Contacts of the helix formed by residues 216 - 225 (chain D) in PDB entry 1LFD
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 LYS 216 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D VAL* 3.6 28.0 - - + +
209D VAL* 3.3 31.4 - - - +
210D GLY* 3.0 12.2 + - - +
211D ALA 3.0 18.6 + - - -
214D VAL* 3.7 11.2 - - + -
215D GLY* 1.3 76.6 - - - +
217D SER* 1.3 60.3 + - - +
219D LEU* 3.5 6.0 - - - +
220D THR* 2.9 28.2 + - - -
257D ASP* 3.6 11.2 - - - +
258D THR* 3.3 27.4 - - - -
260D GLY* 3.5 2.9 - - - +
281D VAL* 4.3 3.6 - - + -
2380D GNP 2.6 46.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 217 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D LYS* 1.3 72.1 - - - +
218D ALA* 1.3 59.4 + - - +
220D THR* 3.1 2.9 + - - -
221D ILE* 2.8 51.7 + - - +
235D THR* 2.9 8.0 + - - -
238D ASP* 4.5 2.3 + - - -
240D TYR* 5.6 0.4 - - - -
257D ASP* 2.6 27.1 + - - -
2373D MG 2.9 21.5 - - - -
2380D GNP 2.9 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D GLY 3.8 1.6 - - - +
216D LYS 3.5 0.2 - - - -
217D SER* 1.3 75.7 - - - +
219D LEU* 1.3 56.4 + - - +
221D ILE* 4.0 6.7 - - - +
222D GLN* 3.0 32.2 + - - +
227D HIS 4.8 0.9 - - - +
228D PHE* 3.9 13.8 - - + -
229D VAL 6.0 0.9 - - - +
346D ALA* 3.4 21.8 - - + +
2380D GNP 2.8 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D VAL* 5.2 1.1 - - + -
215D GLY 3.0 18.4 + - - +
216D LYS* 3.5 5.8 - - - +
218D ALA* 1.3 76.5 - - - +
220D THR* 1.3 62.9 + - - +
222D GLN* 3.2 5.9 + - - +
223D LEU* 3.1 18.0 + - - +
279D LEU* 5.1 4.7 - - + -
281D VAL* 3.8 37.7 - - + -
314D VAL* 4.1 11.0 - - + -
316D ASN* 3.1 29.2 - - - +
344D THR* 3.6 14.6 - - + +
346D ALA* 3.7 19.0 - - + +
352D VAL* 3.6 15.5 - - + +
355D ALA* 6.0 1.3 - - + -
356D PHE* 4.1 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D VAL* 3.7 21.1 - - - +
216D LYS 2.9 15.5 + - - -
217D SER* 3.1 6.1 + - - -
219D LEU* 1.3 77.2 - - - +
221D ILE* 1.3 59.1 + - - +
223D LEU* 3.2 2.4 + - - +
224D ILE* 3.0 39.5 + - + +
240D TYR* 3.6 37.0 - - + -
255D ILE* 3.6 23.3 - - + +
257D ASP* 4.4 6.3 + - + +
356D PHE* 4.0 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LYS* 4.5 12.8 - - - +
54C ASN* 5.9 1.3 - - - +
217D SER* 2.8 36.4 + - - +
218D ALA* 4.0 5.8 - - - +
220D THR* 1.3 71.6 - - - +
222D GLN* 1.3 57.1 + - - +
224D ILE* 4.9 2.2 - - - -
225D GLN* 2.8 36.4 + - - +
226D ASN 3.4 3.8 + - - -
227D HIS* 3.4 44.6 - - + +
228D PHE* 5.6 0.7 - - - -
229D VAL* 6.1 4.5 - - + -
240D TYR* 3.6 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D ALA 3.0 19.5 + - - +
219D LEU 3.4 6.3 - - - +
220D THR 3.2 0.2 - - - -
221D ILE* 1.3 77.6 - - - +
223D LEU* 1.3 58.3 + - - +
226D ASN* 2.9 31.0 + - - +
227D HIS* 3.6 25.0 - - - +
228D PHE* 3.6 13.1 + - + +
346D ALA* 2.8 34.3 - - - +
347D LYS 4.1 4.7 - - - +
348D THR 5.0 0.2 - - - -
349D ARG* 2.9 53.2 + - + +
352D VAL* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D LEU 3.1 9.6 + - - +
220D THR 3.2 6.7 + - - +
222D GLN* 1.3 82.8 - - - +
224D ILE* 1.3 64.3 + - + +
226D ASN* 4.3 1.0 + - - +
242D LYS* 3.3 25.0 + - + +
253D LEU* 4.6 10.5 - - + -
255D ILE* 3.6 26.0 - - + -
349D ARG* 3.5 10.5 + - - +
352D VAL* 4.0 8.9 - - + +
353D GLU* 3.8 28.7 - - + -
356D PHE* 3.4 33.2 - - + -
357D TYR* 3.6 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ASN 3.8 6.6 - - - +
28C GLY* 3.6 35.7 - - - -
220D THR* 3.0 20.9 + - + +
221D ILE* 4.9 0.2 - - - -
223D LEU* 1.3 79.8 - - + +
225D GLN* 1.3 64.2 + - + +
226D ASN* 4.0 0.7 + - - +
240D TYR* 3.8 26.5 - - + -
241D ARG 4.1 5.6 - - - +
242D LYS* 3.6 39.2 - - + +
255D ILE* 3.7 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ASN* 3.2 49.2 + - + +
29C ASN* 4.3 3.5 - - - +
221D ILE* 2.8 24.7 + - + +
224D ILE* 1.3 79.3 - - + +
226D ASN* 1.3 69.8 + - - +
227D HIS* 2.7 49.0 + - + +
240D TYR* 4.3 16.9 - - - -
----------------------------------------------------------
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