Contacts of the helix formed by residues 209 - 223 (chain A) in PDB entry 3TDU
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 PRO 209 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A PHE* 4.0 0.4 - - + -
171A LYS 5.4 0.2 - - - +
172A GLY* 4.9 4.3 - - - -
205A LYS* 4.7 8.3 - - - +
207A SER 3.7 7.6 - - - +
208A ILE* 1.3 92.0 - - + +
210A LYS* 1.3 66.7 + - - +
211A ASP* 4.4 6.1 - - + +
212A THR* 3.1 24.6 + - + +
213A TRP* 3.0 19.1 + - - +
239A LEU* 5.0 3.6 - - + -
758C GLU* 3.4 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLN* 4.8 10.5 + - - +
162A PHE* 3.5 34.3 - - + -
163A ASN* 3.6 31.2 + - - +
171A LYS 4.7 4.9 + - - +
209A PRO* 1.3 71.1 - - - +
211A ASP* 1.3 58.5 + - - +
213A TRP* 3.3 3.1 + - - +
214A ASN* 2.9 57.5 + - - +
60B GLY 4.4 17.7 + - - +
62B ARG* 6.1 6.7 - - + +
758C GLU* 4.4 4.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PRO* 3.3 4.1 - - + +
210A LYS* 1.3 78.4 - - - +
212A THR* 1.3 57.7 + - - +
214A ASN* 4.4 7.1 + - - +
215A LEU* 3.1 32.2 + - - +
237A PRO* 3.7 8.8 - - - +
754C ASP* 4.8 3.5 - - - +
757C ILE* 3.8 31.6 - - + +
758C GLU* 5.5 0.2 + - - -
764C ARG* 2.7 52.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A TRP* 5.7 0.2 - - + -
196A TRP* 4.4 14.6 - - + -
208A ILE* 4.4 6.7 - - + -
209A PRO* 3.1 29.1 + - - +
211A ASP* 1.3 75.0 + - - +
213A TRP* 1.3 67.6 + - - +
215A LEU 3.4 1.2 + - - -
216A LEU* 3.2 20.8 + - - +
237A PRO* 3.6 19.6 - - + +
239A LEU* 3.8 37.2 - - + +
240A ILE* 4.3 10.5 - - + +
754C ASP* 5.2 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A TYR* 2.7 72.0 + + - -
159A GLN* 4.5 0.2 - - - -
161A THR* 3.8 22.0 - - + -
162A PHE* 3.5 44.9 - + + +
173A LEU* 4.0 17.0 - - + -
178A ALA* 3.8 12.8 - - + -
181A TYR* 3.8 24.2 - - + -
182A TRP* 3.2 49.4 - + - -
185A VAL* 4.5 1.3 - - + -
208A ILE* 4.0 7.3 - - + +
209A PRO 3.0 8.6 + - - +
210A LYS 3.4 7.4 - - - +
212A THR* 1.3 79.7 - - - +
214A ASN* 1.3 75.6 + - - +
216A LEU* 3.2 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A TYR* 3.8 4.6 - - - -
159A GLN* 3.4 46.6 + - - +
162A PHE* 5.2 0.3 - - - +
210A LYS* 2.9 48.6 + - - +
211A ASP* 3.7 9.8 + - - +
212A THR 3.3 0.2 - - - -
213A TRP* 1.3 90.3 - - - +
215A LEU* 1.3 70.4 + - + +
217A LEU* 3.4 16.5 + - - +
218A ASP* 3.6 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ASP* 3.1 25.5 + - - +
213A TRP 3.3 0.4 - - - -
214A ASN* 1.3 82.2 - - + +
216A LEU* 1.3 61.0 + - - +
217A LEU 3.1 2.0 - - - -
218A ASP* 3.2 14.4 + - - +
219A PHE* 2.9 24.1 + - - +
235A ALA 6.4 0.2 - - - -
236A TRP* 3.5 20.9 - - + -
237A PRO* 3.8 24.5 - - + -
240A ILE* 4.0 2.5 - - - -
764C ARG* 3.6 31.9 - - - +
769C LYS* 3.7 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A TYR* 3.7 2.5 - - - +
