Contacts of the helix formed by residues 220 - 234 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B LEU* 3.9 22.6 - - - +
19B VAL* 5.1 2.0 - - - +
22B ALA* 3.3 24.7 - - - +
173B VAL* 4.0 13.0 - - - +
174B PHE 2.9 15.8 + - - -
176B PRO* 3.6 16.8 + - - +
218B ILE 3.6 1.4 + - - -
219B TYR* 1.3 70.9 - - - +
221B LEU* 1.3 73.3 + - - +
223B LEU* 3.3 5.4 + - - +
224B ALA 2.8 24.6 + - - -
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ALA* 4.4 10.5 - - + -
25B LYS* 5.6 7.0 - - + -
26B VAL* 4.2 12.2 - - + +
176B PRO* 4.1 21.5 - - + -
219B TYR* 3.2 30.1 - - + +
220B SER* 1.3 91.2 + - - +
222B ASP* 1.3 68.4 + - - +
224B ALA* 3.4 8.3 + - - +
225B GLN* 3.2 32.6 + - - +
307B GLU* 5.0 2.7 - - - +
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Residues in contact with ASP 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ILE* 4.4 4.7 - - + -
219B TYR* 3.0 20.9 + - - +
221B LEU* 1.3 75.8 - - - +
223B LEU* 1.3 63.2 + - - +
225B GLN* 2.9 22.8 + - - +
226B LEU* 3.0 17.9 + - - +
296B PHE* 4.3 12.1 - - + -
297B ARG 5.1 0.4 - - - +
298B PHE* 3.5 30.0 - - + +
299B THR* 2.7 51.3 + - - +
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Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 3.7 27.1 - - + -
170B PRO* 4.0 22.9 - - + -
173B VAL* 3.7 31.4 - - + -
218B ILE* 4.5 11.3 - - + +
219B TYR 3.0 11.4 + - - +
220B SER* 3.5 9.6 - - - +
222B ASP* 1.3 76.4 - - - +
224B ALA* 1.3 52.9 + - - +
226B LEU* 3.2 7.8 + - - -
227B PHE* 2.7 52.9 + - + +
242B LEU* 3.5 35.2 - - + -
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Residues in contact with ALA 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 5.3 0.4 - - - -
22B ALA* 3.6 33.0 - - + +
23B ILE* 3.7 20.8 - - + +
26B VAL* 3.8 8.7 - - + -
220B SER 2.8 16.8 + - - +
221B LEU 3.4 7.0 - - - +
222B ASP 3.2 0.4 - - - -
223B LEU* 1.3 76.9 - - - +
225B GLN* 1.3 63.0 + - - +
227B PHE* 3.4 2.3 + - - +
228B ILE* 3.2 31.5 + - - +
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Residues in contact with GLN 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B VAL* 4.1 22.9 - - + +
221B LEU* 3.4 19.1 - - - +
222B ASP* 2.9 15.3 + - - +
224B ALA* 1.3 74.5 - - - +
226B LEU* 1.3 64.9 + - - +
228B ILE* 3.4 9.0 + - - +
229B TRP* 3.2 21.0 + - - +
296B PHE* 4.4 21.9 - - + -
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ILE* 4.1 12.8 - - + -
222B ASP 3.0 19.2 + - - +
223B LEU* 3.7 6.3 - - - +
225B GLN* 1.3 72.6 - - - +
227B PHE* 1.3 65.4 + - - +
229B TRP* 3.3 8.2 + - + +
230B VAL* 3.0 29.2 + - - +
242B LEU* 3.8 26.9 - - + -
289B LEU* 4.1 28.9 - - + -
293B LEU* 4.1 17.9 - - + -
296B PHE* 4.3 22.9 - - + -
298B PHE* 3.8 31.2 - - + -
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Residues in contact with PHE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 4.0 10.8 - - + -
23B ILE* 3.6 23.1 - - + -
67B ILE* 3.3 28.3 - - + -
69B LEU* 3.4 31.6 - - + -
110B VAL* 3.6 33.0 - - + -
111B SER 4.8 0.2 - - - -
112B CYS* 4.0 16.4 - - + -
168B VAL* 3.9 20.2 - - + -
223B LEU* 2.7 32.3 + - + +
224B ALA 3.5 6.3 - - - +
225B GLN 3.2 0.2 - - - -
226B LEU* 1.3 73.9 - - - +
228B ILE* 1.3 64.0 + - + +
