Contacts of the helix formed by residues 212 - 233 (chain A) in PDB entry 3EFC
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 ARG 212 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A GLU* 5.5 4.9 - - - +
209A VAL* 3.1 27.3 - - + +
211A ASP* 1.3 79.2 - - - +
213A LYS* 1.3 59.9 + - - +
214A TYR 3.2 2.9 - - - -
215A GLN* 3.2 16.5 + - + +
216A LYS* 2.9 26.7 + - - +
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Residues in contact with LYS 213 (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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208A VAL 4.3 5.8 - - - +
209A VAL 2.8 18.8 + - - +
211A ASP* 3.5 3.0 - - + +
212A ARG* 1.3 74.8 - - - +
214A TYR* 1.3 59.4 + - - +
216A LYS* 3.6 7.9 - - - +
217A GLN* 2.8 35.7 + - + +
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Residues in contact with TYR 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLU 5.7 0.2 - - - -
203A VAL* 3.4 20.0 - - + -
204A PRO* 3.5 30.9 - - + +
205A TRP* 5.0 9.1 - + - -
207A ASN* 3.2 26.7 - - - +
208A VAL 4.8 1.3 + - - -
209A VAL* 3.4 23.9 - - + +
213A LYS* 1.3 74.8 - - - +
215A GLN* 1.3 65.8 + - - +
217A GLN* 2.9 20.6 + - - +
218A LYS* 2.6 79.6 + - + +
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Residues in contact with GLN 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A GLU* 3.1 25.8 - - - +
177A ILE* 3.8 19.9 - - + +
199A LEU* 3.9 6.4 - - + +
200A ARG 3.5 12.5 + - - +
202A GLU 3.2 18.9 - - - +
203A VAL* 3.3 32.7 - - - +
209A VAL* 3.8 4.8 - - - +
212A ARG* 3.2 21.1 + - + +
214A TYR* 1.3 81.4 - - - +
216A LYS* 1.3 52.2 + - - +
218A LYS* 3.7 5.7 - - - +
219A LEU* 2.6 39.2 + - - +
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Residues in contact with LYS 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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212A ARG 2.9 13.7 + - - +
213A LYS* 3.6 11.0 - - - +
214A TYR 3.2 0.2 - - - -
215A GLN* 1.3 70.2 - - - +
217A GLN* 1.3 68.9 + - - +
219A LEU* 2.8 8.2 + - - +
220A ALA* 2.8 25.7 + - - +
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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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213A LYS* 2.8 21.4 + - + +
214A TYR* 2.9 27.8 + - - +
216A LYS* 1.3 73.4 - - - +
218A LYS* 1.3 63.7 + - + +
220A ALA* 3.2 7.3 + - - +
221A GLY* 3.0 23.0 + - - -
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Residues in contact with LYS 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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198A GLN* 3.6 38.0 + - + +
199A LEU* 4.1 13.0 - - + -
214A TYR* 2.6 72.1 + - + +
215A GLN* 3.7 6.3 - - - +
217A GLN* 1.3 77.2 - - - +
219A LEU* 1.3 65.5 + - - +
221A GLY* 3.2 2.7 + - - +
222A ASP* 2.9 28.4 + - - +
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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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177A ILE* 5.4 2.7 - - + -
180A ILE* 4.4 11.7 - - + -
199A LEU* 3.5 21.2 - - + +
215A GLN 2.6 22.3 + - - +
216A LYS* 2.8 6.5 + - - +
218A LYS* 1.3 72.7 - - - +
220A ALA* 1.3 59.9 + - - +
222A ASP* 3.5 5.7 + - + +
223A LEU* 3.0 51.7 + - + +
243A THR* 4.6 7.4 - - + -
256A VAL* 3.8 36.3 - - + -
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Residues in contact with ALA 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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216A LYS 2.8 12.7 + - - +
217A GLN* 3.4 11.7 - - - +
219A LEU* 1.3 77.4 - - - +
221A GLY* 1.3 53.3 + - - +
223A LEU* 3.0 8.9 + - - +
224A GLU* 2.8 36.8 + - - +
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Residues in contact with GLY 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 GLN 3.0 13.2 + - - -
218A LYS* 3.7 3.6 - - - -
220A ALA* 1.3 76.5 - - - +
222A ASP* 1.3 61.5 + - - +
224A GLU* 3.0 10.9 + - - +
225A THR* 2.8 27.3 + - - -
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Residues in contact with ASP 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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180A ILE* 4.7 2.6 - - + +
197A PHE* 2.9 53.1 - - + +
198A GLN* 2.9 40.5 + - - +
199A LEU* 3.3 14.4 - - - +
218A LYS* 2.9 11.7 + - - +
219A LEU* 3.7 7.4 - - + +
221A GLY* 1.3 77.1 - - - +
223A LEU* 1.3 58.2 + - + +
225A THR* 2.8 26.2 + - - -
226A LEU 2.9 10.4 + - - -
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Residues in contact with LEU 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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197A PHE* 5.3 1.8 - - + -
219A LEU* 3.0 43.8 + - + +
220A ALA* 3.6 6.5 - - - +
222A ASP* 1.3 76.8 - - + +
224A GLU* 1.3 61.9 + - - +
226A LEU* 3.6 9.0 + - + +
227A ARG* 3.5 16.4 + - - +
