Contacts of the helix formed by residues 213 - 228 (chain D) in PDB entry 2I5B
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 GLY 213 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17D GLY 3.3 15.9 - - - -
18D ALA* 3.7 16.7 - - - +
211D THR 3.3 0.8 + - - -
212D HIS* 1.3 78.8 + - - +
214D ALA* 1.3 57.9 + - - +
215D GLY 3.3 3.1 - - - -
216D CYS* 3.2 6.2 + - - +
217D THR* 2.8 37.5 + - - -
260D THR* 4.7 1.1 - - - -
501D ADP 5.3 1.2 + - - -
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Residues in contact with ALA 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D THR* 3.1 30.6 + - - +
212D HIS 3.2 2.0 + - - -
213D GLY* 1.3 75.2 - - - +
215D GLY* 1.3 52.6 + - - +
217D THR* 3.1 3.5 + - - -
218D PHE* 2.7 35.5 + - - +
243D ILE* 3.7 5.7 - - + +
247D ILE* 4.3 9.9 - - + -
260D THR* 4.1 10.5 - - + -
501D ADP 3.7 31.1 + - + +
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Residues in contact with GLY 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ASP* 2.9 20.1 - - - +
139D THR* 5.1 0.5 + - - -
178D THR* 5.8 1.1 - - - -
213D GLY 3.3 0.4 - - - -
214D ALA* 1.3 79.0 - - - +
216D CYS* 1.3 59.7 + - - +
218D PHE* 3.9 4.3 - - - +
219D SER* 3.2 16.3 + - - -
501D ADP 3.3 40.6 + - - -
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Residues in contact with CYS 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ALA* 4.1 7.9 - - - -
19D GLY* 3.5 25.4 - - - +
22D ALA* 3.9 16.6 - - + -
23D ASP* 3.4 6.7 - - - +
79D LYS* 3.2 11.7 + - - +
81D GLY* 5.8 4.5 - - - -
82D MET 6.1 0.7 - - - -
107D ASP* 4.0 6.7 - - - -
109D VAL* 5.2 12.1 - - - -
213D GLY* 3.2 10.3 + - - +
215D GLY* 1.3 72.3 - - - +
217D THR* 1.3 61.1 + - - +
219D SER* 3.1 8.5 + - - -
220D ALA* 2.9 27.4 + - - +
501D ADP 4.8 0.2 + - - -
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Residues in contact with THR 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D GLY 4.4 0.2 + - - -
22D ALA* 3.8 5.5 - - - +
26D THR* 3.5 19.9 - - - +
213D GLY 2.8 24.3 + - - -
214D ALA* 3.4 4.3 - - - -
216D CYS* 1.3 74.6 - - - +
218D PHE* 1.3 60.2 + - - +
220D ALA* 3.2 3.2 + - - +
221D ALA* 2.8 29.3 + - - +
242D PHE* 3.8 16.2 - - + -
243D ILE* 3.6 20.9 - - + -
246D ALA* 5.0 0.9 - - + -
260D THR* 3.9 6.7 + - - +
262D HIS* 2.9 31.8 + - + -
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Residues in contact with PHE 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D THR* 3.7 29.6 - - + -
176D VAL* 3.7 27.4 - - + -
178D THR* 4.0 14.8 - - + -
190D ASP* 5.2 1.3 - - - -
201D LEU* 5.6 1.1 - - + -
214D ALA 2.7 18.5 + - - +
215D GLY* 3.9 5.8 - - - +
217D THR* 1.3 74.4 - - - +
219D SER* 1.3 58.9 + - - +
221D ALA* 3.3 5.0 + - - +
222D VAL* 3.0 38.9 + - + +
236D ILE* 4.1 13.0 - - + -
239D ALA* 3.8 10.8 - - + -
240D LYS* 3.8 26.7 - - + -
243D ILE* 3.8 31.8 - - + +
501D ADP 4.1 17.3 - - - -
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Residues in contact with SER 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D LYS* 2.8 29.5 + - - -
105D VAL* 3.8 16.7 - - - +
107D ASP* 3.1 21.4 + - - -
139D THR* 3.7 22.9 - - - -
215D GLY 3.2 2.6 + - - -
216D CYS 3.1 3.3 + - - -
218D PHE* 1.3 78.5 - - - +
220D ALA* 1.3 55.2 + - - +
222D VAL* 3.3 5.7 + - - +
223D THR* 2.7 38.2 + - - -
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Residues in contact with ALA 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ASP* 3.4 23.8 - - - +
26D THR* 3.6 23.3 - - - +
27D PHE* 3.3 18.2 - - + -
79D LYS* 3.9 6.0 - - - +
216D CYS 2.9 19.3 + - - +
217D THR* 3.4 4.9 - - - +
219D SER* 1.3 74.2 + - - +
221D ALA* 1.3 53.0 + - - +
223D THR* 3.1 1.4 + - - -
