Contacts of the helix formed by residues 192 - 207 (chain A) in PDB entry 2DFS
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 VAL 192 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ALA* 6.1 0.2 - - - +
190A ALA* 3.5 26.5 - - + -
191A ASN* 1.4 69.2 - - - +
193A GLU* 1.4 62.5 + - - +
195A LYS* 3.2 7.0 + - + +
196A VAL* 3.1 26.6 + - + +
226A ILE* 6.0 4.0 - - + -
234A ILE* 4.2 29.0 - - + +
235A ILE 4.3 4.0 - - - +
236A GLY* 4.1 34.5 - - - +
237A ALA* 4.2 2.9 - - + -
423A LEU* 3.6 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LYS* 4.3 11.4 - - - +
177A MET* 4.5 24.2 - - + +
178A ARG* 2.7 68.2 + - - +
181A ALA* 4.9 14.0 - - + +
191A ASN 2.8 6.3 + - - +
192A VAL* 1.4 73.5 - - - +
194A GLU* 1.3 55.7 + - + +
196A VAL* 3.4 6.2 + - - +
197A LEU* 2.9 59.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ASN* 3.0 26.7 + - + +
193A GLU* 1.3 75.9 - - - +
195A LYS* 1.3 106.5 + - - +
197A LEU* 3.5 8.5 + - - +
198A ALA* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLU 3.2 17.7 + - - -
190A ALA* 2.8 30.1 + - - +
191A ASN* 4.8 0.4 - - - +
192A VAL* 3.2 8.7 + - + +
194A GLU* 1.3 114.9 + - - +
196A VAL* 1.4 62.1 + - - +
198A ALA* 3.4 7.8 + - - +
199A SER* 3.3 16.5 + - - -
314A LEU 5.9 2.5 - - - +
315A LEU* 3.7 25.8 - - + +
422A ALA 4.8 10.5 - - - +
423A LEU* 4.1 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A MET* 3.9 31.9 - - + -
192A VAL* 3.1 22.8 + - + +
193A GLU 3.7 5.6 - - - +
195A LYS* 1.4 75.3 - - - +
197A LEU* 1.3 63.3 + - - +
199A SER* 2.6 31.8 + - - +
200A ASN* 3.7 7.4 + - - +
224A ILE* 4.2 23.6 - - + -
226A ILE* 5.4 1.1 - - + -
237A ALA* 4.3 7.0 - - + -
423A LEU* 3.4 31.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
170A THR 5.9 0.2 - - - +
174A LYS* 3.9 33.7 - - + -
177A MET* 4.1 14.8 - - + -
193A GLU* 2.9 50.5 + - + +
194A GLU* 3.9 7.2 - - - +
196A VAL* 1.3 74.7 - - - +
198A ALA* 1.3 57.6 + - - +
200A ASN* 3.1 40.7 + - - +
201A PRO* 3.7 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A GLU 3.1 17.7 + - - +
195A LYS* 3.6 8.5 - - - +
196A VAL 3.3 0.2 - - - -
197A LEU* 1.3 75.0 - - - +
199A SER* 1.4 59.5 + - - +
200A ASN 3.3 0.4 - - - -
201A PRO* 3.4 20.7 - - - +
202A ILE* 4.1 1.2 - - - +
311A ALA* 3.4 13.7 - - + +
314A LEU* 4.2 31.2 - - + -
315A LEU* 4.2 8.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
195A LYS 3.3 7.3 + - - -
196A VAL* 2.6 28.7 + - - +
198A ALA* 1.4 76.0 - - - +
200A ASN* 1.4 63.8 + - - +
201A PRO 3.6 0.2 - - - -
202A ILE* 3.4 7.5 + - - +
203A MET* 3.1 24.5 + - - +
222A LYS* 6.1 0.7 - - - -
224A ILE* 5.3 0.7 - - - +
239A MET* 3.7 17.1 - - - +
315A LEU* 3.7 20.6 - - - +
419A VAL* 3.8 19.7 - - - -
