Contacts of the helix formed by residues 215 - 228 (chain A) in PDB entry 3ROT
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 THR 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ASP* 4.3 7.4 - - - -
157A PRO* 3.5 10.4 - - + +
158A GLN* 5.0 0.4 - - - +
164A LEU* 3.6 33.0 - - + -
213A CYS* 3.2 9.1 - - - +
214A LEU* 1.3 84.9 - - - +
216A SER* 1.3 63.4 + - - +
217A GLN* 3.0 36.0 + - - +
218A ALA* 3.2 10.0 + - - +
219A LEU 3.4 6.6 + - - -
242A SER* 4.1 6.3 - - - -
243A PHE 4.2 7.4 - - - -
244A ASP* 4.4 2.2 - - - -
317A GOL 4.0 18.6 - - - +
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Residues in contact with SER 216 (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 ASP* 2.5 36.1 + - - -
35A PRO* 4.3 2.9 - - - +
215A THR* 1.3 74.5 - - - +
217A GLN* 1.3 56.2 + - - +
218A ALA 3.1 0.4 - - - -
219A LEU* 3.6 9.6 - - - -
220A ASP* 2.9 41.5 + - - +
242A SER* 4.6 0.4 - - - -
243A PHE 3.8 12.1 + - - -
244A ASP* 4.4 2.7 + - - -
246A THR* 3.7 27.5 - - - +
249A THR* 4.2 7.0 - - - -
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Residues in contact with GLN 217 (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 ASP* 3.7 29.0 - - + +
37A TRP* 5.7 2.2 - - - +
63A ALA* 3.1 35.2 + - - +
157A PRO* 3.8 14.9 - - + +
158A GLN* 2.9 29.4 + - - +
188A GLY 5.2 0.5 - - - +
189A THR* 3.8 21.3 - - + +
194A VAL* 4.6 5.0 - - - +
215A THR* 3.0 16.7 + - - +
216A SER* 1.3 79.1 + - - +
218A ALA* 1.3 56.9 + - - +
220A ASP* 4.6 4.5 - - - -
221A PRO* 3.2 22.5 - - - +
317A GOL 6.1 0.2 - - - -
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Residues in contact with ALA 218 (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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155A LEU* 4.0 31.4 - - + +
157A PRO* 4.4 10.4 - - + +
187A VAL* 4.4 10.1 - - + -
194A VAL* 3.9 9.7 - - - +
213A CYS* 4.0 15.2 - - + -
214A LEU 4.7 0.2 - - - +
215A THR* 3.2 9.6 + - - +
216A SER 3.1 0.4 - - - -
217A GLN* 1.3 78.1 - - - +
219A LEU* 1.3 65.8 + - - +
221A PRO* 3.4 14.8 - - - +
222A LEU* 3.5 12.0 + - - +
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Residues in contact with LEU 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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213A CYS* 3.7 15.4 - - - -
215A THR 3.4 1.8 + - - -
216A SER* 3.2 11.1 + - - +
218A ALA* 1.3 77.9 - - - +
220A ASP* 1.3 56.7 + - - +
222A LEU* 3.0 9.8 + - + +
223A GLY* 2.6 35.6 + - - +
226A LEU* 5.1 0.9 - - + -
240A VAL* 3.8 29.4 - - + -
242A SER* 3.8 21.8 - - - +
249A THR* 3.6 42.6 - - + +
252A LEU* 4.2 11.9 - - + -
258A VAL* 4.0 17.3 - - + -
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Residues in contact with ASP 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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35A PRO* 5.0 11.0 - - - +
216A SER* 2.9 31.1 + - - +
217A GLN* 4.6 3.5 - - - +
219A LEU* 1.3 72.2 - - - +
221A PRO* 1.3 70.8 - - + +
223A GLY* 3.1 11.4 + - - -
224A GLN* 3.1 12.6 + - - +
246A THR* 4.8 5.0 + - - -
248A ASN* 3.3 37.2 + - - +
249A THR* 5.3 1.2 + - - -
35B PRO* 6.3 2.9 - - + -
247B PRO* 6.1 0.3 - - - +
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Residues in contact with PRO 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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189A THR 5.5 0.2 - - - +
191A PRO* 3.6 43.1 - - + +
194A VAL* 3.7 20.0 - - + -
195A GLN* 3.0 34.2 + - + +
217A GLN 3.2 20.4 - - - +
218A ALA 3.4 12.8 - - - +
220A ASP* 1.3 96.3 - - + +
222A LEU* 1.3 59.3 + - - +
224A GLN* 3.5 8.9 + - + +
