Contacts of the helix formed by residues 209 - 230 (chain A) in PDB entry 5CEO
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 209 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A PRO* 3.1 14.4 + - + +
208A VAL* 1.3 73.8 - - - +
210A PRO* 1.4 74.6 - - - +
211A SER* 3.9 7.5 + - - -
212A LEU* 3.0 27.6 + - + +
213A LEU* 2.9 19.9 + - - +
376A GLN* 3.6 33.7 - - - +
380A PHE* 3.6 14.8 - - + -
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Residues in contact with PRO 210 (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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209A THR* 1.4 86.6 - - - +
211A SER* 1.3 59.1 + - - +
213A LEU* 3.5 12.6 + - + +
214A VAL* 3.2 30.1 + - - +
371A VAL* 3.2 35.0 - - + +
372A LEU* 3.9 9.2 - - + +
374A THR 3.9 13.7 - - - +
376A GLN* 4.0 17.9 - - + +
379A TYR* 3.7 32.7 - - + -
380A PHE* 4.5 0.2 - - + -
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Residues in contact with SER 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A THR* 3.1 8.7 - - - -
210A PRO* 1.3 79.3 - - - +
212A LEU* 1.4 57.3 + - - +
214A VAL* 3.3 4.3 + - - +
215A ASP* 2.9 39.6 + - - +
372A LEU* 3.6 20.5 - - - +
376A GLN* 5.9 2.9 - - - -
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Residues in contact with LEU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ARG* 3.4 35.4 - - + +
207A PRO 3.6 22.9 - - - +
208A VAL* 4.0 10.1 - - + -
209A THR* 3.0 21.5 + - + +
211A SER* 1.4 75.4 - - - +
213A LEU* 1.4 61.3 + - - +
215A ASP* 4.4 8.7 - - + +
216A TRP* 3.0 68.7 + - + +
248A ASP* 4.4 10.8 - - + +
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Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A VAL* 3.7 14.5 - - + +
209A THR 2.9 11.8 + - - +
210A PRO* 3.7 8.1 - - + +
211A SER 3.3 0.2 - - - -
212A LEU* 1.4 76.2 - - - +
214A VAL* 1.3 52.2 + - - +
217A SER* 2.8 38.5 + - - -
300A LEU* 4.1 6.7 - - + -
303A LEU* 3.9 24.6 - - + +
304A LEU* 4.0 24.5 - - + +
339A PHE* 3.8 35.2 - - + -
371A VAL* 4.2 17.0 - - + -
379A TYR* 3.3 28.0 - - + +
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Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A PRO 3.2 17.6 + - - +
211A SER 3.6 4.0 - - - +
212A LEU 3.3 0.2 - - - -
213A LEU* 1.3 76.8 - - + +
215A ASP* 1.3 69.7 + - - +
217A SER* 3.9 4.7 - - - -
218A MET* 3.1 46.7 + - + +
339A PHE* 5.2 4.0 - - + -
364A LEU* 5.6 0.9 - - + +
368A SER* 3.8 33.4 - - - -
371A VAL* 4.0 18.6 - - + -
372A LEU* 4.1 16.4 - - + -
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Residues in contact with ASP 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASN* 5.3 0.3 + - - -
211A SER* 2.9 24.5 + - - +
212A LEU* 4.2 10.4 - - + +
214A VAL* 1.3 79.8 - - - +
216A TRP* 1.3 69.5 + - + +
218A MET* 4.5 2.1 - - - +
219A GLY* 3.0 24.9 + - - -
248A ASP 5.4 2.7 - - - +
250A VAL* 4.4 2.1 - - - +
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Residues in contact with TRP 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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198A LEU* 3.6 28.7 - - + -
201A VAL* 3.9 18.8 - - + -
206A ARG* 3.7 28.5 - - + -
208A VAL* 4.3 17.9 - - + -
212A LEU* 3.0 44.1 + - + +
215A ASP* 1.3 82.6 - - + +
217A SER* 1.4 57.3 + - - +
220A ILE* 3.0 38.4 + - + +
244A ILE* 3.9 26.9 - - + +
248A ASP* 2.8 30.6 + - - +
250A VAL* 3.5 24.3 - - + +
303A LEU* 3.8 20.9 - - + -
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Residues in contact with SER 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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213A LEU* 2.8 25.4 + - - +
214A VAL* 3.6 5.5 + - - -
216A TRP* 1.4 77.5 - - - +
218A MET* 1.3 58.1 + - - +
220A ILE* 3.5 1.8 + - - -
221A ALA* 2.9 24.3 + - - +
296A PHE* 3.3 18.6 - - - -
300A LEU* 3.9 19.8 - - - +
303A LEU* 3.8 17.6 - - - +
339A PHE* 5.0 0.5 - - - -
364A LEU* 3.4 23.7 - - - +
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Residues in contact with MET 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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214A VAL* 3.1 34.1 + - + +
215A ASP* 4.5 1.6 - - - +
217A SER* 1.3 73.6 - - - +
219A GLY* 1.3 56.3 + - - +
221A ALA* 3.7 1.5 - - - -
222A GLY* 2.7 31.9 + - - -
361A LEU* 3.4 51.5 - - + +
364A LEU* 3.9 20.0 - - + -
365A ASP* 4.1 31.0 - - + +
368A SER* 5.2 0.7 - - - -
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Residues in contact with GLY 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASN* 3.2 38.8 - - - +
215A ASP 3.0 21.4 + - - -
216A TRP 3.8 0.7 - - - -
217A SER 3.3 0.2 - - - -
218A MET* 1.3 76.6 - - - +
220A ILE* 1.3 61.3 + - - +
222A GLY 3.3 0.2 + - - -
223A GLY 3.0 19.2 + - - -
250A VAL* 3.9 3.6 - - - -
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Residues in contact with ILE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU* 4.3 7.0 - - + -
