Contacts of the helix formed by residues 222 - 235 (chain E) in PDB entry 4SKN
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 TRP 222 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E LEU* 3.9 21.4 - - + +
106E MET* 3.6 31.6 - - + -
109E VAL* 4.3 11.3 - - + +
125E VAL* 3.9 18.4 - - + -
126E PHE* 4.1 6.1 - + - -
205E ALA 3.6 0.9 - - - +
206E VAL* 3.5 42.8 - - + -
207E LEU* 3.3 36.3 - - + +
208E THR* 2.6 40.4 + - + +
217E HIS* 3.6 14.5 - - + +
220E ARG* 4.7 0.6 - - + +
221E GLY* 1.3 75.4 - - - +
223E GLU* 1.3 54.4 + - - +
225E PHE* 2.8 20.4 + + - +
226E THR* 2.7 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 223 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205E ALA* 3.7 7.2 + - + +
206E VAL* 3.3 18.0 - - + +
218E LYS* 3.8 0.2 - - - +
219E GLU* 2.8 41.6 + - - -
220E ARG 3.9 0.5 + - - -
221E GLY* 3.3 1.8 + - - -
222E TRP* 1.3 79.5 + - - +
224E GLN* 1.3 51.7 - - - +
226E THR* 2.9 9.4 + - - -
227E ASP* 2.7 42.6 + - - +
248E TYR* 2.9 41.3 + - + +
252E LYS* 3.1 5.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 224 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E GLU* 4.6 2.4 + - - +
99E LYS* 5.3 4.2 - - - +
101E TYR* 3.4 48.7 + - + +
221E GLY* 3.2 11.3 + - - +
223E GLU* 1.3 76.3 - - - +
225E PHE* 1.3 61.5 + - - +
227E ASP* 3.3 14.4 - - + +
228E ALA* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 225 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E PHE* 4.2 7.6 - + - -
93E LEU* 4.0 36.3 - - + -
96E GLU* 4.5 12.6 - - + -
97E PHE* 5.3 2.0 - + - -
101E TYR* 3.4 20.8 - - + +
102E PHE* 3.6 25.4 - + + -
105E LEU* 5.3 0.2 - - + -
126E PHE* 3.7 21.1 - + - -
128E TRP* 3.9 11.9 - + - -
207E LEU* 3.6 32.8 - - + -
221E GLY 3.1 12.0 + - - +
222E TRP* 2.8 19.6 + + + +
224E GLN* 1.3 76.2 - - - +
226E THR* 1.3 61.1 + - + +
228E ALA* 2.9 19.7 + - - +
229E VAL* 3.0 15.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 226 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203E LEU* 4.5 12.3 - - + +
204E ASN 3.4 16.8 - - - +
205E ALA 2.9 26.4 + - - +
207E LEU* 4.1 24.7 - - + -
222E TRP 2.7 22.4 + - - +
223E GLU* 2.9 13.0 + - - -
225E PHE* 1.3 70.5 - - + +
227E ASP* 1.3 65.1 + - - +
229E VAL* 3.3 9.9 + - + +
230E VAL* 3.0 29.6 + - - +
252E LYS* 2.9 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 227 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223E GLU* 2.7 26.7 + - - +
224E GLN* 3.3 19.6 - - + +
226E THR* 1.3 77.9 - - - +
228E ALA* 1.3 51.5 + - - +
230E VAL* 3.3 4.1 + - - +
231E SER* 2.8 38.2 + - - -
252E LYS* 2.8 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E LEU* 4.6 5.9 - - + +
96E GLU* 3.6 39.9 - - + +
224E GLN 3.0 12.3 + - - +
225E PHE* 2.9 14.6 + - + +
227E ASP* 1.3 76.9 - - - +
229E VAL* 1.3 60.3 + - - +
231E SER* 3.4 7.0 - - - -
232E TRP* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 229 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E TRP* 4.4 9.2 - - + -
93E LEU* 4.2 20.8 - - + +
128E TRP* 3.9 32.1 - - + -
134E ILE* 5.7 2.3 - - + +
201E LEU* 4.0 26.5 - - + -
203E LEU* 4.3 10.5 - - + -
225E PHE* 3.0 18.7 + - + +
226E THR* 3.4 14.6 - - - +
227E ASP 3.2 0.4 - - - -
228E ALA* 1.3 77.6 - - - +
230E VAL* 1.3 65.9 + - - +
232E TRP* 3.3 3.3 + - - +
233E LEU* 3.1 24.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 230 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E VAL* 5.9 3.4 - - + -
142E LEU* 5.0 4.5 - - + -
203E LEU* 4.2 16.8 - - + -
226E THR 3.0 16.7 + - - +
227E ASP* 3.7 4.5 - - - +
229E VAL* 1.3 75.4 - - - +
231E SER* 1.3 66.5 + - - +
233E LEU* 3.0 10.3 + - - +
234E ASN* 2.7 27.4 + - + +
242E PHE* 4.1 24.5 - - + -
252E LYS* 4.0 29.2 - - + +
255E ALA* 5.3 7.2 - - + +
256E ILE* 4.3 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 231 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227E ASP 2.8 22.2 + - - -
228E ALA* 3.4 10.5 - - - -
230E VAL* 1.3 74.9 - - - +
232E TRP* 1.3 64.6 + - - +
234E ASN* 3.0 9.1 + - - +
235E GLN* 3.0 40.6 + - - +
255E ALA* 5.4 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 232 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E HIS* 3.5 59.3 + + + -
93E LEU* 4.9 7.9 - - + -
134E ILE* 3.6 33.2 - - + -
135E LYS* 4.1 19.3 - - + -
228E ALA 3.0 10.5 + - - +
229E VAL 3.6 7.9 - - - +
231E SER* 1.3 77.9 - - - +
233E LEU* 1.3 111.9 + - + +
235E GLN* 3.0 10.8 + - - -
236E ASN* 2.9 58.3 + - + +
237E SER* 4.3 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 233 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E TRP* 5.2 0.2 - - + -
134E ILE* 3.8 24.7 - - + +
137E VAL* 4.3 13.2 - - + +
140E VAL* 3.9 27.8 - - + -
201E LEU* 4.0 20.6 - - + -
229E VAL* 3.1 12.4 + - + +
230E VAL* 3.0 11.5 + - - +
232E TRP* 1.3 107.5 - - + +
234E ASN* 1.3 62.0 + - - +
237E SER* 3.0 40.3 + - - +
240E LEU* 3.5 15.0 - - + +
242E PHE* 5.0 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 234 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E VAL* 2.7 20.2 + - + +
231E SER* 3.2 11.8 + - - +
233E LEU* 1.3 74.8 - - - +
235E GLN* 1.3 72.6 + - - +
237E SER 3.9 2.8 + - - +
240E LEU* 5.0 1.3 - - - -
242E PHE* 5.0 3.1 - - + -
255E ALA 3.6 24.1 + - - +
256E ILE* 3.9 4.6 - - + -
257E ASP* 3.2 29.6 + - - +
260E ARG* 5.0 2.1 + - - -
261E HIS* 2.9 38.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 235 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E SER* 3.1 34.1 + - - +
232E TRP* 3.0 9.4 + - - +
234E ASN* 1.3 87.1 - - - +
236E ASN* 1.3 75.6 + - - +
237E SER 3.6 1.1 + - - -
260E ARG* 3.9 12.6 + - - -
----------------------------------------------------------
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