Contacts of the helix formed by residues 221 - 237 (chain A) in PDB entry 3O75
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 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ASP* 5.8 0.7 - - - -
219A ALA* 2.9 16.5 + - - +
220A PHE* 1.3 74.6 - - - +
222A ARG* 1.3 59.7 + - - +
223A GLU* 3.9 18.5 + - - -
224A CYS* 3.1 25.3 + - - +
225A GLY 2.9 24.3 + - - -
249A VAL* 3.3 11.3 - - - +
250A LEU* 3.5 7.8 - - - +
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Residues in contact with ARG 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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221A SER* 1.3 73.6 - - - +
223A GLU* 1.3 63.1 + - - +
225A GLY 3.3 0.5 + - - -
226A GLN* 3.1 6.8 + - - +
249A VAL* 3.3 23.3 - - + +
252A GLN* 3.9 24.2 - - + +
253A GLY* 3.0 33.7 - - - +
256A ASP* 2.7 42.4 + - - +
277B GLN* 3.6 30.3 - - - +
280B ASP* 5.4 3.6 + - - -
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Residues in contact with GLU 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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221A SER* 3.2 15.5 + - - +
222A ARG* 1.3 80.3 - - - +
224A CYS* 1.3 67.4 + - - +
226A GLN* 3.2 15.4 + - - +
227A ARG* 2.7 67.2 + - - +
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Residues in contact with CYS 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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187A ALA* 5.1 0.2 - - - -
217A GLY* 3.7 21.1 - - - -
218A GLU* 3.0 35.4 - - - +
219A ALA 3.3 21.1 - - - +
221A SER* 3.1 20.4 + - - +
223A GLU* 1.3 84.3 - - + +
225A GLY* 1.3 62.5 + - - +
227A ARG* 3.3 6.8 + - - +
228A LEU* 3.0 38.1 + - - +
250A LEU* 4.5 1.3 - - + -
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Residues in contact with GLY 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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185A ILE* 4.6 3.4 - - - +
221A SER 2.9 12.7 + - - -
222A ARG 3.3 2.4 + - - -
223A GLU 3.3 0.2 - - - -
224A CYS* 1.3 77.0 - - - +
226A GLN* 1.3 61.2 + - - +
228A LEU* 3.6 5.9 + - - +
229A MET* 3.1 24.6 + - - +
250A LEU* 3.7 31.6 - - - +
253A GLY 3.9 7.7 - - - -
254A VAL* 4.1 4.9 + - - +
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Residues in contact with GLN 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 ARG* 3.1 11.6 + - - +
223A GLU* 3.4 15.9 - - - +
224A CYS 3.2 0.2 - - - -
225A GLY* 1.3 74.1 - - - +
227A ARG* 1.3 67.4 + - + +
229A MET 3.3 1.2 + - - -
230A GLN* 3.1 25.5 + - + +
253A GLY* 3.3 19.2 - - - +
256A ASP* 4.5 20.0 - - + +
257A THR* 3.2 25.1 + - - +
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Residues in contact with ARG 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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218A GLU* 3.3 24.5 + - - +
223A GLU* 2.7 56.4 + - - +
224A CYS* 3.3 8.9 + - - +
226A GLN* 1.3 78.7 - - + +
228A LEU* 1.3 65.8 + - + +
230A GLN* 3.2 8.1 + - - +
231A GLN* 2.9 36.3 + - - +
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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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185A ILE* 3.7 28.3 - - + -
186A GLY 3.4 25.8 - - - +
215A TYR* 3.9 28.0 - - + +
216A GLN 4.6 2.5 - - - +
217A GLY* 3.8 22.0 - - - +
218A GLU* 5.9 0.9 - - - +
224A CYS* 3.0 26.3 + - - +
225A GLY* 3.9 3.6 - - - +
227A ARG* 1.3 76.5 - - + +
229A MET* 1.3 59.5 + - - +
231A GLN* 3.1 23.6 + - - +
232A LEU* 2.8 28.9 + - - +
250A LEU* 4.9 1.1 - - + -
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Residues in contact with MET 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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185A ILE* 3.9 12.0 - - - +
225A GLY 3.1 19.0 + - - +