216A TRP 3.0 26.7 + - - +
217A SER* 3.9 4.7 - - - +
219A GLY* 1.3 73.9 - - - +
221A ALA* 1.4 56.9 + - - +
223A GLY 3.3 1.0 + - - -
224A MET* 2.9 42.1 + - + +
237A LEU* 4.4 7.4 - - + -
242A MET* 3.9 25.8 - - + -
250A VAL* 3.7 27.1 - - + +
252A ILE* 3.6 8.6 - - + +
296A PHE* 3.8 21.5 - - + -
299A VAL* 3.9 28.3 - - + -
303A LEU* 4.6 4.7 - - + -
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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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217A SER 2.9 19.3 + - - +
218A MET 3.8 0.7 - - - +
219A GLY 3.4 0.2 - - - -
220A ILE* 1.4 74.3 - - - +
222A GLY* 1.3 56.0 + - - +
224A MET 3.6 0.2 + - - -
225A ASN* 3.0 30.1 + - - +
296A PHE* 3.9 4.0 - - + -
357A PHE* 3.7 19.1 - - + +
360A ILE* 3.9 27.1 - - + -
361A LEU* 3.8 20.8 - - + +
364A LEU* 4.1 4.3 - - + -
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Residues in contact with GLY 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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170A HIS* 3.4 20.4 + - - -
172A ASN* 5.1 0.7 - - - -
218A MET 2.7 21.2 + - - -
219A GLY 3.7 1.3 - - - -
221A ALA* 1.3 72.5 - - - +
223A GLY* 1.3 62.4 + - - +
225A ASN* 3.6 4.2 + - - +
226A TYR* 3.2 16.6 + - - +
361A LEU* 3.7 16.5 - - - +
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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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170A HIS* 3.5 22.0 - - - -
172A ASN* 4.4 1.1 - - - -
173A ILE* 3.7 7.3 - - - +
219A GLY 3.0 12.4 + - - -
222A GLY* 1.3 74.7 - - - +
224A MET* 1.3 58.3 + - - +
226A TYR* 3.5 4.2 - - - +
227A LEU* 3.2 28.6 + - - +
252A ILE* 3.6 19.7 - - - -
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Residues in contact with MET 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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220A ILE* 2.9 22.0 + - + +
223A GLY* 1.3 73.0 - - - +
225A ASN* 1.3 59.9 + - - +
227A LEU* 3.3 23.4 + - + +
228A HIS* 2.9 42.5 + - + +
234A HIS* 3.8 14.1 - - + +
237A LEU* 3.6 30.7 - - + -
252A ILE* 4.0 9.0 - - + -
292A ASP* 3.4 40.6 - - + +
357A PHE* 3.4 32.8 - - + -
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Residues in contact with ASN 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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221A ALA 3.0 19.6 + - - +
222A GLY 3.7 5.8 + - - +
223A GLY 3.4 0.2 - - - -
224A MET* 1.3 73.4 - - - +
226A TYR* 1.3 64.4 + - - +
228A HIS* 3.4 4.9 + - - +
229A LEU* 3.0 51.2 + - - +
357A PHE* 3.7 13.8 - - + +
358A ARG* 3.8 27.4 + - - +
361A LEU* 3.8 22.6 - - + +
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Residues in contact with TYR 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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167A LYS* 3.7 6.9 + - - -
168A LEU* 3.5 29.2 - - + +
169A LYS* 3.1 40.9 + - - +
170A HIS* 3.6 39.0 - + + -
173A ILE* 4.6 3.6 - - + -
222A GLY 3.2 4.1 + - - +
223A GLY 3.5 11.0 - - - +
225A ASN* 1.3 80.5 - - - +
227A LEU* 1.3 65.3 + - + +
229A LEU* 3.4 9.9 + - + +
230A HIS* 2.9 59.8 + + - -
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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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168A LEU* 4.5 7.2 - - + -
173A ILE* 3.8 24.7 - - + -
223A GLY 3.2 11.5 + - - +
224A MET* 3.3 33.8 + - + +
226A TYR* 1.3 87.1 - - + +
228A HIS* 1.3 62.5 + - - +
230A HIS* 3.1 11.7 + - - +
231A LYS 3.3 0.2 + - - -
232A ILE* 3.0 54.1 + - + +
234A HIS* 4.7 2.7 - - + +
252A ILE* 4.6 0.9 - - + -
255A PHE* 4.0 42.6 - - + -
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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 MET* 2.9 20.4 + - + +
225A ASN* 3.9 6.1 - - - +
227A LEU* 1.3 74.4 - - - +
229A LEU* 1.4 58.9 + - - +
231A LYS* 2.9 31.0 + - - +
232A ILE 3.1 22.2 - - - +
289A GLU* 3.2 58.2 + - + +
292A ASP* 2.6 24.8 + - - +
293A ILE* 4.7 4.3 - - + +
356A SER* 6.1 0.4 - - - -
357A PHE* 3.4 37.4 + + + +
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Residues in contact with LEU 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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225A ASN* 3.0 43.9 + - - +
226A TYR* 3.6 10.3 - - + +
227A LEU 3.3 0.2 - - - -
228A HIS* 1.4 76.7 - - + +
230A HIS* 1.3 65.4 + - + +
231A LYS* 3.2 13.3 + - - +
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Residues in contact with HIS 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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167A LYS* 3.4 37.9 + - - -
168A LEU* 3.8 7.4 - - + -
226A TYR* 2.9 49.6 + + - +
227A LEU 3.1 9.7 + - - +
229A LEU* 1.3 81.1 - - + +
231A LYS* 1.4 67.2 + - - +
232A ILE* 3.2 26.2 + - + +
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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