Contacts of the helix formed by residues 188 - 210 (chain A) in PDB entry 5DTM
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 ALA 188 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A GLU* 2.9 16.1 + - - +
187A LYS* 1.4 77.5 - - - +
189A ASP* 1.3 64.2 + - - +
190A ILE 3.6 0.4 - - - -
191A PRO* 3.6 18.5 - - + +
192A ALA* 3.2 25.8 + - - +
220A ARG* 3.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LYS 3.6 0.2 + - - -
188A ALA* 1.3 68.9 - - - +
190A ILE* 1.4 76.6 + - + +
192A ALA* 3.6 2.0 + - - +
193A LYS* 3.0 31.9 + - - +
220A ARG* 3.5 27.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
124A LYS* 3.4 50.5 - - + +
125A LEU* 3.9 3.6 - - + +
188A ALA* 4.9 0.2 - - - +
189A ASP* 1.4 88.5 - - + +
191A PRO* 1.4 74.6 - - + +
193A LYS* 3.2 11.4 + - + +
194A TYR* 2.9 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 3.9 24.9 - - + +
133A PRO* 5.9 0.7 - - + -
165A GLY* 3.5 29.5 - - - +
166A VAL* 3.8 11.2 - - + +
186A GLU* 3.9 8.7 - - + +
188A ALA* 3.6 30.7 - - + +
190A ILE* 1.4 91.5 - - + +
192A ALA* 1.4 52.1 + - - +
194A TYR* 3.2 2.6 + - + +
195A ALA* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A GLU* 4.0 16.4 - - + +
188A ALA 3.2 21.5 + - - +
189A ASP 3.9 2.9 - - - +
191A PRO* 1.4 75.6 - - - +
193A LYS* 1.4 61.4 + - - +
195A ALA* 3.4 20.3 + - - +
196A GLU* 3.4 15.5 + - - +
219A GLU 5.3 0.9 - - - +
220A ARG* 4.0 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ASP* 3.0 25.3 + - - +
190A ILE* 3.7 10.8 - - + +
192A ALA* 1.4 74.1 - - - +
194A TYR* 1.3 64.6 + - + +
196A GLU* 3.3 37.6 + - - +
197A THR* 3.8 7.5 + - - -
200A ARG* 4.1 17.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A SER* 3.3 28.8 - - - -
119A VAL* 3.8 24.7 - - + -
120A THR* 4.1 6.6 + - - -
121A ASP* 3.1 47.7 + - - +
124A LYS* 4.4 4.8 - - + +
125A LEU* 4.2 10.5 - - + -
166A VAL* 3.7 13.9 - - + -
190A ILE* 2.9 38.3 + - + -
191A PRO 3.6 7.2 - - - +
193A LYS* 1.3 75.9 - - + +
195A ALA* 1.4 58.7 + - - +
197A THR* 3.1 10.9 + - - +
198A MET* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A SER* 6.1 0.7 - - - +
165A GLY 4.1 4.9 - - - +
166A VAL* 3.5 28.9 + - - +
167A GLY* 4.5 0.4 - - - +
186A GLU* 6.0 0.9 - - + -
191A PRO 2.8 16.3 + - - +
192A ALA* 3.4 13.7 - - - +
194A TYR* 1.4 72.0 - - - +
196A GLU* 1.3 56.0 + - - +
198A MET* 3.3 2.0 + - - +
199A ASP* 2.9 31.4 + - - +
218A LEU* 3.6 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ALA 3.6 14.2 - - - +
193A LYS* 3.3 40.2 + - - +
194A TYR 3.2 0.6 - - - -
195A ALA* 1.3 78.1 - - - +
197A THR* 1.3 57.5 + - - +
199A ASP* 3.6 8.7 - - - +
200A ARG* 3.3 41.5 + - - +
218A LEU* 6.1 1.1 - - - +
220A ARG* 6.0 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A HIS 4.5 3.4 - - - +
118A SER* 3.6 31.6 - - - +
193A LYS* 3.8 11.3 + - - -
194A TYR* 3.1 13.4 + - - -
196A GLU* 1.3 73.6 - - - +
198A MET* 1.4 59.9 + - - +
200A ARG* 3.2 26.4 + - - +
201A GLU* 2.9 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 4.8 4.3 - - + +
114A VAL* 3.4 17.5 - - + +
115A TYR* 3.6 25.6 - - + +
118A SER* 3.5 27.6 - - - -
119A VAL* 4.3 9.6 - - + -
166A VAL* 3.3 33.7 - - + +
168A GLN* 3.8 29.2 - - + -
171A LEU* 3.9 17.3 - - + -
194A TYR 2.9 17.6 + - - +
195A ALA 3.3 4.9 + - - +
197A THR* 1.4 74.9 - - - +
199A ASP* 1.3 57.4 + - - +
202A PHE* 2.9 33.4 + - - +
218A LEU* 5.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU* 4.9 0.9 - - - -
195A ALA 2.9 17.5 + - - +
196A GLU* 3.6 9.3 - - - +
197A THR 3.2 0.2 - - - -
198A MET* 1.3 75.6 - - - +
200A ARG* 1.4 62.9 + - - +
202A PHE* 4.6 0.4 - - - -
203A ARG* 2.8 46.9 + - - +
216A TYR* 2.7 40.8 + - - +
218A LEU* 4.1 18.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LYS* 4.1 13.7 - - - +
