Contacts of the helix formed by residues 193 - 207 (chain A) in PDB entry 3DAN
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 193 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LYS 5.1 0.5 + - - -
190A LEU* 2.6 21.7 + - - -
192A THR* 1.3 77.1 - - - +
194A ALA* 1.3 66.2 + - - +
195A PRO* 3.3 3.4 - - - -
196A THR* 3.0 23.6 + - - +
197A LEU* 3.0 30.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
173A PHE* 3.3 45.5 - - + -
190A LEU* 4.1 14.9 + - + -
191A GLY 5.3 2.7 - - - +
192A THR 3.5 0.8 - - - -
193A SER* 1.3 77.0 + - - +
195A PRO* 1.3 70.4 - - + +
197A LEU* 3.1 10.9 + - - +
198A ILE* 2.8 32.2 + - + +
240A LEU* 5.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASP 5.6 0.2 - - - +
169A GLU* 3.8 21.8 - - + +
170A GLN* 3.8 34.1 - - + +
173A PHE* 4.8 3.1 - - + -
192A THR 3.7 12.1 - - - +
193A SER 3.5 3.6 - - - -
194A ALA* 1.3 93.9 - - + +
196A THR* 1.3 56.6 + - - +
198A ILE* 4.0 0.9 - - - +
199A SER* 2.8 35.1 + - - -
278A PHE* 4.0 23.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A THR 5.4 0.9 + - - -
193A SER* 3.0 17.1 + - - -
195A PRO* 1.3 76.7 - - - +
197A LEU* 1.3 68.7 + - + +
199A SER* 3.9 4.6 - - - -
200A SER* 3.0 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A LEU* 4.2 17.0 - - + -
193A SER* 3.0 35.9 + - - +
194A ALA* 3.7 5.6 - - - +
196A THR* 1.3 80.3 - - + +
198A ILE* 1.3 62.3 + - - +
200A SER* 3.4 1.5 + - - -
201A TRP* 3.1 19.9 + - - +
236A THR* 3.5 35.7 - - + +
239A LYS* 4.1 42.2 - - + +
240A LEU* 4.3 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A PHE* 3.6 38.4 - - + -
194A ALA 2.8 23.0 + - - +
195A PRO 4.0 3.4 - - - +
197A LEU* 1.3 77.9 - - - +
199A SER* 1.3 56.9 + - - +
201A TRP* 3.2 5.3 + - + +
202A VAL* 2.8 45.8 + - + +
240A LEU* 4.0 15.9 - - + -
274A CYS* 3.6 44.6 - - + +
278A PHE* 3.7 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLU* 4.5 2.6 + - - -
195A PRO 2.8 23.0 + - - -
196A THR* 3.9 5.8 - - - -
198A ILE* 1.3 76.6 - - - +
200A SER* 1.3 59.3 + - - +
202A VAL* 3.5 6.5 + - - +
203A LEU* 3.0 30.0 + - - +
278A PHE* 4.9 2.4 - - - -
282A LYS* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A THR* 3.0 25.4 + - - +
197A LEU* 3.7 6.5 - - - -
198A ILE 3.2 0.2 - - - -
199A SER* 1.3 77.2 - - - +
201A TRP* 1.3 61.8 + - - +
203A LEU* 3.2 10.7 + - - +
204A PHE* 3.2 32.5 + - - -
233A ILE* 4.5 4.7 - - - -
236A THR* 4.7 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 2.9 29.3 + - + -
103A THR* 4.3 4.3 - - + -
197A LEU 3.1 11.0 + - - +
198A ILE* 3.6 7.6 - - + +
200A SER* 1.3 77.2 - - - +
202A VAL* 1.3 78.9 + - + +
204A PHE* 3.2 10.4 + - - +
205A ASN* 2.9 36.1 + - - +
233A ILE* 3.6 39.8 - - + +
237A TYR* 3.5 26.5 - + - -
240A LEU* 4.8 10.1 - - + -
270A LEU* 3.7 14.4 - - + -
271A PHE* 3.7 31.4 - + - -
274A CYS* 4.0 27.1 - - + -
275A PHE* 4.0 21.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ILE* 2.8 40.9 + - + +
199A SER* 3.9 6.5 - - - +
201A TRP* 1.3 83.5 - - + +
203A LEU* 1.3 58.9 + - - +
205A ASN* 3.1 8.7 + - - +
206A LEU* 2.8 52.6 + - + +
210A LEU* 5.4 3.1 - - + -
274A CYS 4.8 3.8 - - - +
275A PHE* 4.3 18.2 - - + -
279A GLY* 6.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A SER 3.0 15.0 + - - +
200A SER* 3.4 13.7 - - - +
201A TRP 3.2 0.2 - - - -
202A VAL* 1.3 77.0 - - - +
204A PHE* 1.3 62.0 + - + +
206A LEU 4.5 0.2 - - - +
207A ALA* 2.8 48.8 + - + +
210A LEU* 4.1 23.1 - - + -
212A LEU* 3.8 36.6 - - + -
223A LEU* 5.4 3.8 - - + -
228A LEU* 4.9 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 3.9 22.3 - - + +
200A SER* 3.2 23.5 + - - -
201A TRP 3.2 10.1 + - - +
203A LEU* 1.3 85.4 - - + +
205A ASN* 1.3 63.1 + - - +
207A ALA* 4.4 3.5 + - - +
208A PRO* 4.7 2.9 - - - +
228A LEU* 3.7 51.5 + - + +
229A PRO 3.1 28.3 - - - -
232A LEU* 3.8 27.8 - - + -
233A ILE* 3.8 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 3.2 16.3 + - - -
98A PRO* 3.3 36.3 - - + +
102A LEU* 3.5 22.1 - - - +
103A THR* 4.6 9.5 - - - +
111A TYR* 4.9 2.3 + - - -
201A TRP* 2.9 54.9 + - - +
202A VAL* 3.1 8.9 + - - +
204A PHE* 1.3 82.3 - - - +
206A LEU* 1.3 61.1 + - + +
208A PRO* 3.9 3.5 - - - +
271A PHE* 5.0 1.0 - - - -
275A PHE* 4.2 20.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A THR* 3.6 32.3 - - + -
96A TYR* 3.4 10.3 - - - +
202A VAL* 2.8 36.1 + - + +
203A LEU 3.8 0.2 - - - -
205A ASN* 1.3 75.1 - - + +
207A ALA* 1.3 64.2 + - - +
208A PRO* 3.2 4.3 - - - -
209A THR* 3.0 20.2 + - - +
210A LEU* 3.2 35.8 + - + +
275A PHE* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU* 2.8 32.9 + - + +
204A PHE 4.7 1.3 - - - +
205A ASN 3.6 0.2 - - - -
206A LEU* 1.3 69.5 - - - +
208A PRO* 1.3 70.9 - - + +
209A THR 3.0 1.0 + - - -
210A LEU* 3.2 15.3 + - - +
223A LEU* 3.6 26.2 - - + +
224A HIS* 3.1 16.8 + - - -
228A LEU* 4.0 23.1 - - + -
----------------------------------------------------------
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