* 5.1 0.2 - - - -
188A PRO 3.0 15.6 + - - -
189A LYS* 2.9 24.9 + - - +
191A ARG* 1.3 75.6 - - - +
193A HIS* 1.3 65.3 + - - +
195A VAL* 3.6 2.6 + - - -
196A ALA* 3.1 20.3 + - - +
228A GLU* 5.6 0.2 - - - -
230A GLU* 4.2 20.7 - - - +
231A VAL* 4.3 10.9 - - - +
234A ASN* 3.2 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLU* 4.4 16.6 + - + +
149A PHE* 3.8 28.5 - - + +
150A GLY* 3.6 31.6 - - - -
153A GLN* 2.4 32.9 + - - +
189A LYS* 3.2 27.1 + - + +
190A ILE* 3.2 10.0 + - + +
192A SER* 1.3 86.6 + - - +
194A ALA* 1.3 61.7 + - - +
196A ALA* 3.3 2.8 + - - +
197A CYS* 3.1 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PHE* 3.8 21.7 - - + -
179A PHE* 3.5 24.4 - - - +
182A PHE* 3.9 10.3 - - + +
183A PHE* 3.7 10.8 - - + -
190A ILE 3.0 13.2 + - - +
191A ARG 3.2 7.6 + - - +
193A HIS* 1.3 77.4 - - - +
195A VAL* 1.3 61.1 + - - +
197A CYS* 3.6 3.0 + - - +
198A VAL* 3.3 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A PHE* 3.7 27.8 - - + -
191A ARG 3.1 19.2 + - - +
192A SER* 4.1 2.2 - - - +
194A ALA* 1.3 74.1 - - - +
196A ALA* 1.3 65.3 + - - +
198A VAL* 3.5 1.9 + - - +
199A ASN* 3.0 40.7 + - - +
216A PHE* 5.1 0.2 - - + -
220A LEU* 4.3 17.0 - - + -
223A LEU* 3.7 19.3 - - + -
231A VAL* 5.3 3.6 - - + -
234A ASN* 3.6 35.0 - - + +
235A VAL* 4.3 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLN* 3.5 33.0 - - + +
157A GLU* 5.0 1.5 - - - +
192A SER 3.1 18.9 + - - +
193A HIS 3.5 5.4 - - - +
195A VAL* 1.3 78.6 - - - +
197A CYS* 1.3 60.4 + - - +
199A ASN* 3.5 15.6 + - - +
200A GLN* 3.5 18.8 + - - +
234A ASN* 4.2 16.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PHE* 4.2 17.0 - - - -
152A LEU 4.2 6.3 - - - -
153A GLN* 3.6 33.2 - - - +
156A CYS* 4.2 13.0 - - - -
179A PHE* 3.7 27.8 - - + -
193A HIS 3.1 24.5 + - - +
194A ALA 3.9 3.4 - - - +
195A VAL 3.3 0.2 - - - -
196A ALA* 1.3 77.9 - - - +
198A VAL* 1.3 61.5 + - - +
200A GLN* 3.2 10.1 + - - +
201A PHE* 3.2 24.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ILE* 5.0 7.0 - - + +
179A PHE* 3.8 24.7 - - + -
180A LEU* 4.0 14.4 - - + -
183A PHE* 4.1 3.6 - - + -
194A ALA 3.3 17.2 + - - +
195A VAL 4.0 2.7 - - - +
196A ALA 3.4 0.2 - - - -
197A CYS* 1.3 76.1 - - - +
199A ASN* 1.3 57.6 + - - +
201A PHE* 3.0 27.6 + - - +
202A ILE* 3.5 7.1 - - - +
209A LEU* 3.7 30.7 - - + -
216A PHE* 3.6 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A VAL* 3.0 25.1 + - - +
196A ALA* 3.7 8.4 - - - +
197A CYS 3.2 0.4 - - - -
198A VAL* 1.3 76.4 - - - +
200A GLN* 1.3 63.7 - - + +
201A PHE 3.1 1.0 + - - -
202A ILE* 3.6 18.8 + - + +
203A ILE* 4.9 1.0 + - - +
216A PHE* 3.8 6.2 - - - -
234A ASN* 3.0 34.2 + - - +
237A ARG* 4.1 15.0 - - - +
238A ALA* 3.3 28.5 - - - +
241A MET* 3.5 28.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A CYS* 3.6 35.2 - - + +
157A GLU* 3.4 34.3 + - + +
160A ALA* 4.1 21.5 - - + +
196A ALA* 3.5 17.2 + - - +
197A CYS 3.4 9.4 - - - +
198A VAL 3.1 1.2 - - - -
199A ASN* 1.3 79.0 - - - +
201A PHE* 1.3 68.8 + - + +
202A ILE 3.6 0.6 + - - -
203A ILE 5.3 0.4 + - - -
204A SER* 4.1 7.4 + - - -
----------------------------------------------------------
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