423A LEU* 5.7 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A THR* 4.9 7.1 - - - +
177A MET* 5.9 0.6 - - - +
196A VAL* 3.7 7.5 + - - +
197A LEU* 3.1 47.0 + - - +
199A SER* 1.4 77.1 + - - +
201A PRO* 1.3 60.1 - - + +
203A MET* 3.2 4.4 + - - +
204A GLU* 2.9 48.0 + - - +
222A LYS* 2.8 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU 3.7 6.3 - - - +
198A ALA* 3.4 19.3 - - - +
200A ASN* 1.3 93.6 - - + +
202A ILE* 1.3 58.2 + - - +
204A GLU* 4.2 5.6 - - + +
205A SER* 3.1 23.9 + - - -
307A ASN* 4.3 27.1 - - - +
308A THR* 4.3 14.5 + - - +
311A ALA* 3.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ALA 4.1 1.3 - - - +
199A SER* 3.5 8.7 - - - +
200A ASN 3.2 0.6 - - - -
201A PRO* 1.3 74.6 - - - +
203A MET* 1.3 63.5 + - + +
205A SER* 2.8 24.6 + - - +
206A ILE* 3.3 13.7 + - + +
308A THR* 4.6 5.8 - - + +
311A ALA* 3.8 17.9 - - + -
312A CYS* 3.9 41.3 - - - +
315A LEU* 3.8 30.1 - - + -
317A ILE* 4.9 2.0 - - + -
415A ILE* 3.8 28.5 - - + -
419A VAL* 4.2 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A SER* 3.1 17.7 + - - +
200A ASN* 3.9 2.5 - - - +
202A ILE* 1.3 79.3 - - + +
204A GLU* 1.3 58.4 + - + +
206A ILE* 3.8 20.4 - - + +
207A GLY* 2.8 31.5 + - - -
208A ASN* 4.0 1.1 + - - -
220A PHE* 3.8 31.7 - - + -
222A LYS* 4.3 22.4 - - + +
239A MET* 3.6 34.5 - - + +
241A THR* 4.0 4.0 - - + -
412A PHE* 4.2 5.6 - - + -
415A ILE* 5.2 4.7 - - - -
416A VAL* 3.9 25.6 - - + -
419A VAL* 5.4 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A THR* 4.3 18.7 - - - +
200A ASN* 2.9 35.9 + - - +
201A PRO* 4.2 5.6 - - + +
203A MET* 1.3 76.0 - - - +
205A SER* 1.3 57.3 + - - +
208A ASN* 3.0 53.0 + - + +
216A ASN* 2.9 32.8 + - - +
222A LYS* 4.9 7.5 + - - +
260A HIS* 3.5 8.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PRO 3.1 16.4 + - - -
202A ILE* 2.8 19.9 + - - +
204A GLU* 1.3 76.2 - - - +
206A ILE* 1.4 65.5 + - - +
207A GLY 3.9 0.2 + - - -
259A TYR 3.9 0.2 - - - -
260A HIS* 3.3 14.0 + - - -
261A ILE* 2.9 37.2 + - - +
264A GLN* 3.3 27.1 - - - -
308A THR* 3.8 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ILE* 3.6 12.3 - - + +
203A MET* 3.8 20.6 - - + +
205A SER* 1.4 87.5 + - - +
207A GLY* 1.3 60.1 + - - +
259A TYR* 3.3 11.0 - - - -
261A ILE* 4.2 16.2 - - + -
325A ILE* 6.0 0.2 - - + -
329A LEU* 5.7 3.1 - - + -
408A TYR* 2.7 30.9 + - + +
412A PHE* 3.6 40.9 - - + +
415A ILE* 4.0 47.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A MET 2.8 14.6 + - - -
206A ILE* 1.3 78.6 - - - +
208A ASN* 1.3 63.8 + - - +
219A ARG* 3.1 23.7 + - - -
220A PHE* 3.3 19.8 - - - -
244A LEU* 4.8 0.4 - - - -
259A TYR* 3.4 14.4 - - - -
412A PHE* 4.0 8.1 - - - -
----------------------------------------------------------
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