Contacts of the helix formed by residues 190 - 205 (chain M) in PDB entry 3FKS
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 ARG 190 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166L ARG* 3.6 11.7 - - - +
309L GLU* 3.6 7.4 - - - -
345L ILE 4.6 1.0 + - - -
346L SER* 2.9 29.0 + - - +
347L ILE 3.4 17.7 + - - +
348L THR 2.9 22.4 + - - -
349L ASP* 3.7 13.0 - - - +
375L ARG* 4.3 5.5 - - - +
160M GLY* 4.7 0.4 - - - +
164M THR* 3.1 17.6 + - - -
189M GLU* 1.3 86.8 + - - +
191M THR* 1.3 64.8 + - - +
192M ARG* 4.5 2.2 - - + +
193M GLU* 3.0 50.3 + - + +
194M GLY 3.5 3.6 + - - -
221M GLN* 3.3 10.6 + - - -
222M MET* 4.3 9.2 - - + -
609M PO4 2.7 36.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 191 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136L PRO 4.0 4.4 + - - +
137L GLY* 3.9 19.1 - - - -
138L ILE* 3.9 17.6 - - + +
141L ARG* 3.7 23.6 - - - +
166L ARG* 5.1 0.2 - - - +
309L GLU* 2.8 28.4 + - - -
189M GLU 3.4 1.4 + - - -
190M ARG* 1.3 71.2 - - - +
192M ARG* 1.3 65.0 - - - +
194M GLY* 3.0 3.5 + - - -
195M ASN* 3.0 19.6 + - - +
221M GLN* 3.4 27.1 - - + +
223M ASN* 4.0 9.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 192 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141L ARG* 3.8 21.7 - - + +
144L VAL* 5.0 17.0 - - + +
164L GLY 5.6 3.1 - - - -
166L ARG* 4.1 15.2 - - - +
309L GLU* 5.0 0.4 + - - -
349L ASP* 3.0 36.2 + - - +
375L ARG* 3.5 39.6 + - - +
376L VAL* 4.2 12.4 - - - +
190M ARG* 4.5 0.9 - - + +
191M THR* 1.3 78.4 - - - +
193M GLU* 1.3 84.6 + - + +
195M ASN* 3.3 9.4 + - - +
196M ASP* 3.0 56.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 193 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375L ARG* 4.1 12.1 + - - +
164M THR* 3.2 32.8 - - + +
165M VAL* 6.1 0.2 - - - +
168M GLN* 3.8 10.5 + - - +
189M GLU* 4.2 1.9 - - - +
190M ARG* 3.0 52.5 + - - +
191M THR 3.2 0.4 - - - -
192M ARG* 1.3 113.0 + - + +
194M GLY* 1.3 60.6 + - - +
195M ASN 3.2 0.2 - - - -
196M ASP* 3.7 10.4 - - - +
197M LEU* 3.1 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 194 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138L ILE* 4.0 9.8 - - - +
190M ARG 3.5 5.5 + - - -
191M THR 3.0 8.4 + - - -
193M GLU* 1.3 75.4 - - - +
195M ASN* 1.3 60.2 + - - +
197M LEU* 3.3 6.3 + - - +
198M TYR* 3.1 25.5 + - - +
217M LEU* 5.7 0.2 - - - +
219M PHE* 3.5 35.1 - - - -
221M GLN* 4.4 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 195 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138L ILE* 3.2 29.4 - - + +
139L LEU 4.6 1.6 - - - +
141L ARG* 3.2 44.9 + - + +
142L ARG* 4.0 11.9 + - - +
143L SER* 4.1 3.6 + - - +
191M THR 3.0 10.6 + - - +
192M ARG* 3.3 10.8 + - - +
193M GLU 3.2 0.2 - - - -
194M GLY* 1.3 74.5 - - - +
196M ASP* 1.3 77.4 + - - +
198M TYR* 3.1 8.7 + - - +
199M ARG* 2.9 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 196 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143L SER* 3.3 27.1 + - - +
168M GLN* 4.3 10.8 - - - +
192M ARG* 3.0 42.5 + - - +
193M GLU* 3.5 12.3 + - - +
194M GLY 3.3 0.2 - - - -
195M ASN* 1.3 83.4 + - - +
197M LEU* 1.3 53.2 + - - +
199M ARG* 3.7 14.3 + - - +
200M GLU* 2.8 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168M GLN* 4.2 25.5 - - + +
