Contacts of the helix formed by residues 214 - 230 (chain A) in PDB entry 1N8T
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 214 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ILE* 3.5 34.3 - - + -
209A SER* 2.9 23.1 + - - -
210A LYS 5.2 0.3 + - - -
211A THR* 3.9 7.7 + - - -
212A PHE 3.6 1.6 - - - -
213A THR* 1.3 73.9 + - - +
215A GLN* 1.3 68.6 + - - +
216A GLU* 4.0 4.9 - - - +
217A THR* 3.1 17.0 + - - +
218A ILE* 2.8 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A THR 3.0 9.7 + - - +
214A THR* 1.3 70.5 - - - +
216A GLU* 1.3 70.2 + - - +
218A ILE* 4.0 3.2 - - - +
219A THR* 2.7 42.5 + - - +
518A LYS* 6.3 1.6 - - - +
521A ALA* 5.9 1.8 - - - +
522A LYS* 3.5 26.8 + - + +
525A GLU* 3.0 26.6 + - - +
423B ILE* 3.7 30.4 - - + +
427B ASN* 4.6 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ILE* 3.4 43.0 - - + +
184A SER 4.6 2.2 - - - +
186A ILE* 3.6 37.5 - - + +
214A THR* 4.0 5.5 - - - +
215A GLN* 1.3 92.2 + - + +
217A THR* 1.3 64.1 + - - +
219A THR* 3.3 1.9 + - - -
220A ASN* 2.9 29.5 + - - -
518A LYS* 4.9 6.9 + - - -
384B THR* 4.2 9.4 + - - +
388B HIS* 2.8 31.0 + - + +
423B ILE* 5.6 1.7 - - + +
427B ASN* 4.8 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 3.6 31.5 - - + +
155A GLY* 3.4 19.2 - - - -
156A ILE* 3.4 14.5 + - - +
207A ILE* 3.8 19.7 - - + -
208A ALA 3.8 11.1 + - - +
209A SER* 4.3 4.7 - - - -
214A THR* 3.1 22.6 + - - +
216A GLU* 1.3 77.8 - - - +
218A ILE* 1.3 54.0 + - - +
220A ASN* 3.0 7.8 + - - +
221A ALA* 2.7 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ILE* 4.4 10.1 - - + -
209A SER* 5.0 2.2 - - - +
212A PHE* 3.1 65.5 - - + +
213A THR* 4.0 3.1 - - - -
214A THR 2.8 25.4 + - - +
215A GLN* 4.1 2.9 - - - +
217A THR* 1.3 75.5 - - + +
219A THR* 1.3 65.1 + - - +
221A ALA* 3.1 5.8 + - + +
222A GLU* 2.9 43.4 + - + +
255A PHE* 5.3 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ILE* 3.8 13.7 - - + -
215A GLN* 2.7 30.7 + - - +
216A GLU 3.6 4.0 - - - -
218A ILE* 1.3 77.8 - - - +
220A ASN* 1.3 63.3 + - - +
222A GLU* 4.3 5.1 + - - +
223A THR* 3.0 7.8 + - - -
416B ARG* 2.9 36.7 + - - +
419B LEU* 4.0 19.1 - - + +
420B HIS* 3.9 20.0 - - + +
423B ILE* 4.0 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 3.7 19.2 - - + +
183A VAL* 3.9 15.5 - - + +
184A SER* 3.8 9.7 + - - +
185A ASN 3.0 30.9 + - - +
186A ILE* 4.2 2.4 - - - +
187A ASP 5.1 0.2 - - - +
191A ILE* 3.5 19.5 + - + +
216A GLU 2.9 20.0 + - - -
217A THR* 3.4 7.5 - - - +
219A THR* 1.3 76.1 - - - +
221A ALA* 1.3 62.6 + - - +
223A THR* 3.1 3.6 + - - -
224A ALA* 3.0 23.6 + - - +
420B HIS* 3.3 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 4.2 5.5 - - + +
207A ILE* 3.6 44.4 - - + -
217A THR 2.7 15.8 + - - +
218A ILE* 3.1 10.7 + - + +
220A ASN* 1.3 72.2 - - - +
222A GLU* 1.3 57.3 + - - +
224A ALA* 3.3 3.5 + - - +
225A LYS 2.9 22.9 + - - -
242A PHE* 4.2 0.9 - - - -
