Contacts of the helix formed by residues 218 - 230 (chain C) in PDB entry 1S9F
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 GLY 218 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C LYS* 2.7 26.6 + - - -
216C MET 3.8 0.2 - - - -
217C ILE* 1.3 75.2 - - - +
219C GLU* 1.3 60.1 + - - -
220C ALA 3.3 2.9 - - - -
221C LYS 3.5 0.7 + - - -
222C ALA* 2.9 30.7 + - - +
12K T 3.5 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C PHE* 3.6 15.9 - - + -
214C LYS* 3.7 30.8 - - + +
218C GLY* 1.3 71.6 - - - -
220C ALA* 1.3 63.0 + - - +
222C ALA* 3.7 3.5 - - - +
223C LYS* 2.9 54.4 + - + +
12K T 3.2 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C GLU* 1.3 79.1 - - - +
221C LYS* 1.3 61.6 + - - +
223C LYS* 4.0 5.8 - - - +
224C TYR* 3.1 22.3 + - - +
11K C 3.2 55.9 - - - +
12K T 3.0 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C GLY* 2.9 31.9 + - - -
186C ILE* 4.1 10.5 - - + -
190C THR* 3.3 37.5 - - + +
217C ILE* 3.9 30.7 - - + +
218C GLY 3.5 2.2 + - - -
219C GLU 3.4 0.4 - - - -
220C ALA* 1.3 76.9 - - - +
222C ALA* 1.3 64.9 + - - +
224C TYR* 3.5 11.4 - - + +
225C LEU* 3.0 29.6 + - - +
10G A 5.0 2.4 - - - -
11G C 4.2 11.0 - - - -
11K C 6.2 2.8 - - - -
12K T 4.5 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 222 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C PHE* 3.8 20.4 - - + -
213C LEU* 3.8 30.5 - - + -
214C LYS* 4.2 6.5 - - - +
217C ILE* 3.8 3.5 - - + +
218C GLY 2.9 20.2 + - - +
219C GLU 3.7 3.6 - - - +
221C LYS* 1.3 76.7 - - - +
223C LYS* 1.3 64.7 + - - +
224C TYR 3.3 0.2 + - - -
225C LEU* 4.0 1.6 - - - +
226C ILE* 3.0 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 223 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C PHE* 3.8 19.6 - - + -
219C GLU* 2.9 43.0 + - + +
220C ALA* 4.0 4.7 - - - +
222C ALA* 1.3 75.4 - - - +
224C TYR* 1.3 64.0 - - - +
226C ILE* 3.9 7.2 - - - +
227C SER* 3.0 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 224 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C VAL* 3.5 20.4 - - + +
183C VAL* 3.8 11.0 - - + +
184C PRO* 2.6 31.8 + - - +
185C GLY* 5.2 2.7 - - - -
186C ILE* 4.9 5.2 - - + -
220C ALA 3.1 19.1 + - - +
221C LYS* 3.5 15.5 - - + +
223C LYS* 1.3 76.0 - - - +
225C LEU* 1.3 83.8 + - + +
227C SER* 2.8 21.4 + - - -
228C LEU* 3.2 34.8 + - + +
233C TYR* 4.0 27.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ILE* 4.0 10.3 - - + -
183C VAL* 4.4 4.0 - - + -
186C ILE* 4.0 25.6 - - + -
194C LEU* 3.8 32.1 - - + -
202C LEU* 3.7 25.0 - - + +
205C THR* 4.0 16.6 - - + -
213C LEU* 5.3 1.1 - - + -
217C ILE* 4.0 21.3 - - + -
221C LYS 3.0 13.0 + - - +
222C ALA* 4.0 2.5 - - - +
224C TYR* 1.3 93.1 - - + +
226C ILE* 1.3 59.6 + - + +
228C LEU* 3.2 6.7 + - + +
229C ALA* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 226 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C THR* 4.1 22.9 - - - +
206C LEU* 4.6 4.0 - - + -
208C ILE 5.8 1.6 - - - +
210C PHE* 4.1 31.0 - - + -
213C LEU* 4.1 21.5 - - + -
222C ALA 3.0 22.0 + - - +
223C LYS* 3.9 5.6 - - - +
225C LEU* 1.3 77.3 - - - +
227C SER* 1.3 58.7 + - - +
229C ALA* 3.2 1.8 + - - +
230C ARG* 2.9 68.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 227 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C LYS 3.0 14.7 + - - -
224C TYR* 2.8 22.7 + - - -
226C ILE* 1.3 78.7 - - - +
228C LEU* 1.3 57.5 + - - +
230C ARG* 4.6 1.8 - - - +
231C ASP 3.3 0.9 + - - -
232C GLU* 2.7 52.9 + - - -
233C TYR* 3.1 19.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C ASN* 4.6 0.4 - - - +
149C VAL* 3.9 28.0 - - + -
150C PHE* 4.2 18.8 - - + -
175C ILE* 3.4 16.1 - - - +
183C VAL* 4.0 10.3 - - + -
202C LEU* 4.2 15.5 - - + -
224C TYR* 3.2 48.0 + - + +
225C LEU* 3.2 11.1 + - - +
226C ILE 3.1 0.6 - - - -
227C SER* 1.3 80.5 + - - +
229C ALA* 1.3 63.4 + - - +
231C ASP* 3.3 10.3 + - - +
233C TYR* 3.5 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C ILE* 3.6 25.8 - - + +
202C LEU* 3.0 35.0 - - + +
205C THR* 3.5 12.1 - - - +
206C LEU* 3.8 25.2 - - + +
225C LEU 3.0 10.7 + - - +
226C ILE 3.2 0.9 + - - +
228C LEU* 1.3 76.2 - - - +
230C ARG* 1.3 57.7 + - - +
231C ASP 3.1 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C LEU* 3.6 22.6 - - + +
226C ILE* 2.9 45.4 + - - +
227C SER* 4.2 2.0 - - - +
229C ALA* 1.3 75.5 - - - +
231C ASP* 1.3 70.3 + - - +
232C GLU* 3.1 39.1 + - + +
----------------------------------------------------------
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