Contacts of the helix formed by residues 190 - 208 (chain A) in PDB entry 3F9B
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 GLY 190 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A SER* 3.3 20.3 + - - +
189A TYR* 1.3 82.2 - - - +
191A PRO* 1.3 75.4 - - - +
192A GLU* 3.2 7.0 + - - -
193A ALA 3.2 3.0 + - - -
194A ARG* 3.1 21.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
190A GLY* 1.3 84.6 - - - +
192A GLU* 1.3 73.1 + - - +
194A ARG* 3.8 9.4 - - + +
195A ALA* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A SER* 5.4 4.0 - - - +
190A GLY* 4.0 3.8 - - - -
191A PRO* 1.3 94.2 - - - +
193A ALA* 1.3 59.6 + - - +
195A ALA* 3.4 6.7 + - - +
196A GLU* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A SER 3.5 17.3 + - - +
188A PRO* 3.4 26.9 - - + +
190A GLY 3.2 6.5 + - - +
192A GLU* 1.3 78.4 - - - +
194A ARG* 1.3 57.7 + - - +
196A GLU* 3.3 3.4 + - - +
197A LEU* 3.0 28.5 + - - +
465A LEU* 4.6 5.8 - - + +
466A LEU* 3.9 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A TYR 3.5 21.4 + - - +
190A GLY 3.1 14.3 + - - +
191A PRO* 3.9 8.3 - - + +
192A GLU 3.3 0.2 - - - -
193A ALA* 1.3 73.5 - - - +
195A ALA* 1.3 59.4 + - - +
197A LEU* 3.4 8.2 + - - +
198A SER* 3.0 28.1 + - - -
451A LEU* 5.7 1.4 - - - +
452A ASP* 3.0 43.2 + - - +
455A ILE* 3.6 33.0 - - + +
456A LYS* 5.6 0.4 - - - +
459A GLU* 5.0 6.7 + - - -
465A LEU* 4.0 17.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
191A PRO 2.9 18.9 + - - +
192A GLU* 3.7 6.7 - - - +
194A ARG* 1.3 75.2 - - - +
196A GLU* 1.3 58.1 + - - +
198A SER* 3.4 7.7 + - - -
199A SER* 2.9 29.4 + - - -
----------------------------------------------------------
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 GLU 3.0 16.4 + - - +
193A ALA* 3.6 5.2 - - - +
194A ARG 3.3 0.2 - - - -
195A ALA* 1.3 72.7 - - - +
197A LEU* 1.3 65.5 + - - +
199A SER* 3.3 12.8 + - - -
200A ARG* 2.9 69.3 + - - +
466A LEU* 3.9 14.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
193A ALA 3.0 13.4 + - - +
194A ARG* 3.6 8.1 - - - +
195A ALA 3.3 0.2 - - - -
196A GLU* 1.3 76.3 - - - +
198A SER* 1.3 58.1 + - - +
200A ARG* 3.3 4.4 + - + +
201A LEU* 3.0 50.5 + - + +
429A VAL* 3.9 24.7 - - + -
430A GLU* 3.7 36.8 - - + +
451A LEU* 4.4 7.9 - - + -
455A ILE* 4.0 26.5 - - + -
465A LEU* 3.8 19.3 - - + +
466A LEU* 3.6 13.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ARG 3.0 17.1 + - - -
195A ALA* 3.6 7.6 - - - -
196A GLU 3.3 0.2 - - - -
197A LEU* 1.3 76.3 - - - +
199A SER* 1.3 56.5 + - - +
201A LEU* 3.3 7.9 + - - +
202A THR* 2.8 41.6 + - - -
448A ASP* 4.9 8.8 + - - -
451A LEU* 5.0 10.6 - - - +
----------------------------------------------------------
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 ALA 2.9 17.9 + - - -
196A GLU* 3.5 17.5 + - - -
198A SER* 1.3 75.9 - - - +
200A ARG* 1.3 63.2 + - - +
202A THR* 3.3 5.7 + - - -
203A THR* 3.1 30.1 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
196A GLU* 2.9 54.3 + - - +
197A LEU 3.7 3.6 - - - +
199A SER* 1.3 75.2 - - - +
201A LEU* 1.3 65.3 + - + +
203A THR* 3.4 7.0 + - - -
204A LEU* 3.2 21.7 + - - +
430A GLU* 2.8 54.8 + - + +
466A LEU* 4.0 14.7 - - - +
467A ASN* 3.3 24.4 + - - +
468A SER* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 3.0 39.9 + - + +
198A SER* 3.9 4.5 - - - +
200A ARG* 1.3 78.3 - - + +
202A THR* 1.3 57.5 + - - +
204A LEU* 3.3 10.6 + - + +
205A ARG 3.0 17.3 + - - -
430A GLU* 4.5 10.8 - - + +
433A VAL* 3.7 40.4 - - + -
434A SER* 4.2 14.6 - - - +
437A ARG* 2.8 32.1 + - - +
451A LEU* 4.0 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A SER* 2.8 29.4 + - - -
199A SER* 3.7 6.5 - - - -
201A LEU* 1.3 73.8 - - - +
203A THR* 1.3 67.1 + - - +
205A ARG* 3.3 10.4 + - + +
206A ASN* 3.1 36.5 + - - +
437A ARG* 4.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A SER* 3.1 16.6 + - - -
200A ARG* 3.6 10.7 - - - -
202A THR* 1.3 77.5 - - - +
204A LEU* 1.3 62.4 + - - +
206A ASN* 3.3 11.1 + - - +
207A THR* 3.0 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ARG 3.2 11.3 + - - +
201A LEU* 3.5 14.4 - - + +
202A THR 3.2 0.2 - - - -
203A THR* 1.3 77.1 - - - +
205A ARG* 1.3 65.5 + - - +
207A THR* 3.2 11.3 + - + -
208A LEU* 3.0 51.4 + - + +
434A SER* 3.6 40.8 - - - +
437A ARG* 4.0 18.4 - - + -
438A VAL* 4.4 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU 3.0 6.6 + - - +
202A THR* 3.6 11.9 - - - +
204A LEU* 1.3 75.1 - - - +
206A ASN* 1.3 68.8 + - - +
208A LEU* 3.3 3.1 + - - +
209A ALA* 3.1 21.8 + - - +
437A ARG* 3.2 33.4 - - - +
442A GLY* 3.0 34.1 + - - +
443A ILE* 3.3 41.9 + - + +
445A VAL 3.4 7.1 + - - -
446A GLN* 3.4 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A THR* 3.1 29.8 + - - +
203A THR* 3.5 10.7 - - + +
204A LEU 3.2 0.2 - - - -
205A ARG* 1.3 82.7 - - - +
207A THR* 1.3 62.8 + - - +
209A ALA* 3.3 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A THR* 3.0 21.6 + - - +
204A LEU* 3.6 15.0 - - + -
206A ASN* 1.3 75.6 - - - +
208A LEU* 1.3 63.9 + - + +
209A ALA 3.5 0.7 + - - +
216A ARG* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 3.0 38.9 + - + +
205A ARG 3.6 3.8 - - - +
207A THR* 1.3 79.2 - - + +
209A ALA* 1.3 65.1 + - - +
210A PRO* 3.3 3.1 - - - +
216A ARG* 3.8 14.6 - - - +
217A TYR* 2.6 33.2 + - - +
235A ARG* 3.6 26.5 - - - +
437A ARG* 3.5 45.3 - - + +
438A VAL* 3.9 7.6 - - + +
442A GLY* 4.0 13.1 + - - -
----------------------------------------------------------
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