240A ILE* 3.5 41.2 - - + +
243A THR* 3.5 26.9 - - + +
258A VAL* 3.3 34.3 - - + -
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Residues in contact with GLU 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 ALA 2.8 13.1 + - - +
221A GLY* 3.2 14.1 - - - +
222A ASP 2.9 0.2 - - - -
223A LEU* 1.3 77.8 - - - +
225A THR* 1.3 59.3 + - - +
227A ARG* 3.0 38.3 + - - +
228A SER* 2.9 41.1 + - - +
231A LEU* 6.1 0.3 - - - +
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Residues in contact with THR 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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193A LEU 5.6 3.6 - - - +
196A HIS* 4.9 18.8 - - + -
197A PHE* 4.5 9.8 - - + -
221A GLY 2.8 15.7 + - - -
222A ASP* 3.2 11.8 + - - -
224A GLU* 1.3 75.5 - - - +
226A LEU* 1.3 65.6 + - - +
228A SER* 3.8 7.1 - - - -
229A TYR* 2.9 27.9 + - + +
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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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182A ILE* 3.9 26.7 - - + -
193A LEU* 4.5 14.6 - - + -
197A PHE* 4.4 13.6 - - + -
222A ASP 2.9 10.4 + - - +
223A LEU* 3.7 20.2 - - + +
225A THR* 1.3 79.5 - - - +
227A ARG* 1.3 65.1 + - - +
229A TYR* 3.2 14.0 - - - +
230A TYR* 3.5 23.0 + - + -
238A PHE* 3.5 24.7 - - + -
240A ILE* 4.9 1.1 - - + -
258A VAL* 3.5 32.1 - - + -
260A ILE* 4.0 4.9 - - + -
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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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223A LEU* 3.5 7.6 + - - +
224A GLU* 3.0 40.7 + - - +
226A LEU* 1.3 78.1 - - - +
228A SER* 1.3 55.9 + - - +
229A TYR 2.7 12.5 + - - -
230A TYR* 2.9 14.4 + - - +
231A LEU* 3.1 37.4 + - + +
238A PHE* 3.3 38.8 + - + -
239A ASN* 5.6 2.4 + - - -
240A ILE* 3.8 31.3 - - + +
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Residues in contact with SER 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 GLU* 2.9 31.9 + - - +
225A THR* 3.3 8.9 + - - -
227A ARG* 1.3 71.3 - - - +
229A TYR* 1.3 57.2 + - - +
231A LEU* 4.6 10.4 - - - +
232A ASP* 2.6 44.2 + - - +
299A THR* 5.0 5.5 + - - -
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Residues in contact with TYR 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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188A PHE* 3.6 27.0 - + - -
192A GLU* 3.7 41.7 + - - +
193A LEU* 3.9 23.8 - - + -
196A HIS* 5.9 6.1 - + - -
225A THR* 2.9 16.4 + - + +
226A LEU* 3.2 13.2 - - - +
227A ARG 2.7 3.4 + - - -
228A SER* 1.3 70.3 - - - +
230A TYR* 1.3 74.0 + + + +
232A ASP* 2.8 15.1 + - - +
233A ARG* 3.0 71.7 + - - +
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Residues in contact with TYR 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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185A ASN* 3.4 11.8 - - - +
187A ALA* 4.5 1.8 - - + -
188A PHE* 3.7 24.7 + + - -
193A LEU* 3.6 18.2 - - + +
226A LEU* 3.7 20.2 - - + -
227A ARG 2.9 8.1 + - - +
229A TYR* 1.3 83.5 - + - +
231A LEU* 1.3 58.5 + - - +
233A ARG* 2.9 16.8 + - - -
235A TYR* 3.3 41.1 + + + -
238A PHE* 3.6 34.3 - + + -
260A ILE* 3.2 26.3 - - + +
262A GLU* 2.5 45.9 + - + -
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Residues in contact with LEU 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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224A GLU* 6.1 0.4 - - - +
227A ARG* 3.1 44.4 + - + +
228A SER* 4.4 6.7 - - - +
229A TYR 2.9 1.0 + - - -
230A TYR* 1.3 68.6 - - - +
232A ASP* 1.3 56.3 + - - +
233A ARG 2.6 15.9 + - - -
234A GLY 3.0 10.7 + - - -
235A TYR 3.4 23.1 - - - +
236A ALA* 4.6 7.0 - - - -
237A ARG 5.2 0.4 - - - +
238A PHE* 4.2 14.1 - - + +
296A TYR* 3.7 13.2 - - + +
297A ASN* 3.5 3.5 - - - -
298A GLY* 3.3 28.8 + - - +
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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
----------------------------------------------------------
228A SER* 2.6 28.1 + - - +
229A TYR* 2.8 10.2 + - - +
231A LEU* 1.3 73.9 - - - +
233A ARG* 1.3 69.3 + - - +
234A GLY 3.7 0.2 - - - -
296A TYR 4.3 0.2 - - - +
297A ASN* 2.8 33.3 + - - +
298A GLY* 3.9 1.8 - - - +
299A THR* 2.7 48.3 + - - -
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Residues in contact with ARG 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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188A PHE* 3.4 29.7 - - + -
229A TYR* 3.0 75.3 + - - +
230A TYR 2.9 9.4 + - - +
231A LEU 2.6 7.7 + - - -
232A ASP* 1.3 86.5 - - - +
234A GLY* 1.3 50.2 + - - +
235A TYR* 3.6 11.2 - - + -
265A GLN* 2.7 32.3 + - - +
295A LEU* 3.7 6.1 - - - +
296A TYR 3.9 2.9 - - - -
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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