Contacts of the helix formed by residues 183 - 189 (chain B) in PDB entry 1S9C
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 ASN 183 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.3 12.0 - - + +
36A ALA 4.6 1.0 + - - -
37A SER* 2.8 34.0 + - - -
38A ILE* 2.6 36.0 + - - +
47A ILE* 4.0 4.0 - - - +
181B SER* 2.9 13.0 + - - +
182B LEU* 1.3 83.1 - - - +
184B GLN* 1.3 64.0 + - - +
185B ALA 3.2 3.4 - - - -
186B ALA* 2.9 21.7 + - + +
187B LEU* 3.0 14.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU 3.8 7.3 + - - -
33B GLY* 3.0 32.7 + - - -
35B GLY* 4.2 0.8 - - - +
179B THR 4.7 1.4 - - - +
180B THR* 3.3 30.2 - - + -
181B SER* 2.9 39.2 + - - +
182B LEU 3.5 0.6 - - - -
183B ASN* 1.3 75.5 - - - +
185B ALA* 1.3 58.4 + - - +
187B LEU* 3.2 7.3 + - - +
188B TYR* 2.8 30.7 + - - +
214B LEU* 3.6 16.8 - - + -
218B CYS* 4.1 2.7 - - - -
222B PHE* 3.6 29.9 - - + -
252B PRO* 4.5 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 5.8 2.9 - - + -
183B ASN 3.2 0.4 - - - -
184B GLN* 1.3 76.5 - - - +
186B ALA* 1.3 66.3 + - - +
188B TYR* 4.4 0.7 - - - +
189B ARG* 3.0 31.2 + - - +
198B HIS* 3.3 27.1 - - + +
213B ILE 4.5 1.8 - - - +
214B LEU* 3.4 13.8 - - + +
215B HIS* 3.8 14.4 - - + +
252B PRO* 3.8 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 4.9 1.0 - - - +
32A LEU* 3.7 13.4 - - + +
38A ILE* 4.2 11.3 - - + +
47A ILE* 3.7 28.7 - - + +
183B ASN* 2.9 28.7 + - + +
185B ALA* 1.3 79.6 - - - +
187B LEU* 1.3 58.1 + - - +
189B ARG* 3.3 25.8 - - - +
190B LEU* 3.8 7.4 - - - +
198B HIS 5.0 0.2 + - - -
199B ILE* 4.5 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.9 14.6 - - + -
187A LEU* 4.0 30.3 - - + -
29B MET* 4.8 13.8 - - + +
32B LEU* 3.9 15.5 - - + +
33B GLY* 3.6 30.2 - - - +
183B ASN* 3.0 12.2 + - + +
184B GLN* 3.7 9.4 - - - +
186B ALA* 1.3 76.5 - - - +
188B TYR* 1.3 67.5 + - - +
189B ARG 3.2 1.3 - - - -
190B LEU* 3.0 37.8 + - + +
191B SER* 4.3 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B MET 5.9 0.4 - - - -
30B TYR* 3.4 39.2 + + - -
33B GLY* 3.7 30.0 - - - +
34B VAL* 4.4 2.7 - - + -
62B VAL* 5.5 1.2 - - - +
63B ILE* 4.5 11.8 - - + +
66B GLN* 5.0 3.5 + - - -
184B GLN 2.8 17.9 + - - +
185B ALA* 4.2 4.0 - - - +
187B LEU* 1.3 78.3 - - - +
189B ARG* 1.3 63.1 + - - +
191B SER* 2.9 23.6 + - - -
193B ASP* 5.3 5.5 + - + -
215B HIS* 3.4 42.8 - + + +
217B LEU* 3.3 28.5 + - + +
218B CYS* 3.7 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 4.6 0.4 - - - +
47A ILE 3.9 14.1 + - - -
48A TYR* 3.8 11.3 - - - -
49A GLU* 2.6 44.7 + - - -
185B ALA 3.0 23.2 + - - +
186B ALA* 3.3 23.3 + - - +
188B TYR* 1.3 71.4 - - - +
190B LEU* 1.3 56.3 + - + +
191B SER 2.7 16.2 + - - -
192B GLY* 2.9 15.4 + - - -
193B ASP 3.4 25.8 + - - +
194B TRP* 3.1 49.9 + - - +
195B ASN 4.8 1.8 + - - -
198B HIS* 5.3 0.8 - - - +
199B ILE* 3.7 28.2 - - - +
215B HIS* 3.6 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