255A PHE* 3.5 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ILE* 2.9 31.1 + - + +
219A THR* 4.3 5.4 + - - +
220A ASN 3.2 0.2 - - - -
221A ALA* 1.3 76.1 - - - +
223A THR* 1.3 57.9 + - - +
225A LYS* 4.3 9.4 - - - +
226A ASP* 2.6 43.4 + - - +
255A PHE* 4.1 16.3 - - + -
416B ARG* 3.1 30.0 + - - +
419B LEU* 5.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ILE* 4.0 22.2 - - + -
195A LEU* 4.6 5.8 - - + -
219A THR 3.0 7.6 + - - -
220A ASN 3.1 7.6 + - - -
222A GLU* 1.3 76.3 - - - +
224A ALA* 1.3 62.3 + - - +
226A ASP* 3.5 2.9 + - - +
227A TRP* 2.9 23.2 + - + +
415B ILE* 4.1 10.1 - - + -
416B ARG* 2.7 32.1 + - + +
420B HIS* 2.6 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 4.2 7.4 - - + -
191A ILE* 4.4 5.6 - - + -
195A LEU* 4.3 11.9 - - + +
205A PHE* 3.7 34.5 - - + -
220A ASN 3.0 12.5 + - - +
221A ALA 3.5 9.0 - - - +
223A THR* 1.3 74.6 - - - +
225A LYS* 1.3 66.9 + - - +
227A TRP* 3.0 7.8 + - - +
228A PHE* 2.8 22.9 + - - +
242A PHE* 4.1 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ALA 2.9 16.4 + - - +
222A GLU* 3.2 8.3 + - - +
224A ALA* 1.3 74.6 - - - +
226A ASP* 1.3 76.3 + - - +
228A PHE* 2.8 13.2 + - - +
229A LEU* 2.8 25.3 + - + +
238A VAL* 3.6 30.5 - - + -
242A PHE* 3.6 14.5 - - + -
254A GLU 4.8 2.0 + - - -
255A PHE* 2.7 63.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A GLU* 2.6 37.6 + - - +
223A THR* 4.0 5.6 - - - +
225A LYS* 1.3 88.4 - - - +
227A TRP* 1.3 60.5 + - - +
229A LEU* 3.3 10.3 + - - +
230A LEU* 3.2 27.6 + - + +
416B ARG* 4.9 17.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 3.5 55.7 + - + +
196A ALA* 5.7 0.4 - - - +
198A LEU* 3.8 26.5 - - + -
200A PRO* 3.7 42.4 - - + +
203A SER* 4.6 0.9 - - - -
205A PHE* 3.7 27.4 - + - -
223A THR* 2.9 18.6 + - + +
224A ALA 3.4 8.3 - - - +
226A ASP* 1.3 77.3 - - - +
228A PHE* 1.3 81.9 + - + +
230A LEU* 3.4 23.2 + - + +
231A SER* 4.1 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR* 3.9 3.4 - + - -
200A PRO* 3.4 32.8 - - + -
205A PHE* 5.1 2.7 - + + -
224A ALA 2.8 12.0 + - - +
225A LYS 2.8 8.0 + - - +
227A TRP* 1.3 89.8 - + + +
229A LEU* 1.3 69.3 + - + +
230A LEU 3.1 0.4 - - - -
231A SER* 3.2 7.8 + - - -
232A ALA* 2.9 39.7 + - + +
237A THR* 3.4 39.7 - - + -
238A VAL* 4.1 3.4 - - + -
241A HIS* 3.2 45.3 - + + -
242A PHE* 4.2 19.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LYS* 2.8 33.4 + - + +
226A ASP* 3.3 9.6 + - - +
228A PHE* 1.3 94.3 - - + +
230A LEU* 1.3 65.1 + - + +
231A SER 3.1 2.0 - - - -
233A LYS* 3.1 39.2 + - - +
234A ASP 3.9 17.7 - - - +
235A PRO* 4.3 15.7 - - + -
238A VAL* 3.7 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ASP 3.2 13.9 + - - +
227A TRP* 3.6 20.0 - - + +
228A PHE 3.1 1.4 - - - -
229A LEU* 1.3 80.6 - - + +
231A SER* 1.3 59.1 + - - +
233A LYS* 3.0 23.5 + - - +
----------------------------------------------------------
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