Contacts of the helix formed by residues 173 - 184 (chain D) in PDB entry 6BCH
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 ASP 173 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D SER* 5.5 0.2 - - - -
20D TRP* 3.8 36.0 + - + -
171D ILE* 3.3 5.7 + - - +
172D PRO* 1.3 83.6 - - - +
174D SER* 1.3 69.0 + - - +
175D ASN* 2.6 43.9 + - - +
176D TRP* 3.0 18.6 + - + +
177D VAL* 3.4 8.7 + - - +
225D TYR* 4.0 5.4 - - - -
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Residues in contact with SER 174 (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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173D ASP* 1.3 78.7 + - - +
175D ASN* 1.3 61.4 + - - +
177D VAL* 3.1 8.3 + - - +
178D ALA* 2.9 23.6 + - - +
225D TYR* 3.3 23.4 + - - -
264D PHE* 3.8 13.0 - - - -
268D ASN* 2.7 35.6 + - - +
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Residues in contact with ASN 175 (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 SER* 3.6 25.5 + - - +
20D TRP* 4.4 0.4 - - + -
21D THR* 3.2 32.5 + - - +
173D ASP* 2.6 24.3 + - - +
174D SER* 1.3 73.3 + - - +
176D TRP* 1.3 63.1 + - - +
178D ALA* 3.2 6.8 + - - +
179D GLY 2.9 18.5 + - - -
267D LYS 5.3 0.7 - - - +
268D ASN* 3.6 20.4 - - - +
269D HIS 5.2 0.7 + - - -
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Residues in contact with TRP 176 (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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20D TRP* 3.3 36.7 + + + +
23D THR* 4.0 3.3 - - + +
24D GLY* 3.4 24.5 - - - +
27D ASP* 2.9 33.9 + - - -
105D ILE* 3.8 21.5 - - + +
106D THR* 4.3 3.4 - - + -
171D ILE* 4.2 13.2 - - + -
172D PRO* 3.9 20.2 - - + -
173D ASP* 3.0 15.4 + - - +
175D ASN* 1.3 78.2 - - - +
177D VAL* 1.3 67.9 + - + +
179D GLY 3.2 1.4 + - - -
180D PHE* 2.9 63.0 + + + -
218D LEU* 4.5 18.6 - - + -
222D LEU* 4.2 19.1 - - + -
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Residues in contact with VAL 177 (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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171D ILE* 3.5 30.5 - - + -
173D ASP 3.7 5.6 - - - +
174D SER 3.1 8.5 + - - +
176D TRP* 1.3 84.7 - - + +
178D ALA* 1.3 52.5 + - - +
180D PHE* 3.8 1.5 - - + +
181D THR* 2.7 51.1 + - + +
222D LEU* 4.3 17.0 - - + -
225D TYR* 4.0 17.5 - - + -
226D LEU* 4.8 10.5 - - + -
264D PHE* 3.5 23.1 - - + -
265D PHE* 4.6 1.1 - - + -
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Residues in contact with ALA 178 (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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21D THR* 4.8 4.9 - - + +
174D SER 2.9 12.0 + - - +
175D ASN* 3.2 16.1 + - - +
177D VAL* 1.3 77.4 - - - +
179D GLY* 1.3 55.9 + - - +
181D THR* 2.9 18.7 + - - -
182D ALA* 2.9 20.0 + - - +
264D PHE* 4.8 0.2 - - - -
265D PHE* 4.6 4.9 - - - -
268D ASN* 3.9 19.3 - - + +
269D HIS 3.5 22.9 - - - +
270D ILE* 4.1 3.0 - - - +
271D ILE* 6.1 0.4 - - - -
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Residues in contact with GLY 179 (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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21D THR* 3.6 32.2 - - - +
25D PHE* 3.4 18.5 - - - -
175D ASN 2.9 11.9 + - - -
176D TRP 3.7 1.3 - - - -
178D ALA* 1.3 72.4 - - - +
180D PHE* 1.3 65.9 + - - +
182D ALA* 3.1 9.3 + - - +
183D GLY 3.0 17.7 + - - -
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Residues in contact with PHE 180 (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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24D GLY 3.6 20.9 - - - +
27D ASP* 4.2 2.2 - - + -
28D ALA* 4.0 12.3 - - + -
106D THR* 3.7 23.8 - - + -
176D TRP* 2.9 47.8 + + + +
177D VAL* 3.8 4.0 - - - +
179D GLY* 1.3 75.0 - - - +
181D THR* 1.3 58.0 + - + +
183D GLY* 3.1 1.6 + - - +
184D GLU* 2.9 47.2 + - + +
209D ILE* 3.8 34.1 - - + -
211D GLN* 4.3 19.5 - - + -
218D LEU* 5.4 4.7 - - + -
219D MET* 5.3 7.6 - - - -
222D LEU* 5.3 9.2 - - + -
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Residues in contact with THR 181 (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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177D VAL* 2.7 33.4 + - + +
178D ALA 2.9 11.6 + - - -
180D PHE* 1.3 76.3 - - + +
182D ALA* 1.3 62.1 + - - +
185D GLY* 2.8 35.0 + - - +
187D PHE* 5.3 3.0 - - - -
207D PHE* 4.0 7.0 - - + -
209D ILE* 3.7 28.0 - - + -
226D LEU* 6.0 0.4 - - + -
265D PHE* 3.1 39.2 - - + -
270D ILE* 3.3 9.5 - - - +
274D LYS* 6.1 0.2 - - - +
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Residues in contact with ALA 182 (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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25D PHE* 3.9 11.2 - - + -
178D ALA 2.9 20.1 + - - +
179D GLY 3.1 7.6 + - - +
181D THR* 1.3 78.2 + - - +
183D GLY* 1.3 59.1 + - - +
185D GLY 5.6 0.3 - - - +
270D ILE* 4.4 11.0 - - + -
271D ILE* 3.7 45.8 - - + +
274D LYS* 4.9 10.0 - - - +
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Residues in contact with GLY 183 (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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25D PHE* 3.9 11.4 - - - -
28D ALA* 3.8 14.8 - - - -
29D ASP* 4.0 11.4 - - - +
179D GLY 3.0 10.8 + - - -
180D PHE 3.1 2.4 + - - -
181D THR 3.1 0.2 - - - -
182D ALA* 1.3 79.9 - - - +
184D GLU* 1.3 68.7 + - - +
185D GLY 3.6 2.1 - - - +
16F G 3.8 11.8 + - - +
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Residues in contact with GLU 184 (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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28D ALA* 2.9 45.7 - - + +
29D ASP* 3.8 2.9 - - - +
180D PHE* 2.9 29.4 + - + +
183D GLY* 1.3 74.0 - - - +
185D GLY* 1.3 65.4 + - - +
186D SER* 4.0 0.9 + - - -
209D ILE* 4.0 12.7 - - + -
210D THR* 3.8 28.7 + - - +
211D GLN* 3.3 20.8 + - - +
15F C 4.2 7.6 + - - +
16F G 3.2 38.0 + - - +
17G A 4.1 7.0 + - - -
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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