Contacts of the helix formed by residues 210 - 228 (chain A) in PDB entry 3GG0
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 ASP 210 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ILE* 4.0 12.1 - - + +
207A ALA* 2.8 28.4 + - - +
209A GLU* 1.3 94.4 - - - +
211A ARG* 1.3 58.2 + - - +
212A TYR 3.4 2.9 - - - -
213A ARG* 3.4 27.8 + - - +
214A PHE* 2.8 31.0 + - - +
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Residues in contact with ARG 211 (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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203A PHE* 3.1 58.6 + - + +
204A ALA* 3.9 14.6 + - - +
206A ILE* 3.3 15.9 + - + +
207A ALA 3.8 5.2 - - - +
208A ALA* 3.4 34.4 + - - +
209A GLU 3.4 0.6 - - - -
210A ASP* 1.3 76.6 - - - +
212A TYR* 1.3 64.0 + - + +
214A PHE* 3.9 4.4 - - - -
215A ASP* 2.9 30.9 + - - +
241A LEU* 6.3 2.5 - - + -
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Residues in contact with TYR 212 (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 GLU 5.0 5.7 + - - +
210A ASP 3.4 0.4 - - - -
211A ARG* 1.3 77.1 - - + +
213A ARG* 1.3 64.6 + - - +
215A ASP 3.3 0.9 + - - -
216A LEU* 3.2 19.8 + - - +
241A LEU* 3.9 27.9 - - + +
243A GLY* 3.6 36.8 + - - +
244A SER* 3.4 33.8 - - - -
247A HIS* 4.6 11.2 - - + -
277A GLU* 5.7 1.4 + - - -
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Residues in contact with ARG 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ILE* 4.4 4.2 - - - +
209A GLU 5.4 1.2 + - - +
210A ASP* 3.4 34.8 + - - +
212A TYR* 1.3 77.8 - - - +
214A PHE* 1.3 91.8 + - - +
216A LEU* 3.1 5.4 + - - +
217A GLU* 2.8 61.8 + - + +
247A HIS* 3.4 40.3 - - + +
248A HIS* 5.2 2.2 - - - +
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Residues in contact with PHE 214 (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 PRO* 3.9 25.6 - - + -
169A CYS* 4.0 9.2 - - + -
191A ILE* 4.0 11.7 - - + -
202A MET* 3.7 47.3 - - + -
203A PHE* 4.2 12.8 - + - -
206A ILE* 3.7 32.1 - - + -
210A ASP 2.8 21.2 + - - +
211A ARG* 3.9 3.6 - - - +
213A ARG* 1.3 98.5 - - - +
215A ASP* 1.3 58.6 + - - +
217A GLU* 3.8 4.0 - - + +
218A SER* 2.8 38.3 + - - -
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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
----------------------------------------------------------
203A PHE* 3.8 13.0 - - + -
211A ARG 2.9 19.0 + - - +
212A TYR 3.5 0.7 - - - +
213A ARG 3.2 0.2 - - - -
214A PHE* 1.3 76.7 - - - +
216A LEU* 1.3 58.8 + - - +
218A SER* 2.9 10.4 + - - -
219A LYS* 2.7 53.0 + - - +
240A LEU* 3.4 7.9 - - - +
241A LEU* 3.1 24.1 + - + +
244A SER* 2.7 26.3 + - - +
501A C2E 2.8 25.2 + - - -
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Residues in contact with LEU 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 TYR 3.2 8.5 + - - +
213A ARG* 3.1 9.2 + - - +
215A ASP* 1.3 77.8 - - - +
217A GLU* 1.3 68.2 + - - +
219A LYS* 3.3 12.0 + - - +
240A LEU* 4.0 20.4 - - + +
244A SER* 3.6 23.8 - - - +
245A LEU* 5.0 0.9 - - + -
247A HIS* 4.6 5.4 - - + +
248A HIS* 4.2 21.8 - - + -
251A ALA* 3.8 25.4 - - + +
254A TRP* 3.1 33.4 - - + -
255A LEU* 4.1 30.1 - - + -
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Residues in contact with GLU 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 ARG* 2.8 53.2 + - + +
214A PHE* 3.8 6.3 - - + +
216A LEU* 1.3 76.7 - - - +
218A SER* 1.3 63.4 + - - +
219A LYS 3.0 1.4 + - - -
220A ALA* 3.1 22.2 + - - +
221A TYR* 4.3 6.3 - - + -
248A HIS* 4.8 14.0 + - - -
254A TRP* 3.6 28.6 + - - -
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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
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169A CYS* 3.6 25.4 - - - -
171A PHE* 3.2 18.4 - - - -
191A ILE* 3.6 19.8 - - - +
214A PHE* 2.8 25.5 + - - -
215A ASP* 2.9 19.8 + - - -
217A GLU* 1.3 73.2 - - - +
219A LYS* 1.3 70.2 + - - +
220A ALA 3.1 0.2 - - - -
221A TYR* 3.0 20.6 + - - +
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Residues in contact with LYS 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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171A PHE* 4.3 8.5 - - + -
215A ASP* 2.7 46.5 + - - +
216A LEU 3.4 10.8 - - - +
217A GLU 3.0 1.0 + - - -
218A SER* 1.3 83.4 + - - +
220A ALA* 1.3 56.6 + - - +
222A ALA* 3.2 5.0 + - - +
223A PHE* 3.0 40.0 + - + -
