Contacts of the helix formed by residues 218 - 226 (chain C) in PDB entry 6D6U
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 ILE 218 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C LEU* 4.0 38.3 - - + +
215C LYS* 4.8 18.6 - - - +
216C ARG 4.1 8.3 - - - +
217C ASN* 1.3 79.0 - - - +
219C GLY* 1.3 69.5 + - - +
220C TYR 3.1 3.9 + - - -
221C PHE* 3.6 7.4 + - - +
222C ILE* 3.3 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C ASN* 5.1 0.8 - - - +
218C ILE* 1.3 82.1 - - - +
220C TYR* 1.3 61.5 + - - +
222C ILE* 4.1 3.0 + - - -
223C LEU* 3.4 28.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ARG* 4.5 22.2 + - - +
279B LYS* 4.9 25.6 - - + +
280B VAL 4.6 18.4 - - - +
281B ALA* 4.6 13.7 - - - +
282B TYR 5.8 1.3 - - - -
287B ASP* 5.5 7.2 - - - -
217C ASN* 5.8 6.9 - - + +
218C ILE 3.1 1.6 + - - +
219C GLY* 1.3 79.8 - - - +
221C PHE* 1.3 94.0 + + + +
222C ILE 3.6 0.3 + - - -
223C LEU* 4.1 2.4 + - - +
224C GLN* 3.2 43.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LYS* 5.3 16.2 - - + -
143C TYR* 4.1 21.5 - + - -
144C PRO* 4.4 25.1 - - + -
145C LEU* 6.3 0.2 - - + -
185C GLN* 3.1 39.3 - - + -
216C ARG* 5.0 5.2 - - - -
217C ASN 4.8 13.7 - - - +
218C ILE 3.6 5.3 + - - +
220C TYR* 1.3 108.0 - + + +
222C ILE* 1.3 65.4 + - + +
223C LEU 3.4 0.2 - - - -
224C GLN* 3.2 5.6 + - + +
225C THR* 2.9 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 222 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C PRO* 4.3 5.4 - - + -
145C LEU* 3.7 26.0 - - + -
218C ILE* 3.3 30.7 + - + +
219C GLY* 4.7 1.3 - - - +
220C TYR 3.4 0.6 - - - -
221C PHE* 1.3 76.6 - - + +
223C LEU* 1.3 73.6 + - + +
226C TYR* 2.9 62.2 + - + +
227C MET* 4.0 3.5 + - + +
336C TRP* 4.6 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 223 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B Y01 3.4 37.6 - - + +
219C GLY* 3.4 22.4 - - - +
220C TYR 4.1 3.1 + - - +
221C PHE 3.4 0.4 - - - -
222C ILE* 1.3 87.7 - - + +
224C GLN* 1.3 67.6 + - - +
225C THR 3.4 0.3 + - - -
227C MET* 3.7 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 224 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ARG* 2.9 42.0 + - - +
410B Y01 3.8 35.2 - - - +
220C TYR* 3.2 38.6 + - + +
221C PHE* 3.2 11.4 + - + +
222C ILE 3.2 1.0 - - - -
223C LEU* 1.3 82.9 - - + +
225C THR* 1.3 64.3 + - + +
228C PRO* 4.3 6.4 - - - +
268C LEU* 5.4 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 225 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C PRO* 5.6 1.6 - - + +
221C PHE* 2.9 28.4 + - + +
224C GLN* 1.3 85.2 - - + +
226C TYR* 1.3 90.3 + - - +
227C MET 3.5 0.7 - - - -
228C PRO* 3.3 13.1 - - - +
229C SER* 4.9 4.3 + - - -
264C ILE* 6.0 0.9 - - - +
268C LEU* 4.2 32.3 - - + +
272C LEU* 4.7 10.5 - - + -
281C ILE* 3.8 23.1 - - + +
285C LEU* 5.4 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 226 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C PRO* 3.5 27.9 - - + +
222C ILE* 2.9 53.3 + - + +
225C THR* 1.3 98.2 + - - +
227C MET* 1.3 70.3 - - + +
228C PRO 3.2 0.9 - - - -
229C SER* 3.3 15.0 + - - -
230C ILE* 3.6 20.1 + - + +
281C ILE* 4.4 17.9 - - + +
284C TYR* 3.4 41.9 - + + -
285C LEU* 6.3 1.1 - - + -
335C TYR* 3.8 18.0 + + - -
336C TRP* 4.2 24.1 - + + -
----------------------------------------------------------
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