Contacts of the helix formed by residues 146 - 157 (chain B) in PDB entry 1SZP
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 146 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B VAL* 1.3 86.9 - - - +
147B ALA* 1.3 67.2 + - - +
148B ALA* 2.8 18.2 + - - +
149B ASP* 3.1 24.9 + - + +
150B PHE* 3.3 12.6 + - - +
245C ASN* 3.7 38.9 - - - +
247C VAL 3.3 8.7 - - - -
248C ALA* 4.7 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B VAL 4.2 0.9 - - - -
146B THR* 1.3 78.6 + - - +
148B ALA* 1.3 60.3 + - - +
150B PHE* 3.3 8.7 + - - +
151B HIS 3.2 14.4 + - - -
224C PHE* 4.8 14.4 - - + -
226C PRO* 3.8 14.7 - - + +
229C LEU* 5.4 1.1 - - + -
244C LEU* 3.6 16.6 + - + +
247C VAL* 2.7 40.1 + - + +
249C TYR* 4.7 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B THR* 2.8 6.3 + - - +
147B ALA* 1.3 76.3 - - - +
149B ASP* 1.3 69.2 + - - +
150B PHE 2.8 2.4 + - - -
151B HIS* 2.9 20.2 + - + +
152B MET* 3.0 11.3 + - - +
241C ASP* 4.7 7.6 - - + +
244C LEU* 3.7 28.3 - - + +
245C ASN* 4.3 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B VAL* 4.0 22.2 - - - +
146B THR* 3.1 31.9 + - + +
148B ALA* 1.3 76.7 - - - +
150B PHE* 1.3 64.3 + - - +
152B MET* 3.2 19.8 + - - +
153B ARG* 3.6 26.2 + - - +
245C ASN* 5.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B VAL* 4.2 14.6 - - + -
146B THR 3.3 10.7 + - - +
147B ALA* 3.4 10.1 - - - +
148B ALA 2.8 2.2 - - - -
149B ASP* 1.3 83.7 + - - +
151B HIS* 1.3 59.8 + - - +
152B MET 3.3 0.7 + - - -
153B ARG* 3.6 22.8 + - + +
154B ARG* 3.4 23.2 + - + +
224C PHE* 3.5 24.5 - + - -
225C ARG* 4.4 18.6 - - - -
226C PRO* 3.8 19.7 - - + -
249C TYR* 4.0 37.7 - + + -
251C ARG* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ALA 3.2 5.3 + - - +
148B ALA* 2.9 12.1 + - + +
150B PHE* 1.3 76.1 - - - +
152B MET* 1.3 67.8 + - - +
154B ARG* 4.0 11.6 - - - +
155B SER* 3.6 21.2 + - - -
226C PRO* 3.8 24.8 - - + +
227C VAL* 3.6 40.3 - - + +
244C LEU* 4.9 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ALA 3.0 10.2 + - - +
149B ASP* 3.4 13.2 - - - +
150B PHE 3.2 0.4 - - - -
151B HIS* 1.3 77.1 - - - +
153B ARG* 1.4 54.9 + - + +
155B SER* 2.6 38.8 + - - -
156B GLU* 3.6 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PRO* 4.4 29.4 + - - +
143B GLY 5.8 0.4 + - - -
145B VAL* 3.9 34.1 - - - +
149B ASP* 3.6 20.9 + - - +
150B PHE* 3.6 23.0 + - + +
152B MET* 1.4 75.5 - - - +
154B ARG* 1.3 62.4 + - - +
155B SER 3.3 0.2 - - - -
156B GLU* 3.4 13.2 + - - +
157B LEU* 3.3 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B PHE* 3.4 20.8 + - + +
151B HIS* 4.3 13.5 - - - +
152B MET 2.8 5.7 + - - -
153B ARG* 1.3 74.1 - - - +
155B SER* 1.3 60.5 + - - +
157B LEU* 3.2 20.3 + - - +
176B GLU* 5.5 4.5 - - - +
225C ARG* 3.4 34.8 + - - +
226C PRO* 5.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B HIS* 3.6 23.5 + - - -
152B MET* 2.6 16.7 + - - -
154B ARG* 1.3 68.2 - - - +
156B GLU* 1.3 68.3 + - - -
157B LEU 2.6 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B MET 3.6 3.5 + - - +
153B ARG* 3.4 18.1 + - - +
155B SER* 1.3 77.7 - - - +
157B LEU* 1.3 66.5 + - - +
158B ILE* 3.5 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ARG 3.3 8.1 + - - +
154B ARG* 3.2 18.4 + - - +
155B SER 2.6 14.7 + - - +
156B GLU* 1.3 82.6 - - - +
158B ILE* 1.3 68.2 + - - +
159B CYS* 4.1 6.0 + - - -
176B GLU* 5.2 7.4 - - + -
177B THR* 4.0 20.6 - - - +
178B GLY* 5.9 0.2 - - - -
----------------------------------------------------------
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