238A ILE* 3.5 30.3 - - + -
239A ASN 3.0 20.6 + - - +
240A LEU* 3.7 20.1 - - + +
254A TRP* 4.6 0.2 - - + -
255A LEU* 4.2 15.7 - - + -
501A C2E 2.8 20.9 + - - -
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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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217A GLU 3.1 13.9 + - - +
218A SER 3.1 0.4 - - - -
219A LYS* 1.3 79.6 - - - +
221A TYR* 1.3 64.8 + - + +
223A PHE* 3.7 3.3 + - - +
224A ALA* 3.1 25.6 + - - +
254A TRP* 3.9 14.3 - - + -
258A SER* 3.4 25.2 + - - +
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Residues in contact with TYR 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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164A LEU* 6.0 1.0 - - - +
166A GLY 4.7 4.0 + - - -
167A GLN* 3.7 43.2 - - + +
168A PRO* 3.5 30.3 - - + +
169A CYS* 4.2 23.3 - - - +
171A PHE* 4.3 7.0 - - + -
217A GLU* 4.3 8.3 - - + -
218A SER* 3.0 21.0 + - - +
220A ALA* 1.3 81.9 - - + +
222A ALA* 1.3 60.0 + - - +
224A ALA* 3.8 9.1 - - + +
225A LEU* 3.2 24.4 + - - +
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Residues in contact with ALA 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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171A PHE* 3.9 33.5 - - + -
173A LEU* 6.0 0.9 - - - +
189A ALA* 4.0 8.3 - - + -
218A SER 3.6 2.2 + - - -
219A LYS* 3.2 9.8 + - - +
221A TYR* 1.3 78.2 - - - +
223A PHE* 1.3 60.6 + - - +
225A LEU* 3.2 8.3 + - - +
226A ALA* 2.9 28.1 + - - +
236A LEU* 4.1 4.3 - - - +
238A ILE* 3.9 24.7 - - + -
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Residues in contact with PHE 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 LYS* 3.0 26.4 + - + +
220A ALA 3.8 4.5 - - - +
221A TYR 3.4 0.2 - - - -
222A ALA* 1.3 74.0 - - - +
224A ALA* 1.3 58.8 - - - +
226A ALA* 3.1 3.5 + - - +
227A GLY 2.8 25.8 + - - -
236A LEU* 3.7 19.1 - - + -
238A ILE* 4.3 12.1 - - + -
254A TRP* 5.3 0.2 - + - -
255A LEU* 3.9 43.1 - - + -
258A SER* 3.4 22.4 - - - +
259A LEU* 3.7 16.2 - - + -
262A ALA* 3.4 22.8 - - + +
264A LEU* 3.7 13.9 - - + +
269A VAL* 3.7 34.1 - - + -
271A ILE* 5.8 0.7 - - + -
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Residues in contact with ALA 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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167A GLN* 5.9 2.2 - - - +
220A ALA 3.1 15.9 + - - +
221A TYR* 3.8 11.7 - - + +
223A PHE* 1.3 77.7 - - - +
225A LEU* 1.3 61.8 + - - +
227A GLY* 3.3 1.6 + - - -
228A GLN* 3.1 34.8 + - - +
262A ALA* 4.0 9.1 - - - +
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Residues in contact with LEU 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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164A LEU* 4.4 5.6 - - + -
171A PHE* 3.6 39.3 - - + +
173A LEU* 3.8 28.7 - - + -
189A ALA* 6.1 0.2 - - + -
221A TYR 3.2 16.5 + - - +
222A ALA* 3.2 9.2 + - + +
224A ALA* 1.3 76.1 - - - +
226A ALA* 1.3 61.6 + - - +
228A GLN* 3.6 27.8 - - + +
229A LEU* 3.4 24.5 - - + +
389A ASN* 3.7 39.0 - - + +
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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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173A LEU* 5.8 2.2 - - + +
222A ALA 2.9 12.9 + - - +
223A PHE 3.5 7.4 - - - +
225A LEU* 1.3 75.9 - - - +
227A GLY* 1.3 63.6 + - - +
229A LEU* 3.4 16.7 + - - +
230A PRO 3.5 1.9 - - - +
231A LEU* 3.3 36.9 - - + +
236A LEU* 3.7 28.0 - - + -
264A LEU* 3.9 12.1 - - + -
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Residues in contact with GLY 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 PHE 2.8 12.8 + - - -
224A ALA 3.3 2.9 + - - -
226A ALA* 1.3 78.6 - - - +
228A GLN* 1.3 56.6 + - - +
229A LEU 3.2 3.3 + - - -
230A PRO* 3.5 17.7 - - - +
262A ALA* 3.4 26.4 - - - +
264A LEU* 4.0 6.5 - - - +
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Residues in contact with GLN 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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162A GLN* 4.8 5.7 + - - -
164A LEU* 4.1 31.4 - - - +
224A ALA* 3.1 27.0 + - - +
225A LEU* 3.6 21.6 - - + +
227A GLY* 1.3 75.0 - - - +
229A LEU* 1.3 62.8 + - + +
230A PRO* 3.8 2.5 - - - -
389A ASN 5.6 0.8 + - - -
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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