Contacts of the helix formed by residues 217 - 233 (chain A) in PDB entry 6HBU
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 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A LEU* 1.3 72.8 - - - +
218A SER* 1.3 64.0 + - - +
219A SER* 3.9 5.6 + - - -
220A THR* 2.9 26.8 + - - -
221A ALA* 3.2 12.8 + - - +
80B GLY 3.7 2.2 - - - +
81B PRO* 3.2 26.3 - - - +
82B THR* 3.8 5.2 - - - +
243B HIS* 3.3 27.3 + - + +
244B GLN* 3.1 16.6 + - - -
295B LEU* 3.6 21.6 - - + +
299B ASN* 3.4 14.4 + - - -
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Residues in contact with SER 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ASP* 1.3 78.1 - - - +
219A SER* 1.3 59.9 + - - +
221A ALA* 4.3 1.5 - - - +
222A ASN 3.7 9.0 + - - -
246A ARG* 3.3 34.9 + - - +
249A ILE* 5.1 1.1 - - - +
79B LEU* 6.1 0.3 - - - +
244B GLN* 3.7 27.9 + - - +
245B PRO* 5.0 1.6 - - - +
291B ALA 4.3 7.4 + - - -
292B ASP* 3.0 32.6 + - - -
295B LEU* 4.4 12.5 - - - +
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Residues in contact with SER 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ASP* 3.3 3.5 - - - -
218A SER* 1.3 78.7 - - - +
220A THR* 1.3 64.4 + - - +
221A ALA 3.3 0.7 - - - -
222A ASN* 3.6 3.0 + - - +
223A ALA* 3.2 20.1 + - - +
246A ARG* 4.5 3.3 + - - +
295B LEU* 3.4 26.3 + - - +
296B ASP* 3.5 18.1 + - - -
299B ASN* 3.4 15.9 + - - +
305B VAL* 3.5 25.2 - - - +
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Residues in contact with THR 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LEU 4.6 2.2 - - - +
193A ARG* 3.6 42.5 + - - +
216A LEU* 4.3 12.6 - - + -
217A ASP* 2.9 21.7 + - - -
219A SER* 1.3 73.5 - - - +
221A ALA* 1.3 59.0 + - - +
223A ALA* 3.0 6.3 + - - -
224A VAL* 2.8 31.1 + - + +
81B PRO* 5.4 0.2 - - - +
82B THR* 4.0 10.2 + - - +
299B ASN* 3.5 12.6 + - - +
304B ALA* 4.9 8.7 - - + -
305B VAL* 5.2 1.9 - - - +
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Residues in contact with ALA 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A THR* 3.7 24.2 - - + -
216A LEU* 4.2 8.8 - - + +
217A ASP 3.2 20.4 + - - +
218A SER* 4.5 1.3 - - - +
220A THR* 1.3 79.5 - - - +
222A ASN* 1.3 60.2 + - - +
224A VAL* 3.4 1.4 + - - +
225A LEU* 3.1 29.6 + - - +
249A ILE* 3.9 12.9 - - + +
244B GLN* 3.4 18.4 - - - +
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Residues in contact with ASN 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A SER 3.7 7.5 + - - +
219A SER* 3.6 5.7 + - - +
220A THR 3.3 0.6 - - - -
221A ALA* 1.3 77.1 - - - +
223A ALA* 1.3 58.3 + - - +
225A LEU 3.5 0.4 + - - +
226A LEU* 2.9 49.9 + - - +
246A ARG* 2.7 37.6 + - - +
248A SER* 3.3 27.5 + - - -
249A ILE* 4.0 16.7 - - + +
252A LEU* 4.4 3.4 - - - +
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Residues in contact with ALA 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLU 4.9 1.0 - - - +
219A SER 3.2 12.0 + - - +
220A THR* 3.0 9.7 + - - +
222A ASN* 1.3 79.1 - - - +
224A VAL* 1.3 62.4 + - + +
226A LEU* 4.0 2.0 - - - -
227A LEU* 3.3 9.9 + - - +
304B ALA* 3.6 41.5 - - + +
305B VAL* 4.1 7.6 - - + +
308B ASN* 2.9 30.8 + - + +
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Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLU 6.1 0.4 - - - +
168A LEU* 4.3 22.2 - - + +
193A ARG* 4.7 4.3 - - + -
196A ILE* 4.4 24.0 - - + -
212A PRO* 4.9 6.1 - - + -
213A THR* 5.0 1.3 - - + -
216A LEU* 3.8 21.1 - - + -
220A THR* 2.8 26.4 + - + +
221A ALA* 3.8 7.0 - - - +
222A ASN 3.2 0.2 - - - -
223A ALA* 1.3 78.4 - - + +
225A LEU* 1.3 65.4 + - + +
227A LEU* 3.1 11.7 + - + +
228A LEU* 3.0 39.0 + - + +
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 4.4 10.4 - - + +
212A PRO* 4.9 5.2 - - + -
