Contacts of the helix formed by residues 220 - 234 (chain C) in PDB entry 5ICS
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 GLN 220 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C ILE* 3.6 6.1 - - - +
188C TRP* 4.9 0.7 - - + -
217C ARG* 4.5 7.2 - - - +
218C MET 5.2 0.4 - - - +
219C GLY* 1.3 76.3 - - - +
221C PRO* 1.3 73.4 - - + +
222C ALA* 3.9 14.6 - - + +
223C GLU* 2.8 43.7 + - + +
224C VAL* 3.4 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C GLY* 3.4 36.1 - - - +
21C ILE* 4.0 6.4 - - - +
24C GLY* 3.9 16.5 - - - -
25C ILE 4.5 0.2 + - - -
187C ILE* 3.5 7.8 - - + -
188C TRP 3.5 23.8 - - - +
189C THR* 3.9 7.2 - - + -
190C PRO* 6.4 0.2 - - + -
220C GLN* 1.3 83.8 - - + +
222C ALA* 1.3 56.0 + - - +
224C VAL* 3.2 7.5 + - + +
225C GLY* 2.9 25.1 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
24C GLY* 4.4 10.0 - - - -
28C ALA* 5.1 2.2 - - - +
220C GLN* 3.1 13.1 + - + +
221C PRO* 1.3 79.4 - - - +
223C GLU* 1.3 60.0 + - + +
225C GLY* 3.4 1.1 + - - +
226C ALA* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 223 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A GLU 4.9 5.3 - - - +
235A ALA 6.2 0.2 - - - -
236A ASN* 3.4 23.3 + - + +
237A PHE* 3.5 21.2 - - + +
217C ARG* 2.8 39.3 + - - -
219C GLY* 3.4 4.2 - - - -
220C GLN* 2.8 47.6 + - + +
222C ALA* 1.3 77.0 - - + +
224C VAL* 1.3 65.0 + - - +
226C ALA* 3.4 7.0 + - - +
227C ALA* 3.2 21.1 + - - +
245C VAL* 4.5 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 224 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ILE* 3.8 30.1 - - + -
25C ILE* 4.1 11.7 - - + -
139C ILE* 4.5 5.2 - - + -
182C ILE* 4.0 19.6 - - + +
184C PRO* 4.3 13.0 - - + -
187C ILE* 4.0 33.0 - - + -
220C GLN 3.4 4.7 + - - +
221C PRO 3.2 6.1 + - - +
223C GLU* 1.3 76.1 - - - +
225C GLY* 1.3 63.4 + - - +
227C ALA* 3.1 8.3 + - - +
228C ALA* 3.0 20.6 + - - +
245C VAL* 4.2 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 225 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLY 3.9 1.3 - - - -
25C ILE* 3.8 22.8 - - - +
28C ALA* 3.5 21.4 - - - +
221C PRO 2.9 12.3 + - - -
222C ALA 3.4 2.9 + - - -
223C GLU 3.3 0.2 - - - -
224C VAL* 1.3 76.9 - - - +
226C ALA* 1.3 56.6 + - - +
228C ALA* 3.1 4.2 + - - +
229C VAL* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PHE* 4.0 4.3 - - - -
234A GLU* 3.7 32.4 - - + +
6C ARG* 5.6 2.1 - - - -
28C ALA* 4.1 3.5 - - - +
222C ALA 2.9 16.3 + - - +
223C GLU* 3.8 5.4 - - - +
224C VAL 3.3 0.2 - - - -
225C GLY* 1.3 75.0 - - - +
227C ALA* 1.3 62.9 + - - +
229C VAL* 3.4 7.1 + - - +
230C PHE* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 227 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PHE* 3.9 18.7 - - + -
182C ILE* 3.9 8.1 - - + -
223C GLU 3.2 12.6 + - - +
224C VAL 3.1 9.4 + - - +