225A MSE 3.7 2.6 - - - +
38B THR* 6.1 0.2 - - + -
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Residues in contact with LEU 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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155A LEU* 4.3 7.0 - - + -
194A VAL* 4.9 3.8 - - + +
198A VAL* 4.6 5.4 - - + -
211A ILE* 3.8 30.3 - - + -
213A CYS* 3.8 25.1 - - - -
218A ALA 3.6 9.9 - - - +
219A LEU* 3.0 8.6 + - + +
221A PRO* 1.3 81.2 - - - +
223A GLY* 1.3 65.1 + - - +
225A MSE 3.0 37.9 + - + +
226A LEU* 3.1 21.3 + - + +
234A PHE* 4.1 18.6 - - + -
240A VAL* 4.2 15.9 - - + -
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Residues in contact with GLY 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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219A LEU* 2.6 21.1 + - - -
220A ASP 3.1 2.9 + - - -
222A LEU* 1.3 73.8 - - - +
224A GLN* 1.3 60.1 + - - +
226A LEU* 3.3 13.4 + - - +
227A LEU* 3.1 34.1 + - - +
248A ASN* 5.2 1.8 - - - -
252A LEU* 4.0 22.2 - - - +
247B PRO* 5.8 0.2 - - - -
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Residues in contact with GLN 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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195A GLN* 3.3 7.7 + - - +
220A ASP 3.1 10.3 + - - +
221A PRO* 3.7 11.2 - - + +
222A LEU 3.1 0.6 - - - -
223A GLY* 1.3 77.1 - - - +
225A MSE 1.3 62.0 + - - +
227A LEU* 3.4 11.2 + - - +
228A HIS* 3.2 25.4 + - + +
232A TYR* 3.0 28.7 + - + +
35B PRO* 3.0 40.5 + - - +
38B THR* 2.6 25.8 + - - -
39B SER* 3.4 10.5 + - - -
247B PRO* 4.4 18.2 - - + +
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Residues in contact with MSE 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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195A GLN* 3.6 32.1 - - - +
198A VAL* 4.0 26.2 - - + -
199A LYS* 3.7 30.5 - - + -
221A PRO 3.7 2.5 - - - +
222A LEU* 3.0 31.6 + - + +
224A GLN* 1.3 74.9 - - - +
226A LEU* 1.3 60.2 + - - +
227A LEU 3.1 0.4 - - - -
228A HIS 3.1 0.7 - - - -
229A PRO* 2.9 34.7 - - - +
232A TYR* 3.6 33.7 - - + -
234A PHE* 4.0 24.8 - - + +
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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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219A LEU* 5.1 0.9 - - + -
222A LEU* 3.1 19.3 + - + +
223A GLY* 3.3 20.6 + - - +
225A MSE 1.3 76.5 - - - +
227A LEU* 1.3 60.3 + - - +
229A PRO* 3.7 11.3 - - - +
234A PHE* 4.3 15.5 - - + +
237A GLN* 5.2 4.3 - - - -
238A PRO* 4.1 31.9 - - + +
240A VAL* 4.1 14.8 - - + -
252A LEU* 5.0 0.9 - - + -
257A LEU* 3.8 57.8 - - + +
258A VAL* 4.9 5.6 - - + -
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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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223A GLY 3.1 21.7 + - - +
224A GLN* 3.7 2.7 - - - +
225A MSE 3.1 0.4 - - - -
226A LEU* 1.3 78.8 - - - +
228A HIS* 1.3 82.5 + - + +
229A PRO* 3.5 5.7 - - - +
248A ASN* 5.2 1.6 - - - +
252A LEU* 4.0 13.0 - - + -
255A LYS* 3.6 27.8 - - + -
257A LEU* 3.5 20.4 - - + -
247B PRO* 3.7 37.9 - - + -
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Residues in contact with HIS 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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224A GLN* 3.2 18.8 + - + +
225A MSE 3.1 3.6 - - - -
227A LEU* 1.3 101.9 + - + +
229A PRO* 1.3 66.1 - - - +
230A ASP 3.3 2.5 - - - -
231A ARG* 3.2 59.4 + - + -
232A TYR* 3.2 23.6 - + + -
247B PRO* 5.7 4.7 - - + -
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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