213A THR* 3.6 30.5 - - + -
221A ALA 3.1 16.5 + - - +
222A ASN 4.4 1.1 - - - +
224A VAL* 1.3 80.8 - - + +
226A LEU* 1.3 60.3 + - - +
227A LEU 3.2 0.2 - - - -
228A LEU* 3.6 17.0 - - + +
229A LYS* 2.8 28.6 + - - +
240A PHE* 3.6 32.5 - - + -
242A ILE* 4.4 6.3 - - + -
249A ILE* 3.7 27.4 - - + +
252A LEU* 3.7 14.9 - - + +
253A PHE* 3.9 7.2 - - + -
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Residues in contact with LEU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ASN* 2.9 42.0 + - - +
223A ALA* 4.8 1.6 - - - -
225A LEU* 1.3 75.0 - - - +
227A LEU* 1.3 61.6 + - - +
229A LYS* 4.0 5.9 - - + +
230A ARG* 3.1 26.7 + - - +
252A LEU* 3.9 27.8 - - + -
308B ASN* 4.1 23.4 - - + +
309B ARG* 3.7 42.4 - - + +
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLU* 3.6 31.6 - - + +
168A LEU* 3.9 30.7 - - + -
200A LEU* 4.2 19.5 - - + -
223A ALA 3.3 14.6 + - - +
224A VAL* 3.1 13.8 + - + +
226A LEU* 1.3 77.3 - - - +
228A LEU* 1.3 59.7 + - + +
230A ARG* 3.5 33.2 + - - +
231A MET* 3.1 36.8 + - + +
308B ASN* 4.0 15.6 - - - +
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 4.0 14.6 - - + -
196A ILE* 5.9 0.7 - - + -
200A LEU* 4.6 14.8 - - + -
207A LEU* 4.1 24.5 - - + -
209A LEU* 4.1 29.6 - - + -
212A PRO* 5.1 3.6 - - + -
224A VAL* 3.0 28.9 + - + +
225A LEU* 3.8 21.8 - - + +
226A LEU 3.3 0.2 - - - -
227A LEU* 1.3 76.8 - - + +
229A LYS* 1.3 55.6 + - - +
231A MET* 3.1 12.8 + - - +
232A SER* 2.7 36.4 + - - -
238A ILE* 3.3 15.3 - - + +
240A PHE* 5.1 3.6 - - + -
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Residues in contact with LYS 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 4.0 10.5 - - + +
225A LEU 2.8 18.3 + - - +
226A LEU* 4.1 11.2 - - + +
228A LEU* 1.3 74.7 - - - +
230A ARG* 1.3 63.4 + - - +
232A SER* 2.9 24.2 + - - +
233A LYS* 3.3 37.2 - - - +
252A LEU* 3.2 45.3 + - + +
254A ASP* 3.1 33.5 + - - -
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Residues in contact with ARG 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ARG* 6.0 0.4 - - - +
167A GLU* 3.2 27.9 + - - -
226A LEU 3.1 19.0 + - - +
227A LEU* 3.5 28.2 + - - +
229A LYS* 1.3 76.6 - - - +
231A MET* 1.3 65.7 + - - +
233A LYS* 3.8 20.3 + - - +
234A GLN* 3.8 31.4 + - - +
307B LEU 5.6 2.2 + - - -
308B ASN* 4.4 9.3 + - - +
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Residues in contact with MET 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU* 3.8 38.8 - - + +
203A ASP* 5.9 7.6 - - + -
204A PRO 5.9 0.4 - - - +
207A LEU* 4.2 24.9 - - - -
227A LEU* 3.1 26.9 + - + +
228A LEU* 3.1 18.0 + - + +
230A ARG* 1.3 82.4 - - - +
232A SER* 1.3 62.8 + - - +
233A LYS 3.3 0.7 - - - -
234A GLN* 3.3 21.3 + - - +
236A ARG* 3.4 33.8 - - + +
238A ILE* 4.4 7.0 - - + -
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Residues in contact with SER 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PRO* 4.9 1.7 - - - +
74A GLY* 3.3 38.5 + - - -
75A LEU* 4.4 3.4 - - - +
228A LEU 2.7 18.0 + - - -
229A LYS* 2.9 28.5 + - - +
231A MET* 1.3 72.4 - - - +
233A LYS* 1.3 60.8 + - - +
234A GLN 3.2 2.7 - - - -
235A GLY* 3.4 11.5 + - - -
236A ARG 3.5 15.1 + - - +
238A ILE* 3.8 9.4 - - - +
254A ASP* 4.7 1.6 + - - -
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Residues in contact with LYS 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A LYS* 3.3 44.9 + - - +
230A ARG* 4.1 14.4 - - - +
231A MET 3.3 1.0 - - - -
232A SER* 1.3 78.6 + - - +
234A GLN* 1.3 60.8 + - - +
235A GLY 3.3 1.6 - - - -
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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
------------------------------------------------------------
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