Contacts of the helix formed by residues 216 - 234 (chain A) in PDB entry 1DQU
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 PRO 216 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A VAL* 1.3 103.8 - - + +
217A ILE* 1.3 68.2 + - - +
218A SER* 3.4 17.2 + - - +
219A GLU* 3.5 17.0 + - + +
220A HIS* 3.7 1.9 + - - +
252A ILE* 4.3 7.4 - - + -
253A THR* 3.3 16.4 - - - +
254A SER* 4.2 12.8 - - - +
256A ILE* 4.0 23.3 - - + -
257A ASP* 4.2 7.6 - - + +
260A ASP* 3.5 12.3 - - - +
381A ARG* 4.2 1.0 + - - -
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Residues in contact with ILE 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A PRO* 1.3 74.1 - - - +
218A SER* 1.3 65.4 + - - +
220A HIS* 3.3 3.8 + - - +
221A ILE* 3.0 38.2 + - + +
257A ASP* 3.3 12.2 + - - +
259A ARG* 4.0 19.5 - - + +
260A ASP* 3.0 28.7 + - - +
380A ASN* 4.4 8.3 - - - +
381A ARG* 3.6 44.6 - - + +
384A ALA* 4.0 11.0 - - + -
385A TYR* 3.8 19.6 - - + -
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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
----------------------------------------------------------
216A PRO* 3.8 12.3 - - - +
217A ILE* 1.3 77.3 - - - +
219A GLU* 1.3 67.6 + - - +
221A ILE* 2.8 19.9 + - - +
222A ASN* 2.9 20.6 + - - -
256A ILE* 5.6 2.6 - - - +
257A ASP* 3.2 17.5 + - - +
259A ARG* 4.6 9.9 - - - +
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Residues in contact with GLU 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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176A LEU* 4.9 3.2 - - + +
215A VAL* 2.8 42.7 - - + +
216A PRO* 3.5 15.5 + - + +
217A ILE 3.3 0.4 - - - -
218A SER* 1.3 81.1 + - - +
220A HIS* 1.3 57.3 + - - +
222A ASN* 2.6 33.3 + - + +
223A ARG* 3.3 17.9 + - - +
253A THR* 5.0 0.2 + - - -
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Residues in contact with HIS 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ILE* 3.4 21.3 + - + +
197A GLU 2.6 38.8 + - - -
198A ASP* 3.4 6.3 - - + -
215A VAL* 4.1 6.9 - - + +
216A PRO 3.7 5.1 + - - +
217A ILE 3.3 7.7 + - - +
218A SER 3.2 0.4 - - - -
219A GLU* 1.3 74.7 - - - +
221A ILE* 1.3 63.9 + - - +
222A ASN 2.7 5.9 + - - -
223A ARG* 3.1 34.5 + - - +
224A LEU* 3.3 36.7 + - + +
242A ALA* 4.2 3.8 - - + -
243A ARG 3.9 11.2 - - - -
385A TYR* 3.6 28.0 - + + +
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Residues in contact with ILE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ILE* 3.0 36.6 + - + +
218A SER* 2.8 10.0 + - - +
220A HIS* 1.3 77.6 - - - +
222A ASN* 1.3 55.8 + - - +
224A LEU* 3.9 8.5 + - - +
225A VAL* 2.3 41.9 + - + +
259A ARG* 4.2 22.2 - - - +
384A ALA* 4.1 20.0 - - + +
385A TYR* 3.9 13.9 - - + -
388A PHE* 3.4 38.1 - - + -
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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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176A LEU* 4.1 28.3 - - + +
218A SER* 2.9 15.0 + - - +
219A GLU* 2.6 20.7 - - + +
220A HIS 2.7 0.4 - - - -
221A ILE* 1.3 84.6 + - - +
223A ARG* 1.3 64.0 + - - +
225A VAL* 3.5 9.9 + - - +
226A ALA* 3.0 20.3 + - - +
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Residues in contact with ARG 223 (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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171A THR* 3.3 29.0 + - - +
174A GLY 5.1 5.7 + - - -
176A LEU* 4.7 7.2 - - + -
179A VAL* 4.5 16.1 - - + +
196A ILE* 4.2 18.2 - - + -
197A GLU 2.7 30.3 + - - -
198A ASP* 3.9 3.0 - - - +
199A GLN 3.1 27.3 + - - -
201A PRO* 3.4 21.0 - - - +
215A VAL* 4.0 17.2 - - - +
219A GLU* 3.7 18.3 + - - +
220A HIS* 3.1 24.3 + - - +
222A ASN* 1.3 72.3 - - - +
224A LEU* 1.3 71.5 + - - +
225A VAL 2.5 2.9 + - - -
226A ALA* 2.6 19.3 + - - +
227A ILE* 2.8 13.7 + - - -
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Residues in contact with LEU 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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196A ILE* 3.0 36.6 - - + -
220A HIS* 3.4 32.1 - - + +
221A ILE* 4.2 6.5 - - - +
223A ARG* 1.3 75.1 - - - +
225A VAL* 1.3 61.4 + - - +
227A ILE* 3.3 13.5 + - + +
228A ARG* 3.1 20.8 + - - +
240A ALA* 5.4 5.6 - - + -
241A ILE 4.8 2.5 - - - +
242A ALA* 3.7 25.4 - - + +
385A TYR* 4.4 19.3 - - + +
388A PHE* 3.6 32.7 - - + +
389A ALA* 4.6 3.6 - - + -
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Residues in contact with VAL 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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33A PRO* 3.5 35.2 - - + -
34A PHE* 4.3 9.5 - - + -
221A ILE* 2.3 43.7 - - + +
222A ASN* 3.6 12.6 - - - +
223A ARG 2.5 4.8 + - - -
224A LEU* 1.3 71.5 - - - +
226A ALA* 1.3 58.7 + - - +
228A ARG* 2.8 7.5 + - + +
