Contacts of the helix formed by residues 213 - 223 (chain D) in PDB entry 3IFS
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 213 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D LEU* 3.7 24.2 - - + -
200D VAL 4.7 0.6 + - - -
201D ILE* 5.1 0.2 - - - -
202D PRO* 4.0 23.6 - - + +
205D VAL* 3.9 22.9 - - + -
210D SER* 2.6 22.8 + - - +
211D VAL 3.2 0.2 - - - +
212D LEU* 1.3 83.2 - - - +
214D PRO* 1.3 76.5 - - - +
215D VAL* 3.0 22.5 + - - +
216D GLY 3.2 9.4 + - - -
217D LEU* 3.2 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D GLU* 3.3 37.0 - - - +
63D ILE* 4.0 25.6 - - + -
141D ASN* 5.1 0.5 - - - +
179D THR* 4.2 9.7 + - + +
199D PHE* 3.8 23.3 - - + -
200D VAL 3.6 13.7 - - - +
202D PRO* 5.3 0.9 - - + -
213D THR* 1.3 90.5 - - - +
215D VAL* 1.3 63.1 + - - +
216D GLY 3.1 1.1 + - - -
217D LEU* 3.7 2.9 - - + -
218D LEU* 3.2 24.9 + - + +
219D PRO* 3.9 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D GLY 3.4 25.4 - - - +
85D SER* 3.7 17.3 - - - +
89D ALA* 4.4 5.6 - - + +
143D ILE* 3.5 27.8 - - + +
179D THR* 4.0 7.3 - - + +
201D ILE* 3.7 35.7 - - + -
210D SER* 3.5 22.4 - - - +
211D VAL* 4.9 1.6 - - - -
213D THR* 3.0 17.4 + - - +
214D PRO* 1.3 78.8 - - - +
216D GLY* 1.3 60.1 + - - +
219D PRO* 3.5 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D ALA* 4.1 13.7 - - - -
211D VAL* 3.3 18.9 + - - -
213D THR 3.2 3.8 + - - -
214D PRO 3.1 0.2 - - - -
215D VAL* 1.3 80.2 - - - +
217D LEU* 1.3 66.3 + - - +
218D LEU 3.4 2.2 - - - -
219D PRO* 3.3 3.6 - - - +
220D ILE* 3.0 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D TYR* 6.1 1.3 - - + -
60D PHE* 3.7 33.0 - - + -
63D ILE* 4.0 20.4 - - + -
211D VAL 4.2 6.3 - - - +
212D LEU* 3.4 28.5 - - + +
213D THR* 3.2 15.8 + - - +
214D PRO* 5.3 0.4 - - + -
216D GLY* 1.3 76.6 - - - +
218D LEU* 1.3 57.3 + - - +
220D ILE* 3.6 3.8 - - - +
221D ALA* 2.8 32.9 + - - +
227D ILE* 3.7 23.0 - - + +
230D MSE 4.1 20.9 - - + -
231D MSE 4.3 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ILE* 3.6 35.8 - - + +
66D CYS* 4.3 7.9 - - + -
67D ALA* 4.2 7.0 - - + +
70D ILE* 4.5 6.1 - - + -
77D LEU* 5.7 0.7 - - + -
141D ASN* 3.7 32.1 - - + +
177D TYR* 4.1 12.8 - - + -
179D THR* 4.7 0.9 - - - +
199D PHE* 3.8 27.6 - - + -
214D PRO* 3.2 13.1 + - + +
217D LEU* 1.3 77.9 - - - +
219D PRO* 1.3 73.3 - - + +
221D ALA* 3.8 0.9 - - - +
222D VAL* 3.0 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D LEU* 4.1 15.0 - - + -
79D VAL* 4.0 25.1 - - + -
89D ALA* 4.1 12.3 - - + -
93D ILE* 3.6 22.8 - - + +
114D VAL* 4.6 2.3 - - + +
141D ASN* 3.6 17.7 - - - +
143D ILE* 4.4 2.5 - - + -
215D VAL 3.5 19.7 - - - +
216D GLY 3.3 10.1 - - - +
218D LEU* 1.3 95.2 - - + +
220D ILE* 1.3 61.0 + - - +
222D VAL* 3.3 2.3 + - - +
223D SER* 3.1 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D ALA* 4.3 8.7 - - - +
92D ALA* 3.3 31.4 - - + -
93D ILE* 4.1 10.8 - - + -
211D VAL* 4.5 8.1 - - + -
216D GLY* 3.0 35.5 + - - +
217D LEU* 3.6 4.9 - - + +
219D PRO* 1.3 76.5 - - - +
221D ALA* 1.3 61.4 + - - +
223D SER* 2.7 24.6 + - - -
225D LEU* 3.3 30.6 + - + -
227D ILE* 3.9 14.6 - - + -
230D MSE 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ILE* 4.6 4.3 - - + -
64D GLN* 5.3 3.4 - - + -
67D ALA* 3.8 18.8 - - + +
71D LYS* 3.1 15.1 + - - -
217D LEU 2.8 21.2 + - - +
218D LEU 3.8 3.1 - - - +
220D ILE* 1.3 71.9 - - - +
222D VAL* 1.3 60.5 + - - +
224D GLY* 2.9 17.7 + - - -
225D LEU 3.8 13.2 + - - +
227D ILE* 4.1 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D ALA* 3.8 22.4 - - - -
70D ILE* 3.8 32.8 - - + -
71D LYS* 3.3 19.5 - - + +
77D LEU* 4.0 22.7 - - + -
111D THR* 3.7 0.7 - - - -
112D PRO* 3.5 36.9 - - + +
114D VAL* 4.8 4.3 - - + -
218D LEU* 3.0 24.1 + - + +
219D PRO 3.7 4.9 - - - +
221D ALA* 1.3 74.8 - - - +
223D SER* 1.3 56.8 + - - +
224D GLY 3.0 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ILE* 3.7 21.5 - - - +
97D ASN* 3.1 36.1 + - - -
101D TYR* 3.4 20.1 + - - -
111D THR* 3.4 14.6 + - - +
114D VAL* 4.3 6.0 - - - +
219D PRO 3.1 12.2 + - - -
220D ILE 2.7 18.5 + - - -
222D VAL* 1.3 75.3 - - - +
224D GLY* 1.3 56.2 + - - +
225D LEU* 3.4 9.9 - - - +
----------------------------------------------------------
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