230B VAL* 3.3 6.2 + - + +
231B LEU* 3.1 21.2 + - - +
242B LEU* 4.6 2.7 - - - +
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Residues in contact with ILE 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ILE* 4.8 10.1 - - + +
26B VAL* 3.8 26.0 - - + -
27B VAL* 3.7 24.7 - - + -
31B ALA* 4.3 7.0 - - + +
38B TRP* 4.1 18.8 - - + -
67B ILE* 5.5 1.8 - - + -
224B ALA 3.2 16.9 + - - +
225B GLN* 3.8 6.5 - - - +
226B LEU 3.2 0.2 - - - -
227B PHE* 1.3 76.4 - - + +
229B TRP* 1.3 66.7 + - - +
231B LEU* 3.3 8.8 + - - +
232B ARG* 3.2 59.7 + - - +
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Residues in contact with TRP 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B GLN 3.2 11.6 + - - +
226B LEU* 3.5 11.9 - - + +
228B ILE* 1.3 80.7 - - - +
230B VAL* 1.3 87.1 + - + +
232B ARG* 3.8 3.9 - - - +
233B GLU* 2.9 53.0 + - + +
234B TYR* 3.8 23.3 - + + -
240B ILE* 4.6 7.2 - - + -
289B LEU* 4.8 8.3 - - + -
292B TYR* 3.4 51.6 - + + -
293B LEU* 3.7 38.0 - - + +
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Residues in contact with VAL 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LYS* 3.0 18.4 + - - -
110B VAL* 3.8 29.8 - - + -
166B THR* 4.7 2.2 - - + -
168B VAL* 3.9 23.6 - - + -
226B LEU 3.0 19.7 + - - +
227B PHE* 3.5 8.7 - - - +
229B TRP* 1.3 95.0 - - + +
231B LEU* 1.3 65.7 + - - +
234B TYR* 3.3 28.1 + - + +
240B ILE* 4.4 7.9 - - + -
242B LEU* 4.7 7.2 - - + -
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Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B MET* 5.9 1.2 - - - +
10B ILE* 5.8 5.6 - - + -
38B TRP* 5.5 5.4 - - + -
65B HIS* 4.5 15.6 + - + -
67B ILE* 4.3 24.5 - - + -
108B LYS* 3.2 24.3 + - - +
110B VAL* 4.4 11.6 - - + +
227B PHE 3.1 13.1 + - - +
228B ILE* 3.3 11.4 + - + +
230B VAL* 1.3 76.5 - - - +
232B ARG* 1.3 61.1 + - + +
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Residues in contact with ARG 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B MET* 4.8 19.0 - - + +
31B ALA* 2.8 27.5 + - - +
32B GLY* 4.1 0.2 - - - -
33B LEU* 3.8 11.1 - - - +
36B GLU* 3.0 38.9 + - - +
38B TRP* 4.3 3.0 - - - -
108B LYS* 4.5 2.6 + - - -
228B ILE* 3.2 37.7 + - - +
229B TRP* 4.0 2.7 - - - +
231B LEU* 1.3 82.1 - - + +
233B GLU* 1.3 74.3 + - + +
234B TYR 3.8 1.3 + - - -
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Residues in contact with GLU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B TRP* 2.9 44.3 + - + +
232B ARG* 1.3 89.9 - - + +
234B TYR* 1.3 59.6 + - - +
235B ASN* 4.0 2.0 + - - +
292B TYR* 5.1 4.7 - - - -
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Residues in contact with TYR 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LYS* 2.4 32.1 + - - -
166B THR* 3.8 13.0 - - + -
229B TRP* 3.8 26.6 + + + -
230B VAL* 3.3 28.7 + - + +
232B ARG 3.8 0.6 - - - -
233B GLU* 1.3 76.9 - - - +
235B ASN* 1.3 57.8 + - - +
236B GLU* 3.2 46.0 - - + +
238B GLU 2.7 20.6 + - - -
239B PRO 3.2 3.3 + - - -
240B ILE* 3.5 41.0 - - + +
288B LYS* 3.2 18.2 + - + -
292B TYR* 4.1 14.8 - + - -
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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