224D ALA* 2.8 32.7 + - - +
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Residues in contact with ALA 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D THR* 3.4 16.9 - - + +
30D LYS* 4.3 7.9 - - - +
217D THR 2.8 19.5 + - - +
218D PHE* 3.5 7.6 - - - +
220D ALA* 1.3 69.8 - - - +
222D VAL* 1.3 64.9 + - - +
224D ALA* 3.4 3.9 + - - +
225D GLU* 3.1 24.8 + - - +
239D ALA* 3.6 23.5 - - + +
242D PHE* 4.2 17.7 - - + -
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Residues in contact with VAL 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D VAL* 3.8 20.4 - - + -
137D VAL* 4.1 15.9 - - + -
139D THR* 5.0 4.0 - - + -
218D PHE* 3.0 40.4 + - + +
219D SER* 3.7 8.3 - - - +
221D ALA* 1.3 75.7 - - - +
223D THR* 1.3 58.4 + - - +
225D GLU* 3.3 2.3 + - - +
226D LEU* 2.9 40.1 + - + +
235D ALA* 4.5 7.9 - - + -
236D ILE* 4.2 19.1 - - + -
239D ALA* 3.6 17.5 - - + +
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Residues in contact with THR 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ALA* 4.2 3.1 - - + -
27D PHE* 3.9 20.2 - - + -
77D ALA* 3.3 10.3 - - + +
78D MET* 3.4 39.0 - - - +
79D LYS* 3.3 18.3 - - - +
105D VAL* 3.3 14.7 - - + +
219D SER 2.7 22.5 + - - -
220D ALA 3.1 4.9 + - - -
222D VAL* 1.3 76.2 - - - +
224D ALA* 1.3 55.6 + - - +
226D LEU* 3.5 2.6 + - - -
227D ALA* 3.0 23.8 + - - +
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Residues in contact with ALA 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D THR 5.0 0.4 - - - +
27D PHE* 3.9 20.6 - - + -
30D LYS* 3.9 22.7 - - + -
32D VAL* 3.6 25.1 - - + +
220D ALA 2.8 19.6 + - - +
221D ALA* 3.7 4.7 - - - +
223D THR* 1.3 73.3 - - - +
225D GLU* 1.3 59.4 + - - +
227D ALA* 2.9 21.5 + - - +
228D LYS* 3.1 12.7 + - - +
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Residues in contact with GLU 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LYS* 2.7 39.2 + - - +
221D ALA 3.1 13.6 + - - +
222D VAL 3.6 0.2 - - - +
224D ALA* 1.3 78.4 - - - +
226D LEU* 1.3 60.7 + - - +
228D LYS* 3.3 29.0 + - - +
229D GLY 3.6 0.2 + - - -
230D ALA* 3.2 30.6 + - + +
234D GLU* 5.1 2.0 - - + +
235D ALA* 3.6 31.4 - - + +
238D ALA* 3.7 20.2 - - + +
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Residues in contact with LEU 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D ASP* 5.0 0.3 - - - +
77D ALA* 4.1 1.8 - - + -
103D ASN* 3.7 52.6 - - + +
105D VAL* 3.6 30.1 - - + -
136D THR* 4.8 2.5 - - + -
137D VAL* 4.5 9.2 - - + -
222D VAL* 2.9 24.0 + - + +
223D THR 3.7 4.3 - - - +
225D GLU* 1.3 75.5 - - - +
227D ALA* 1.3 61.9 + - - +
229D GLY* 3.1 14.7 + - - -
230D ALA 3.8 20.5 + - - +
232D VAL* 3.9 28.9 - - + -
235D ALA* 4.0 8.0 - - + +
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Residues in contact with ALA 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D HIS* 3.2 23.4 + - + +
5D LYS 4.0 12.6 - - - +
6D ALA* 4.5 1.1 - - + -
32D VAL* 4.1 18.2 - - + -
76D ASP* 3.4 14.6 - - + +
77D ALA* 3.8 21.1 - - + +
223D THR 3.0 13.9 + - - +
224D ALA 2.9 13.7 + - - +
226D LEU* 1.3 76.1 - - - +
228D LYS* 1.3 57.4 + - - +
229D GLY 3.3 1.1 + - - -
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Residues in contact with LYS 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D HIS* 3.7 33.9 + - + +
30D LYS* 2.9 44.4 + - + +
31D ASN* 4.8 8.2 - - - +
32D VAL* 3.7 16.2 - - + -
224D ALA 3.1 13.4 + - - +
225D GLU* 3.7 24.5 + - - +
226D LEU 3.1 0.6 - - - -
227D ALA* 1.3 76.7 - - - +
229D GLY* 1.3 57.0 + - - +
230D ALA* 3.5 2.8 + - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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