Contacts of the helix formed by residues 185 - 195 (chain B) in PDB entry 5L26
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 ALA 185 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ILE 5.3 1.3 - - - -
151B PHE 4.0 4.5 - - - -
152B VAL* 4.0 1.8 - - - -
153B GLY* 3.6 26.9 - - - +
184B VAL* 1.3 79.0 - - - +
186B GLY* 1.3 60.4 + - - +
187B SER* 3.6 19.1 - - - +
188B VAL* 3.2 8.7 - - + +
189B LEU* 3.0 29.0 + - - +
366B PHE* 3.2 7.0 - - + -
504B URI 3.8 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PHE* 4.1 14.2 - - - -
112B MET* 6.2 2.5 - - - -
150B ILE 4.9 1.7 + - - -
151B PHE* 2.8 24.0 + - - -
185B ALA* 1.3 72.9 - - - +
187B SER* 1.3 61.0 + - - +
189B LEU* 3.4 13.9 - - - +
190B ALA* 3.3 21.5 + - - +
503B 6ZL 4.8 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B MET* 4.3 9.4 - - - +
105B ILE* 3.7 36.9 + - - +
108B PHE* 3.8 21.7 - - - +
109B SER* 4.6 5.1 + - - -
112B MET* 6.2 1.0 - - - +
185B ALA* 3.6 13.9 - - - +
186B GLY* 1.3 78.0 - - - +
188B VAL* 1.3 73.9 + - - +
189B LEU 3.4 0.2 + - - -
190B ALA* 3.4 6.2 + - - +
191B GLY* 3.3 13.7 + - - -
504B URI 4.5 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ILE* 4.4 16.4 - - + -
185B ALA* 3.2 17.7 - - + +
187B SER* 1.3 86.4 + - - +
189B LEU* 1.3 60.3 + - - +
191B GLY* 3.0 4.0 + - - +
192B TYR* 2.9 59.2 + - + +
263B VAL* 5.6 0.9 - - + -
333B PHE* 3.7 28.7 - - + -
366B PHE* 3.5 20.4 - - + -
504B URI 4.1 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 5.0 10.1 - - + -
150B ILE 5.8 0.9 - - - +
184B VAL* 4.3 9.6 - - + -
185B ALA 3.0 16.9 + - - +
186B GLY* 3.4 13.5 - - - +
187B SER 3.2 0.4 - - - -
188B VAL* 1.3 78.6 - - - +
190B ALA* 1.3 66.0 + - + +
192B TYR* 3.1 16.2 + - - +
193B VAL* 3.1 24.9 + - + +
199B LEU* 3.7 28.5 - - + -
202B LEU* 3.6 27.5 - - + +
203B ILE* 4.2 10.8 - - + -
206B SER* 3.3 28.0 - - - +
503B 6ZL 6.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 6.1 0.2 - - + -
67B ILE* 3.7 24.6 - - + +
104B MET* 4.3 11.0 - - + -
108B PHE* 3.5 34.3 - - + -
186B GLY 3.3 4.8 + - - +
187B SER 3.8 7.2 - - - +
189B LEU* 1.3 81.6 - - + +
191B GLY* 1.3 59.8 + - - +
193B VAL* 3.5 3.8 - - - +
194B GLN* 3.1 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 3.7 32.5 - - - +
104B MET* 4.6 0.8 - - - +
105B ILE* 6.3 0.7 - - - -
187B SER 3.3 7.8 + - - -
188B VAL* 3.0 12.1 + - - -
190B ALA* 1.3 76.6 - - - +
192B TYR* 1.3 65.7 + - - +
194B GLN* 3.4 4.4 + - - +
195B MET* 3.1 25.9 + - - +
333B PHE* 4.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B VAL* 3.5 21.2 - - + +
188B VAL* 2.9 44.2 + - + +
189B LEU* 3.1 15.7 + - - +
191B GLY* 1.3 74.9 - - - +
193B VAL* 1.3 63.1 + - - +
195B MET* 3.0 19.1 + - - +
196B GLY 3.2 0.2 + - - -
197B VAL* 3.1 34.7 + - + +
202B LEU* 3.7 27.8 - - + -
332B GLU* 3.0 39.3 + - + +
333B PHE* 3.6 32.3 - + - -
336B TYR* 4.1 20.2 - + - -
364B CYS* 5.1 0.2 - - - -
366B PHE* 3.5 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER* 6.0 1.6 - - - +
67B ILE* 4.0 16.6 - - + -
189B LEU 3.1 15.8 + - - +
190B ALA* 3.5 11.9 - - - +
192B TYR* 1.3 75.5 - - - +
194B GLN* 1.3 64.4 + - - +
196B GLY* 2.9 21.5 + - - -
197B VAL 3.6 13.3 + - - +
199B LEU* 3.6 41.7 - - + -
202B LEU* 3.9 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 3.3 24.8 - - + +
71B ASN* 3.4 24.9 + - - +
95B PHE* 3.1 24.5 - - + -
100B ARG* 3.7 33.0 + - - +
101B VAL* 4.4 4.5 - - + -
104B MET* 4.2 11.2 - - + -
190B ALA 3.1 17.2 + - - +
191B GLY* 3.8 5.6 - - - +
192B TYR 3.3 0.2 - - - -
193B VAL* 1.3 82.1 - - - +
195B MET* 1.3 60.5 + - - +
196B GLY* 3.3 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE* 4.2 10.8 - - + -
97B PHE* 3.9 25.4 - - + -
101B VAL* 3.8 14.8 - - + -
191B GLY 3.1 17.3 - - - +
192B TYR* 3.0 18.7 + - - +
194B GLN* 1.3 78.4 - - - +
196B GLY* 1.3 56.8 + - - +
197B VAL* 3.7 1.1 - - + -
333B PHE* 4.0 21.8 - - + +
336B TYR* 4.1 5.8 - - - -
337B SER* 3.6 41.7 - - - +
340B VAL* 3.5 27.9 - - + +
76C PHE* 5.3 0.9 - - + -
----------------------------------------------------------
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