229A ALA* 2.8 28.3 + - + +
388A PHE* 4.2 17.7 - - + -
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Residues in contact with ALA 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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176A LEU* 4.1 19.5 - - + +
179A VAL* 4.1 11.9 - - + -
180A MET* 3.5 33.7 - - + +
222A ASN 3.0 14.2 + - - +
223A ARG 2.6 12.2 + - - +
225A VAL* 1.3 68.3 - - - +
227A ILE* 1.3 64.0 + - - +
229A ALA* 3.7 8.6 - - - +
230A GLN* 3.2 19.9 + - - +
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Residues in contact with ILE 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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179A VAL* 3.8 14.6 - - + -
183A THR* 3.8 25.6 - - + +
194A ILE* 3.9 30.5 - - + +
196A ILE* 3.9 34.3 - - + +
223A ARG 2.8 10.0 + - - +
224A LEU* 3.4 18.4 - - + +
226A ALA* 1.3 78.3 - - - +
228A ARG* 1.3 64.7 + - - +
231A ALA* 3.4 20.4 + - - +
238A LEU* 5.0 5.4 - - + -
240A ALA* 4.4 21.8 - - + -
241A ILE 6.1 0.4 - - - +
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Residues in contact with ARG 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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27A TRP* 3.7 25.0 - - - -
30A THR* 4.1 24.3 - - - +
32A ARG* 4.1 22.0 - - + +
34A PHE* 4.5 7.0 - - + -
224A LEU 3.1 11.0 + - - +
225A VAL* 2.8 10.6 + - + +
227A ILE* 1.3 81.8 + - + +
229A ALA* 1.3 67.2 + - - +
230A GLN 3.2 0.2 - - - -
231A ALA* 3.7 20.8 - - - +
232A ASP* 2.9 36.0 + - - +
238A LEU* 2.6 32.3 + - - +
240A ALA* 4.0 16.5 - - - +
388A PHE 5.4 4.4 + - - +
390A ASP* 3.8 18.0 + - - -
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Residues in contact with ALA 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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34A PHE* 3.9 25.7 - - + -
39A ILE* 4.2 9.3 - - + +
180A MET* 4.7 9.9 - - - -
225A VAL* 2.8 14.0 + - + +
226A ALA* 3.7 10.5 - - - +
228A ARG* 1.3 79.5 - - - +
230A GLN* 1.3 57.8 + - - +
232A ASP* 3.2 4.0 + - - +
233A ILE* 2.9 35.1 + - + +
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Residues in contact with GLN 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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180A MET* 3.3 56.9 + - + +
181A LYS* 5.6 0.2 - - - +
183A THR* 3.9 16.6 - - + -
184A LYS* 4.3 14.4 + - - +
226A ALA 3.2 9.7 + - - +
227A ILE 4.0 0.2 - - - +
229A ALA* 1.3 73.5 - - - +
231A ALA* 1.3 69.2 + - - +
232A ASP 2.9 1.1 - - - -
233A ILE* 2.6 33.5 + - - +
234A MET* 2.9 41.2 + - + +
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Residues in contact with ALA 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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183A THR* 4.5 4.1 - - - +
227A ILE 3.4 14.6 + - - +
228A ARG* 3.5 32.1 + - - +
230A GLN* 1.3 76.7 - - - +
232A ASP* 1.3 52.5 + - - +
234A MET* 3.4 3.7 - - - -
235A GLY 2.7 29.3 + - - -
236A THR* 3.0 39.9 + - + +
238A LEU* 4.2 8.7 - - + -
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Residues in contact with ASP 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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21A TRP* 3.5 20.2 - - + -
22A TRP* 3.2 21.4 - - + -
27A TRP* 4.9 0.2 - - - -
32A ARG* 3.2 36.9 + - - -
34A PHE* 3.5 11.4 - - - -
39A ILE* 3.9 18.4 - - + +
43A ARG* 3.3 10.2 + - - -
228A ARG* 2.9 27.0 + - - +
229A ALA 3.2 5.4 - - - +
230A GLN 2.7 1.2 + - - -
231A ALA* 1.3 75.4 - - - +
233A ILE* 1.3 67.6 + - - +
235A GLY* 3.0 9.9 + - - -
236A THR 4.8 0.3 - - - +
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Residues in contact with ILE 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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39A ILE* 4.0 31.0 - - + +
42A LYS* 3.5 35.4 - - + +
43A ARG* 2.8 44.4 + - + +
47A LYS* 4.2 2.4 + - - -
180A MET* 6.3 2.7 - - - -
184A LYS* 6.3 0.7 - - - +
229A ALA* 2.9 21.5 + - + +
230A GLN* 2.6 27.3 + - - +
232A ASP* 1.3 66.3 - - - +
234A MET* 1.3 59.5 + - + +
235A GLY 2.8 14.1 + - - -
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Residues in contact with MET 234 (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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47A LYS* 4.3 7.9 + - - +
48A ILE 4.4 1.8 - - - +
50A TYR* 3.8 44.6 + - + +
184A LYS* 3.4 41.1 - - + +
187A VAL* 2.7 53.6 - - + +
230A GLN* 2.9 28.9 + - - +
231A ALA* 3.7 3.4 - - - +
233A ILE* 1.3 76.7 - - + +
235A GLY* 1.3 68.1 + - - +
236A THR* 3.5 3.6 + - + -
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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
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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