Contacts of the helix formed by residues 220 - 234 (chain D) in PDB entry 4BL5
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 SER 220 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D LEU* 4.2 16.4 - - - +
19D VAL* 5.1 1.9 - - - +
22D ALA* 3.7 19.3 - - - +
173D VAL* 4.0 20.2 - - - -
174D PHE 2.8 14.0 + - - -
175D GLY* 3.6 16.3 - - - -
176D PRO* 4.0 4.0 + - - +
218D ILE 3.5 1.6 + - - -
219D TYR* 1.3 70.4 - - - +
221D LEU* 1.3 68.5 + - - +
223D LEU* 2.9 8.8 + - - +
224D ALA* 2.7 34.8 + - - +
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Residues in contact with LEU 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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22D ALA* 4.4 19.1 - - + +
25D LYS* 5.3 10.8 - - + -
26D VAL* 4.5 8.5 - - + +
176D PRO* 4.7 11.9 - - + -
219D TYR* 3.2 31.9 - - + +
220D SER* 1.3 92.8 + - - +
222D ASP* 1.3 66.4 + - - +
224D ALA* 3.3 13.1 + - - +
225D GLN* 3.1 22.7 + - - +
307D GLU* 5.8 1.1 - - - +
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Residues in contact with ASP 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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218D ILE* 4.3 4.3 - - + -
219D TYR* 2.9 26.0 + - - +
221D LEU* 1.3 73.6 - - - +
223D LEU* 1.3 65.5 + - - +
225D GLN* 3.1 22.4 + - - +
226D LEU* 3.3 16.0 + - - +
296D PHE* 3.9 10.5 - - + -
297D ARG 5.1 0.6 - - - +
298D PHE* 3.1 32.3 - - + +
299D THR* 2.7 50.0 + - - +
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Residues in contact with LEU 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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19D VAL* 3.8 28.5 - - + -
170D PRO* 3.9 24.9 - - + -
173D VAL* 4.0 29.6 - - + -
218D ILE* 4.2 17.4 - - + +
219D TYR 3.1 6.3 + - - +
220D SER* 2.9 9.9 + - - +
222D ASP* 1.3 75.8 - - - +
224D ALA* 1.3 57.7 + - - +
226D LEU* 3.1 4.9 + - - -
227D PHE* 2.7 49.1 + - + +
242D LEU* 3.6 31.6 - - + -
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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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19D VAL* 5.5 2.0 - - - +
22D ALA* 3.9 5.8 - - + -
23D ILE* 3.8 33.8 - - + +
26D VAL* 3.6 20.6 - - + -
220D SER 2.7 15.8 + - - +
221D LEU 3.4 11.0 - - - +
222D ASP 3.2 0.2 - - - -
223D LEU* 1.3 74.9 - - - +
225D GLN* 1.3 62.1 + - - +
227D PHE* 3.3 5.2 - - - +
228D ILE* 3.1 28.1 + - - +
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Residues in contact with GLN 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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26D VAL* 4.2 20.6 - - + -
221D LEU* 3.1 20.9 - - - +
222D ASP* 3.1 17.4 + - - +
224D ALA* 1.3 76.6 - - - +
226D LEU* 1.3 58.7 + - - +
228D ILE* 3.3 12.5 + - - +
229D TRP* 3.0 27.9 + - - +
296D PHE* 4.2 22.9 - - + -
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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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218D ILE* 4.5 4.7 - - + -
222D ASP 3.3 10.9 + - - +
223D LEU 3.1 6.7 + - - +
225D GLN* 1.3 73.8 - - - +
227D PHE* 1.3 60.4 + - - +
229D TRP* 3.3 7.1 + - + +
230D VAL* 2.8 36.0 + - + +
242D LEU* 3.9 26.5 - - + -
289D LEU* 4.1 18.2 - - + -
293D LEU* 3.7 22.2 - - + -
296D PHE* 3.5 34.1 - - + -
298D PHE* 3.8 35.0 - - + -
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Residues in contact with PHE 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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19D VAL* 4.0 13.2 - - + -
23D ILE* 4.3 10.5 - - + -