182A TRP* 3.5 27.6 - - + +
186A LEU* 4.1 5.8 - - + -
190A PHE* 4.0 15.7 - - + -
196A TRP* 3.4 60.6 - - + +
212A THR 3.2 12.3 + - - +
213A TRP* 3.2 12.5 + - - +
215A LEU* 1.3 76.8 - - - +
217A LEU* 1.3 57.7 + - - +
219A PHE* 3.3 22.7 + - + +
220A SER* 2.9 28.9 + - - -
240A ILE* 3.9 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PRO 5.7 0.2 - - - +
154A PHE* 3.9 24.2 - - + -
155A LYS* 3.9 27.4 - - + -
158A TYR* 3.7 49.1 + - + -
186A LEU* 4.2 10.5 - - + -
189A ARG* 4.0 14.4 - - - +
214A ASN 3.4 7.4 + - - +
215A LEU 3.1 0.4 - - - -
216A LEU* 1.3 77.5 - - - +
218A ASP* 1.3 65.6 + - - +
220A SER* 2.7 30.4 + - - +
221A THR* 3.2 19.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LYS* 5.0 17.0 + - - +
159A GLN* 5.8 0.3 + - - -
214A ASN 3.6 14.4 - - - +
215A LEU* 3.2 23.8 + - + +
217A LEU* 1.3 76.9 - - - +
219A PHE* 1.3 62.6 + - - +
221A THR* 2.6 24.7 + - - +
222A MET* 3.3 12.3 + - - +
236A TRP* 3.8 6.5 - - + -
769C LYS* 3.7 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PHE* 3.7 33.7 - + - -
192A PHE* 4.8 1.1 - + - -
215A LEU 2.9 13.6 + - - +
216A LEU* 3.5 19.1 - - + +
217A LEU 3.2 0.2 - - - -
218A ASP* 1.3 76.1 - - - +
220A SER* 1.3 64.1 + - - +
221A THR 3.2 0.3 + - - -
222A MET* 3.3 3.6 + - + +
223A ILE* 3.0 58.1 + - + +
227A MET* 4.5 3.1 - - + -
230A TYR* 3.6 32.5 - + - -
236A TRP* 3.6 13.8 - + + -
240A ILE* 3.5 19.5 - - + -
243A PHE* 4.0 22.7 - + - -
244A VAL* 3.6 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 4.7 5.1 - - - +
189A ARG* 4.0 14.0 + - - +
190A PHE* 3.4 47.1 - - - -
191A LYS* 5.6 2.3 + - - +
216A LEU 2.9 13.1 + - - -
217A LEU* 2.7 32.4 + - - +
219A PHE* 1.3 76.9 - - - +
221A THR* 1.3 61.5 + - - +
222A MET 3.7 0.2 + - - -
223A ILE* 4.2 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ARG* 5.0 8.3 - - - +
217A LEU* 3.3 26.0 - - + +
218A ASP* 2.6 26.9 + - - +
220A SER* 1.3 82.1 - - - +
222A MET* 1.3 61.7 + - - +
223A ILE 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ASP 3.3 21.4 + - - +
219A PHE* 3.3 8.6 + - + +
221A THR* 1.3 85.3 + - - +
223A ILE* 1.3 98.1 + - + +
224A ALA* 3.3 0.7 + - - -
229A ASN* 2.7 40.0 + - - +
230A TYR* 4.6 9.2 - - + -
236A TRP* 3.6 31.2 - - + +
769C LYS* 4.6 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PHE* 4.6 2.2 - - + -
191A LYS* 2.8 26.8 + - + -
192A PHE* 3.9 21.3 - - + -
219A PHE* 3.0 58.4 + - + +
220A SER* 4.2 12.2 - - - +
221A THR 3.8 0.9 - - - +
222A MET* 1.3 84.0 - - + +
224A ALA* 1.3 68.3 + - - +
227A MET* 3.7 28.3 - - + -
229A ASN* 3.7 14.4 - - - +
230A TYR* 3.8 16.6 - - + -
----------------------------------------------------------
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