171M ILE* 4.5 26.9 - - + -
184M PHE* 3.4 52.3 - - + -
193M GLU 3.1 16.7 + - - +
194M GLY* 3.6 7.0 - - - +
195M ASN 3.2 0.2 - - - -
196M ASP* 1.3 77.5 - - - +
198M TYR* 1.3 59.8 + - - +
200M GLU* 4.1 5.8 - - + +
201M MET* 3.2 38.4 + - + +
217M LEU* 4.4 10.8 - - + -
219M PHE* 4.5 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 198 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138L ILE* 4.3 13.9 - - + -
139L LEU* 4.5 20.1 - - + +
93M GLY 5.0 6.7 + - - -
95M ILE* 3.4 35.9 - - + -
104M ASP* 4.6 7.3 + - + +
106M ARG* 4.2 12.3 - - - -
194M GLY 3.1 12.7 + - - +
195M ASN* 3.1 13.4 + - - +
197M LEU* 1.3 78.9 - - - +
199M ARG* 1.3 61.3 + - + +
201M MET* 4.4 4.0 - - - -
202M LYS* 3.2 58.7 + - + +
207M ILE* 3.9 17.1 - - + +
209M LEU* 4.1 13.0 - - - +
217M LEU* 3.7 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 199 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142L ARG* 5.9 3.8 - - - +
143L SER* 3.0 34.4 + - - +
195M ASN* 2.9 19.6 + - - +
196M ASP* 3.8 11.9 + - - +
198M TYR* 1.3 78.9 - - + +
200M GLU* 1.3 81.7 + - - +
201M MET 3.2 0.4 - - - -
202M LYS* 3.5 4.7 + - - +
203M GLU* 3.3 55.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 200 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168M GLN* 5.4 6.7 - - - +
196M ASP* 2.8 21.5 + - + +
197M LEU* 4.1 10.1 - - + +
198M TYR 3.5 0.2 - - - -
199M ARG* 1.3 93.8 - - - +
201M MET* 1.3 57.5 + - + +
203M GLU* 4.5 2.4 - - - +
204M THR* 2.6 41.8 + - - -
420M VAL* 4.9 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 201 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171M ILE* 5.0 16.4 - - + -
184M PHE* 6.1 1.1 - - - -
197M LEU* 3.2 37.3 + - + +
198M TYR 4.5 0.2 - - - +
199M ARG 3.2 0.2 - - - -
200M GLU* 1.3 78.7 - - + +
202M LYS* 1.3 63.6 + - - +
204M THR 4.0 0.2 - - - -
205M GLY 3.2 2.8 + - - -
206M VAL* 3.1 34.3 + - + -
207M ILE* 3.1 39.9 + - + -
215M VAL* 3.8 25.1 - - + -
217M LEU* 3.4 43.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 202 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198M TYR* 3.2 51.1 + - + +
199M ARG* 3.5 5.9 + - - +
200M GLU 3.4 0.4 - - - -
201M MET* 1.3 78.7 - - - +
203M GLU* 1.3 67.9 + - + +
204M THR 3.5 0.5 + - - -
205M GLY* 3.8 5.5 + - - -
207M ILE* 3.9 35.2 - - + +
209M LEU* 3.6 43.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199M ARG* 3.3 49.6 + - + +
200M GLU* 4.6 2.0 - - - +
202M LYS* 1.3 76.3 - - + +
204M THR* 1.3 68.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 204 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176M LYS* 5.2 19.3 - - + +
200M GLU* 2.6 32.8 + - - -
201M MET 4.0 2.7 - - - -
202M LYS 3.3 0.6 - - - -
203M GLU* 1.3 83.6 - - - +
205M GLY* 1.3 59.9 + - - +
206M VAL* 4.1 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 205 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201M MET 3.2 4.5 + - - -
202M LYS 3.8 3.1 + - - -
203M GLU 3.6 0.8 - - - -
204M THR* 1.3 78.6 - - - +
206M VAL* 1.3 70.1 + - - +
207M ILE 3.2 14.2 + - - +
208M ASN* 5.0 5.1 + - - +
212M GLU 5.1 2.6 - - - +
----------------------------------------------------------
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