196A GLU* 3.3 25.2 + - - +
197A THR* 3.2 40.5 + - + +
199A ASP* 1.4 81.8 - - - +
201A GLU* 1.3 58.9 + - + +
203A ARG* 3.6 6.5 + - - +
204A LYS* 3.1 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A VAL* 3.9 13.2 - - + +
117A HIS* 3.4 24.9 + - + +
118A SER* 3.4 23.6 - - - +
197A THR* 2.9 27.9 + - + +
200A ARG* 1.3 72.0 - - + +
202A PHE* 1.3 59.1 + - - +
204A LYS* 2.8 35.6 + - - +
205A TRP* 2.8 52.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 4.5 3.8 - - + -
110A ILE* 4.2 11.4 - - + -
111A LEU* 4.1 22.9 - - + -
114A VAL* 3.7 10.9 - - + +
171A LEU* 3.7 43.7 - - + -
175A ALA* 4.0 7.0 - - + -
198A MET 2.9 19.0 + - - +
199A ASP 3.7 2.9 - - - +
201A GLU* 1.3 77.3 - - - +
203A ARG* 1.3 57.3 + - - +
205A TRP* 3.9 0.3 - - - +
206A MET* 2.9 66.3 + - + +
213A HIS* 3.7 27.8 - + + -
216A TYR* 3.4 28.7 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASP* 2.8 32.8 + - - +
200A ARG* 4.0 5.6 - - - +
202A PHE* 1.3 72.9 - - - +
204A LYS* 1.3 62.1 + - - +
206A MET* 4.0 1.6 - - - +
207A LYS* 3.1 38.0 + - - +
213A HIS* 3.7 32.3 + - - +
215A GLU* 5.9 2.0 - - - +
216A TYR* 3.1 55.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A HIS* 4.5 5.9 + - - -
200A ARG 3.1 19.1 + - - +
201A GLU* 2.8 37.7 + - - +
202A PHE 3.3 0.2 - - - -
203A ARG* 1.3 75.7 - - - +
205A TRP* 1.3 87.9 + - - +
207A LYS* 3.3 9.8 + - - +
208A TRP* 2.9 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 5.8 0.2 - - + -
18A ALA* 3.5 22.4 - - + -
20A TYR* 3.4 18.2 - + - -
40A THR* 4.8 2.2 - - + -
110A ILE* 4.6 4.7 - - + -
113A GLN* 3.3 40.4 - - + +
114A VAL* 4.2 20.0 - - + -
117A HIS* 3.9 20.7 - + - -
201A GLU* 2.8 52.3 + - + +
202A PHE 4.1 2.0 - - - +
204A LYS* 1.3 85.9 - - - +
206A MET* 1.3 59.0 + - - +
208A TRP* 3.0 38.1 + + + +
209A TYR* 2.9 59.8 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PRO* 3.9 14.6 - - + -
107A LEU* 5.1 0.4 - - - -
110A ILE* 3.8 27.1 - - + -
175A ALA* 4.3 2.0 - - + -
202A PHE* 2.9 57.5 + - + +
203A ARG 4.0 2.9 - - - +
205A TRP* 1.3 71.3 - - - +
207A LYS* 1.3 55.1 + - - +
209A TYR* 3.4 2.7 + - - -
210A GLY 2.9 8.3 + - - -
211A LYS* 2.8 53.0 + - + +
212A LYS 3.3 27.1 - - - +
213A HIS* 3.8 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.3 14.7 - - - +
15A ALA* 3.8 11.8 - - + +
203A ARG* 3.1 28.7 + - - +
204A LYS* 3.5 7.2 - - - +
206A MET* 1.3 73.7 - - + +
208A TRP* 1.4 63.7 + - - +
210A GLY* 3.1 11.6 + - - +
211A LYS 5.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.3 33.3 + - + -
10A LYS 3.2 17.7 - - - -
11A SER* 2.7 37.9 + - - +
12A PRO* 3.3 17.7 - - + +
13A VAL* 3.7 1.2 - - - +
15A ALA* 4.0 5.1 - - + +
16A GLU 3.2 23.3 + - - -
18A ALA* 3.3 18.7 - - + +
40A THR* 3.6 23.3 - - + -
44A VAL* 3.9 3.4 - - + -
78A TYR* 3.5 19.1 - + - -
204A LYS* 2.9 16.2 + - + +
205A TRP* 3.0 28.9 + + + +
207A LYS* 1.4 75.6 - - - +
209A TYR* 1.3 92.7 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PRO* 4.2 9.9 - - + +
13A VAL* 4.1 8.7 - - - +
40A THR* 3.4 12.9 - - + +
43A TRP* 5.2 0.7 - - + -
44A VAL* 4.1 17.0 - - + -
106A LEU* 3.8 24.7 - - + -
109A HIS* 2.9 24.3 + + - -
110A ILE* 3.6 26.7 - - + -
113A GLN* 2.7 28.8 + - - -
205A TRP* 2.9 42.0 + + + +
206A MET 4.0 1.1 - - - +
208A TRP* 1.3 97.8 - + - +
210A GLY* 1.3 60.5 + - - +
211A LYS* 3.8 29.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.7 20.8 - - - +
99A ASN* 3.8 23.7 - - - +
100A THR 4.2 1.0 + - - -
206A MET 2.9 5.6 + - - -
207A LYS* 3.1 15.1 + - - -
208A TRP 3.3 0.2 - - - -
209A TYR* 1.3 78.6 - - - +
211A LYS* 1.3 65.8 + - - +
----------------------------------------------------------
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