226A GLN 3.6 4.7 - - - +
227A ARG 3.3 0.2 - - - -
228A LEU* 1.3 76.6 - - - +
230A GLN* 1.3 56.8 + - - +
232A LEU* 3.4 10.0 + - - +
233A ILE* 3.1 47.9 + - + +
239A LEU* 4.6 1.6 - - + -
240A PRO* 4.4 11.4 - - + -
243A LEU* 3.7 32.1 - - + -
254A VAL* 4.0 22.9 - - + +
257A THR* 3.7 26.0 - - + +
258A LEU* 4.3 14.8 - - + -
268A LEU* 4.3 13.2 - - + -
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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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226A GLN* 3.1 17.0 + - + +
227A ARG* 3.5 10.8 - - - +
228A LEU 3.1 0.2 - - - -
229A MET* 1.3 75.6 - - - +
231A GLN* 1.3 65.0 + - - +
233A ILE* 3.5 14.2 + - - +
234A ASP* 3.2 23.2 + - - +
257A THR* 3.7 26.6 + - - +
260A ALA* 5.8 3.1 - - - +
261A ARG* 6.1 0.4 - - - +
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Residues in contact with GLN 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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215A TYR* 3.7 32.5 + - + +
227A ARG* 2.9 26.2 + - - +
228A LEU* 3.4 23.5 - - - +
230A GLN* 1.3 77.7 - - + +
232A LEU* 1.3 63.0 + - - +
234A ASP* 3.3 12.6 - - - +
235A ASP* 3.1 20.6 + - - +
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Residues in contact with LEU 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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183A ALA* 3.4 24.7 - - + -
185A ILE* 4.5 6.1 - - + -
213A ARG* 3.6 36.8 - - + -
215A TYR* 3.6 18.6 - - + -
228A LEU 2.8 15.7 + - - +
229A MET* 3.7 13.9 - - - +
230A GLN 3.2 0.2 - - - -
231A GLN* 1.3 77.7 - - - +
233A ILE* 1.3 58.0 + - - +
235A ASP* 3.1 5.4 - - + +
236A LEU* 3.0 33.6 + - + +
240A PRO* 3.7 26.0 - - + -
243A LEU* 4.1 12.3 - - + -
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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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229A MET* 3.1 30.7 + - + +
230A GLN* 4.0 13.9 - - - +
232A LEU* 1.3 73.4 - - - +
234A ASP* 1.3 57.1 + - - +
237A GLY* 2.8 32.1 + - - -
238A GLY* 3.0 28.7 + - - +
239A LEU* 3.5 29.4 - - + -
240A PRO* 4.9 1.3 - - + -
257A THR* 3.7 25.6 - - + -
258A LEU* 5.4 0.4 - - + -
261A ARG* 3.8 26.0 - - - +
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Residues in contact with ASP 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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230A GLN 3.2 15.1 + - - +
231A GLN* 3.3 9.2 - - - +
233A ILE* 1.3 77.3 - - - +
235A ASP* 1.3 71.4 + - - +
237A GLY* 3.6 7.6 + - - -
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Residues in contact with ASP 235 (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 ARG* 3.1 39.9 + - - -
215A TYR* 2.8 29.9 + - + +
231A GLN 3.1 7.3 + - - +
232A LEU* 3.1 12.8 - - + +
234A ASP* 1.3 83.9 + - - +
236A LEU* 1.3 62.3 + - + +
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Residues in contact with LEU 236 (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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181A SER* 4.1 11.4 - - - +
182A ILE 6.3 0.4 - - - -
183A ALA* 5.6 0.2 - - + -
211A GLU* 4.8 11.7 - - + -
213A ARG* 3.8 39.3 - - + +
232A LEU* 3.0 25.0 + - + +
235A ASP* 1.3 77.3 - - - +
237A GLY* 1.3 60.3 + - - +
238A GLY* 3.3 15.6 + - - +
239A LEU 4.4 1.3 - - - +
240A PRO* 3.6 41.5 - - + -
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Residues in contact with GLY 237 (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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233A ILE* 2.8 10.2 + - - -
234A ASP* 3.6 7.0 + - - -
235A ASP 3.4 3.2 + - - -
236A LEU* 1.3 78.8 - - - +
238A GLY* 1.3 56.9 + - - +
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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