67D ILE* 3.4 30.7 - - + -
69D LEU* 3.2 27.1 - - + -
110D VAL* 3.7 26.2 - - + -
111D SER 4.4 1.6 - - - -
112D CYS* 3.9 19.3 - - + -
168D VAL* 3.5 26.2 - - + -
223D LEU* 2.7 37.4 + - + +
224D ALA* 3.3 12.6 - - - +
226D LEU* 1.3 71.8 - - - +
228D ILE* 1.3 61.9 + - - +
230D VAL* 3.1 8.8 + - - +
231D LEU* 3.0 20.8 + - - +
242D LEU* 4.3 3.9 - - - +
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Residues in contact with ILE 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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23D ILE* 4.6 10.8 - - + -
26D VAL* 3.5 35.9 - - + -
27D VAL* 4.3 12.3 - - + -
31D ALA* 4.9 5.4 - - + +
38D TRP* 4.2 20.6 - - + -
67D ILE* 5.6 2.9 - - + -
224D ALA 3.1 17.6 + - - +
225D GLN* 3.3 9.4 + - - +
227D PHE* 1.3 77.8 - - - +
229D TRP* 1.3 63.8 + - - +
231D LEU* 3.1 17.8 + - - +
232D ARG* 3.1 53.1 + - - +
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Residues in contact with TRP 229 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225D GLN 3.0 13.6 + - - +
226D LEU* 3.5 10.3 - - + +
228D ILE* 1.3 79.7 - - - +
230D VAL* 1.3 89.1 + - + +
232D ARG* 3.1 6.9 + - + +
233D GLU* 2.8 63.8 + - + +
234D TYR* 3.9 22.7 - + + -
240D ILE* 4.5 9.9 - - + -
289D LEU* 5.2 3.6 - - + -
292D TYR* 3.6 47.3 - + + -
293D LEU* 4.0 37.7 - - + +
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Residues in contact with VAL 230 (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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108D LYS* 3.2 8.9 + - - -
110D VAL* 4.2 16.2 - - + -
166D THR* 4.8 2.9 - - + -
168D VAL* 3.6 34.1 - - + -
226D LEU 2.8 22.3 + - - +
227D PHE 3.1 7.2 + - - +
229D TRP* 1.3 96.1 - - + +
231D LEU* 1.3 64.7 + - - +
234D TYR* 3.1 41.1 + - + +
240D ILE* 4.2 8.7 - - + -
242D LEU* 4.4 9.2 - - + -
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Residues in contact with LEU 231 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D MET* 6.3 0.4 - - - -
10D ILE* 5.9 7.0 - - + -
38D TRP* 5.5 4.7 - - + -
65D HIS* 4.6 15.9 - - + -
67D ILE* 4.5 23.1 - - + -
108D LYS* 2.8 28.8 + - - +
110D VAL* 4.3 13.4 - - + +
227D PHE 3.0 11.6 + - - +
228D ILE* 3.1 13.2 + - - +
230D VAL* 1.3 76.1 - - - +
232D ARG* 1.3 59.9 + - + +
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Residues in contact with ARG 232 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D MET* 5.0 17.9 - - + +
31D ALA* 3.0 29.1 + - - +
32D GLY* 3.8 2.4 - - - -
33D LEU* 3.5 12.2 - - - +
36D GLU* 2.6 43.0 + - - +
38D TRP* 4.0 7.9 - - - -
108D LYS* 4.5 2.0 + - - -
228D ILE* 3.1 35.5 + - + +
229D TRP* 3.1 9.5 + - + +
231D LEU* 1.3 82.8 - - + +
233D GLU* 1.3 69.6 + - + +
235D ASN* 4.8 4.2 + - - +
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Residues in contact with GLU 233 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229D TRP* 2.8 51.1 + - + +
232D ARG* 1.3 85.1 - - + +
234D TYR* 1.3 61.2 + - - +
235D ASN* 3.5 17.2 + - - +
292D TYR* 5.8 2.1 - - - -
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Residues in contact with TYR 234 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108D LYS* 2.5 31.6 + - - +
166D THR* 3.8 11.5 - - + +
229D TRP* 3.9 17.6 + + + -
230D VAL* 3.1 37.7 + - + +
233D GLU* 1.3 75.2 - - - +
235D ASN* 1.3 57.0 + - - +
236D GLU* 3.2 45.9 + - + -
238D GLU 2.5 23.7 + - - -
239D PRO 3.3 8.1 + - - -
240D ILE* 3.9 23.3 - - + -
288D LYS* 3.4 3.7 + - + -
292D TYR* 3.6 42.4 - + - -
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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