Contacts of the helix formed by residues 215 - 226 (chain B) in PDB entry 4N36
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 215 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LYS* 1.3 76.2 - - - +
216B TRP* 1.3 66.5 + - - +
217B TYR* 3.9 2.6 + - - +
218B SER* 3.3 18.9 + - - -
219B ALA* 2.8 20.3 + - - +
311B CYS 3.6 8.1 - - - -
312B ASP* 3.3 31.0 - - + +
313B ILE 3.4 9.0 - - - -
314B THR* 3.8 12.2 - - + +
312D ASP* 2.7 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B THR* 1.3 72.2 - - - +
217B TYR* 1.3 70.6 + + - +
219B ALA* 3.2 3.5 + - - +
220B GLU* 2.8 35.8 + - + +
230B LEU* 3.4 17.8 - - + +
252B TRP* 3.3 44.1 - + + +
253B ILE 2.8 22.0 + - - -
254B GLY 4.1 6.3 - - - -
255B LEU 3.5 9.3 + - - -
256B THR* 3.7 18.6 - - + -
267B VAL* 3.7 34.3 - - + -
295B CYS* 3.5 22.4 - - + -
311B CYS* 3.1 15.7 + - + +
217D TYR* 3.4 42.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B THR* 3.2 4.4 + - - +
216B TRP* 1.3 86.5 - + - +
218B SER* 1.3 61.7 + - - +
220B GLU* 3.2 12.8 + - + +
221B GLN* 2.9 57.7 + - + +
311B CYS* 4.7 1.0 + - - +
216D TRP* 3.4 29.5 - + - -
217D TYR* 3.4 45.7 - + + -
256D THR* 2.6 37.7 + - - +
257D LYS 4.1 2.4 + - - -
295D CYS* 4.0 4.5 - - - -
311D CYS* 4.3 12.3 - - + -
312D ASP* 5.7 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LYS* 3.8 23.6 + - - +
215B THR* 3.3 16.5 + - - -
217B TYR* 1.3 78.2 - - - +
219B ALA* 1.3 62.0 + - - +
221B GLN* 3.5 12.1 + - - +
222B PHE* 3.1 22.0 + - - +
311D CYS* 4.7 8.8 - - - +
312D ASP* 2.8 26.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LYS* 3.9 12.0 - - + +
215B THR 2.8 19.2 + - - +
216B TRP* 3.3 7.9 - - - +
218B SER* 1.3 74.1 - - - +
220B GLU* 1.3 66.1 + - - +
222B PHE* 3.1 5.4 + - - +
223B CYS* 3.0 27.0 + - - -
230B LEU* 4.1 5.8 - - + -
252B TRP* 4.6 2.9 - - + -
317B PHE* 3.5 39.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B TRP* 2.8 31.0 + - + +
217B TYR* 3.2 16.8 + - + +
219B ALA* 1.3 73.1 - - - +
221B GLN* 1.3 62.1 + - - +
223B CYS* 3.3 1.8 + - - +
224B VAL* 3.0 31.6 + - + +
229B HIS* 2.7 30.5 + - - -
230B LEU* 2.9 41.6 + - + +
267B VAL* 3.4 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TYR* 2.9 41.1 + - + +
218B SER* 3.8 10.2 + - - +
219B ALA 3.2 0.2 - - - -
220B GLU* 1.3 76.0 - - + +
222B PHE* 1.3 62.5 + - - +
224B VAL* 3.4 7.2 + - - +
225B SER* 3.0 23.0 + - - -
256D THR* 3.1 25.7 + - - -
257D LYS* 3.2 19.8 + - - +
294D HIS* 3.4 40.6 + - + +
311D CYS* 3.6 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B TYR* 3.7 36.8 - + - -
214B LYS* 4.0 20.9 - - - -
218B SER 3.1 15.1 + - - +
219B ALA 3.1 8.9 + - - +
221B GLN* 1.3 76.3 - - - +
223B CYS* 1.3 66.1 + - - +
225B SER* 2.6 23.6 + - - -
226B ARG* 3.2 54.6 + - + +
317B PHE* 3.6 24.7 - + + -
319B CYS* 4.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ALA 3.0 18.1 + - - -
220B GLU 3.3 7.2 + - - +
222B PHE* 1.3 76.4 - - - +
224B VAL* 1.3 58.1 + - - +
226B ARG* 2.9 13.6 + - - -
228B SER* 2.8 35.6 + - - +
229B HIS* 3.7 16.4 - - - -
230B LEU* 3.7 23.3 - - - +
317B PHE* 4.1 1.3 - - - -
319B CYS* 2.0 51.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B GLU* 3.0 41.7 + - + +
221B GLN* 3.8 8.5 - - + +
222B PHE 3.2 0.2 - - - -
223B CYS* 1.3 75.5 - - - +
225B SER* 1.3 57.1 + - - +
226B ARG 3.0 0.2 - - - -
227B ASN* 3.0 18.2 + - - -
228B SER 3.3 14.1 - - - +
229B HIS* 3.9 11.0 - - + +
258D ALA* 4.2 9.4 - - + -
259D GLY* 3.1 42.4 - - - +
260D MET* 4.2 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLN 3.0 13.0 + - - -
222B PHE* 2.6 23.2 + - - -
224B VAL* 1.3 75.5 - - - +
226B ARG* 1.3 84.6 + - - +
227B ASN 3.4 1.3 - - - -
259D GLY 4.2 11.2 - - - -
260D MET* 3.7 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B TRP* 4.0 19.7 - - + -
222B PHE* 3.4 54.0 - - + +
223B CYS* 2.9 9.4 + - - +
225B SER* 1.3 104.9 + - - +
227B ASN* 1.3 68.3 + - - +
228B SER* 3.3 5.4 + - - +
319B CYS* 5.9 0.4 - - - -
321B ARG* 3.2 19.1 + - - +
260D MET* 4.2 2.5 - - - -
----------------------------------------------------------
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