Contacts of the helix formed by residues 185 - 198 (chain I) in PDB entry 5T0G
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 THR 185 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183I GLU* 3.9 6.0 - - + +
184I MET* 1.3 80.1 + - - +
186I LEU* 1.3 65.3 + - - +
187I LYS* 3.1 15.7 - - - +
188I SER* 2.4 40.3 + - - -
189I ALA* 3.6 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I ALA* 3.8 16.4 - - + -
40I ASN 3.3 7.6 - - - +
41I ASP* 3.1 28.9 - - - +
42I GLY* 3.8 29.8 - - - -
43I VAL 4.0 9.4 - - - +
44I LEU* 3.9 8.6 - - + +
184I MET* 4.3 4.3 - - + -
185I THR* 1.3 77.9 - - - +
187I LYS* 1.3 60.7 + - + +
189I ALA* 3.2 9.8 + - - +
190I LEU* 2.8 37.3 + - + +
215I THR* 5.5 6.3 - - + -
217I THR* 4.9 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 187 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185I THR* 3.1 15.0 - - - +
186I LEU* 1.3 78.6 - - + +
188I SER* 1.3 59.8 + - - +
190I LEU* 3.5 15.8 - - + +
191I ALA* 2.9 29.8 + - - +
236I LEU* 5.6 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 188 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180I LYS* 4.8 5.2 - - - +
183I GLU* 4.5 4.3 + - - +
185I THR* 2.4 42.8 + - - -
187I LYS* 1.3 78.6 - - - +
189I ALA* 1.3 61.3 + - - +
191I ALA* 3.4 5.7 + - - +
192I LEU* 2.9 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I ILE* 4.6 7.8 - - + +
38I LEU 4.5 7.2 - - - +
39I ALA* 5.2 1.8 - - + -
44I LEU* 3.7 20.1 - - + +
180I LYS* 3.8 27.6 - - - +
184I MET* 6.1 0.2 - - + -
185I THR 3.6 2.9 + - - +
186I LEU* 3.2 11.7 + - - +
188I SER* 1.3 80.8 + - - +
190I LEU* 1.3 57.5 + - - +
192I LEU* 3.4 10.7 - - - +
193I ALA* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I LEU* 3.7 35.9 - - + -
186I LEU* 2.8 26.8 + - + +
187I LYS* 3.5 18.2 - - + +
188I SER 3.1 0.2 - - - -
189I ALA* 1.3 75.0 - - - +
191I ALA* 1.3 60.1 + - - +
193I ALA* 3.3 5.6 + - + +
194I ILE* 2.9 28.8 + - - +
213I ILE* 4.2 23.1 - - + -
215I THR* 4.5 11.0 - - + -
228I LEU* 5.3 6.7 - - + -
236I LEU* 4.6 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 191 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I LYS 2.9 16.5 + - - +
188I SER* 3.9 5.2 - - - +
190I LEU* 1.3 74.6 - - - +
192I LEU* 1.3 58.7 + - - +
194I ILE* 4.0 5.6 - - - +
195I LYS* 2.9 27.6 + - - +
236I LEU* 5.6 11.3 - - + +
240I HIS* 3.5 26.8 + - + +
243I GLU* 6.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I ILE* 5.5 5.8 - - + -
174I MET* 6.3 0.2 - - + -
175I LEU* 3.6 31.2 - - + -
178I ASP* 3.5 42.6 - - + +
180I LYS* 4.5 20.2 - - + +
188I SER 2.9 18.4 + - - +
189I ALA* 3.4 9.0 - - - +
190I LEU 3.1 0.2 - - - -
191I ALA* 1.3 75.0 - - - +
193I ALA* 1.3 62.8 + - + +
195I LYS* 2.9 30.2 + - - +
196I VAL* 2.9 18.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 193 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I LEU* 3.8 31.4 - - + +
37I ILE* 5.9 2.2 - - + -
44I LEU* 4.7 6.7 - - + -
46I ALA* 5.8 1.3 - - + -
189I ALA 2.9 17.9 + - - +
190I LEU* 3.3 7.6 + - + +
192I LEU* 1.3 79.2 - - + +
194I ILE* 1.3 60.5 + - - +
196I VAL* 3.2 24.7 + - - +
197I LEU* 3.5 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 194 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190I LEU 2.9 17.8 + - - +
191I ALA* 4.0 6.5 - - - +
193I ALA* 1.3 73.7 - - - +
195I LYS* 1.3 61.0 + - - +
197I LEU* 3.5 2.5 + - - +
198I ASN* 2.9 29.8 + - - +
206I LEU* 3.2 25.3 - - + +
237I ILE* 5.6 6.7 - - + -
240I HIS* 4.0 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 195 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174I MET* 3.5 33.3 - - + +
178I ASP* 2.9 30.5 + - - -
191I ALA 2.9 14.8 + - - +
192I LEU* 2.9 21.0 + - - +
194I ILE* 1.3 76.3 - - - +
196I VAL* 1.3 62.8 + - - +
198I ASN* 3.5 9.2 + - + +
199I LYS* 3.5 15.0 + - + +
240I HIS* 3.3 25.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I LEU* 5.5 5.8 - - + -
168I SER* 5.4 1.3 - - - +
171I ALA* 3.5 30.3 - - + -
174I MET* 3.7 24.5 - - + -
175I LEU* 4.9 13.2 - - + -
192I LEU* 2.9 17.7 + - + +
193I ALA* 3.3 15.3 - - - +
194I ILE 3.1 0.4 - - - -
195I LYS* 1.3 76.9 - - - +
197I LEU* 1.3 68.7 + - + +
199I LYS 3.2 1.6 + - - -
200I THR* 2.5 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I THR* 5.6 11.7 - - + -
35I LEU* 3.7 28.3 - - + -
46I ALA* 6.2 1.1 - - + -
47I ALA 5.5 1.6 - - - +
48I GLU* 4.8 13.9 - - + +
193I ALA 3.5 8.2 + - - +
194I ILE* 3.5 4.9 + - - +
196I VAL* 1.3 91.7 - - + +
198I ASN* 1.3 59.9 + - - +
199I LYS 3.1 5.9 + - - -
200I THR* 4.0 1.6 - - - +
201I MET* 3.1 38.5 + - + +
203I VAL 4.0 7.4 - - - +
206I LEU* 4.4 14.9 - - + +
211I VAL* 3.7 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 198 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194I ILE 2.9 19.3 + - - +
195I LYS* 3.8 10.2 - - + +
196I VAL 3.2 0.6 - - - -
197I LEU* 1.3 77.1 - - - +
199I LYS* 1.3 57.5 + - + +
201I MET 5.2 1.1 - - - -
203I VAL 5.7 0.9 - - - -
204I SER* 5.6 4.4 + - - +
205I LYS* 5.0 8.7 + - - -
206I LEU* 3.9 20.6 - - + +
240I HIS* 3.7 21.9 + - - +
241I GLU* 5.3 9.9 - - - +
244I GLU* 4.9 15.2 - - - +
----------------------------------------------------------
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