226C ALA* 1.3 76.1 - - - +
228C ALA* 1.3 58.2 + - - +
230C PHE* 3.4 5.0 + - - +
231C LEU* 3.0 30.8 + - - +
243C LEU* 3.9 19.5 - - + -
245C VAL* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ILE* 4.3 16.4 - - + -
29C PHE* 3.8 19.5 - - + -
87C VAL* 5.1 0.9 - - + -
137C ILE* 3.2 21.4 - - + +
182C ILE* 3.5 17.2 - - + +
224C VAL 3.0 12.2 + - - +
225C GLY* 3.1 8.7 + - - +
227C ALA* 1.3 74.9 - - - +
229C VAL* 1.3 66.1 + - - +
231C LEU 3.2 0.9 + - - -
232C ALA* 2.9 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ARG* 3.8 27.1 - - + +
7C TYR* 5.4 0.9 - - + -
28C ALA* 3.7 33.7 - - + +
29C PHE* 3.9 25.4 - - + +
32C SER* 4.1 17.7 - - - +
225C GLY 2.9 19.0 + - - +
226C ALA* 3.8 6.5 - - - +
228C ALA* 1.3 75.2 - - - +
230C PHE* 1.3 59.6 + - - +
232C ALA* 3.3 0.5 + - - +
233C SER* 2.7 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ALA 4.0 3.4 - - - -
227A ALA* 3.9 25.8 - - + -
230A PHE* 3.6 57.9 - + + -
243A LEU* 4.2 18.8 - - + -
6C ARG* 5.1 2.8 - - - -
226C ALA 3.0 9.1 + - - +
227C ALA 3.5 9.4 - - - +
228C ALA 3.2 0.2 - - - -
229C VAL* 1.3 76.6 - - - +
231C LEU* 1.3 73.1 + - + +
233C SER* 4.3 3.4 - - - -
234C GLU* 2.9 50.8 + - + +
235C ALA* 3.1 32.9 + - + -
238C CYS* 4.9 4.0 - - - -
243C LEU* 4.1 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 231 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C ASN* 4.0 2.4 - - - +
137C ILE* 3.8 17.0 - - + -
178C ARG* 2.8 29.1 + - - -
180C ASN* 4.1 31.2 - - + +
181C CYS 4.2 5.4 - - - +
182C ILE* 3.5 36.1 - - + -
227C ALA 3.0 14.4 + - - +
228C ALA 3.2 4.2 + - - +
230C PHE* 1.3 79.2 - - + +
232C ALA* 1.3 61.2 + - - +
235C ALA* 3.8 18.2 + - + +
238C CYS* 4.8 0.2 - - + -
241C ILE* 4.0 26.0 - - + -
243C LEU* 4.1 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TYR* 3.6 26.7 + - + +
29C PHE* 3.6 27.1 - - + -
85C CYS* 4.0 4.7 - - - -
135C ASN* 3.5 19.6 + - - +
137C ILE* 3.9 0.6 - - + +
178C ARG* 3.2 16.6 + - - -
228C ALA 2.9 16.3 + - - +
229C VAL 3.8 1.3 - - - +
231C LEU* 1.3 79.4 - - - +
233C SER* 1.3 60.0 + - - +
234C GLU 3.8 0.2 - - - -
236C ASN* 4.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 233 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ARG* 3.7 20.0 + - - +
7C TYR* 3.5 29.2 - - - -
229C VAL* 2.7 30.2 + - - +
232C ALA* 1.3 78.4 - - - +
234C GLU* 1.3 75.8 + - - +
235C ALA 3.9 0.2 - - - -
236C ASN* 4.2 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 234 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 3.3 39.7 - - - -
223A GLU* 5.0 6.4 - - - +
226A ALA* 3.8 30.0 - - + +
6C ARG* 3.8 19.1 - - + +
230C PHE* 2.9 28.9 + - + +
233C SER* 1.3 90.7 - - - +
235C ALA* 1.3 59.4 + - - +
236C ASN* 3.3 14.7 + - - +
----------------------------------------------------------
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