Contacts of the helix formed by residues 199 - 214 (chain B) in PDB entry 3G33
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 PRO 199 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B GLU* 3.9 12.6 - - + +
39B VAL* 4.5 7.0 - - + -
197B MET 3.9 4.9 - - - +
198B TYR* 1.3 88.5 - - + +
200B PRO* 1.3 76.6 - - + +
201B SER* 4.0 7.6 - - - +
202B MET* 3.0 39.8 + - + +
203B ILE* 3.2 9.7 + - - +
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Residues in contact with PRO 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B GLU* 3.4 28.3 - - + +
38B TYR 5.0 3.1 - - - +
39B VAL* 3.9 11.9 - - + -
155B VAL 3.2 22.2 - - - +
156B ILE* 3.6 6.5 - - - -
157B ALA* 3.3 38.1 - - + +
160B PHE* 3.8 10.1 - - + -
198B TYR 3.5 6.4 - - - +
199B PRO* 1.3 82.0 - - + +
201B SER* 1.3 56.6 + - - +
203B ILE* 3.2 7.1 + - + -
204B ALA* 2.9 25.5 + - - +
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Residues in contact with SER 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 3.9 11.1 - - - +
35B GLU* 2.7 40.4 + - - -
160B PHE* 3.5 23.9 - - - -
199B PRO* 4.0 6.6 - - - +
200B PRO* 1.3 74.2 - - - +
202B MET* 1.3 58.0 + - - +
204B ALA* 3.4 1.7 + - - +
205B THR* 2.8 33.9 + - - +
233B THR* 4.4 11.9 - - - +
235B THR* 4.6 8.2 - - - +
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Residues in contact with MET 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B TYR* 3.9 18.8 - - + -
199B PRO* 3.0 32.7 + - + +
201B SER* 1.3 77.8 + - - +
203B ILE* 1.3 61.0 + - - +
205B THR* 3.3 11.9 - - + +
206B GLY* 2.8 28.4 + - - -
235B THR* 4.8 14.8 - - + -
239B CYS* 4.2 27.4 - - + +
240B LEU* 5.1 6.7 - - + -
243B CYS* 3.7 32.6 - - + -
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Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B ALA* 3.6 18.8 - - + -
186B LEU* 4.1 7.4 - - + +
189B CYS* 3.5 32.1 - - + -
195B PHE* 3.5 32.3 - - + +
196B ALA 5.5 0.2 - - - +
198B TYR* 3.6 34.1 - - + +
199B PRO 3.2 5.1 + - - +
200B PRO* 3.5 11.0 - - + +
202B MET* 1.3 75.2 - - - +
204B ALA* 1.3 51.8 + - - +
207B SER* 2.7 38.3 + - - -
243B CYS* 4.8 5.2 - - - -
247B ILE* 4.2 2.8 - - - +
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Residues in contact with ALA 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B ALA 3.2 27.1 - - - +
160B PHE* 3.5 21.5 - - + -
161B LEU* 5.0 3.9 - - + +
164B ILE* 4.1 5.4 - - + -
186B LEU* 4.1 6.7 - - + -
200B PRO 2.9 13.7 + - - +
201B SER 3.6 2.0 - - - +
203B ILE* 1.3 73.3 - - - +
205B THR* 1.3 61.2 + - - +
206B GLY 3.0 1.3 - - - -
207B SER* 3.4 5.1 + - - -
208B ILE* 2.9 36.0 + - - +
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Residues in contact with THR 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ILE* 4.0 5.5 - - - +
201B SER 2.8 29.2 + - - +
202B MET* 3.3 15.0 - - + +
204B ALA* 1.3 72.4 - - - +
206B GLY* 1.3 62.1 + - - +
208B ILE* 3.4 20.5 - - - +
209B GLY* 3.4 5.2 + - - -
229B LEU* 3.4 40.5 + - - +
233B THR* 4.0 23.9 + - - +
235B THR* 4.4 4.7 - - - +
240B LEU* 3.3 20.7 - - + +
244B GLN* 5.3 0.2 - - - +
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Residues in contact with GLY 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B MET 2.8 18.9 + - - -
203B ILE 3.9 0.2 - - - -
205B THR* 1.3 77.1 - - - +
207B SER* 1.3 59.5 + - - +
208B ILE 3.2 0.2 - - - -
209B GLY 3.3 0.9 + - - -
210B ALA* 3.1 22.0 + - - +
240B LEU* 3.7 13.2 - - - -
243B CYS* 4.6 2.0 - - - -
244B GLN* 3.5 21.4 - - - +
247B ILE* 3.8 11.4 - - - -
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Residues in contact with SER 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B LEU* 5.7 0.3 - - - +
182B ALA* 4.1 3.8 + - - +
185B PHE* 3.3 36.0 - - - -
186B LEU* 3.0 26.4 - - - +
189B CYS* 4.8 0.9 - - - -
203B ILE 2.7 22.6 + - - -
204B ALA 3.4 2.3 + - - -
206B GLY* 1.3 74.9 - - - +
208B ILE* 1.3 61.2 + - - +
210B ALA* 3.5 6.2 + - - +
211B ALA* 3.1 25.5 + - - +
247B ILE* 3.6 14.2 - - - +
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Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B LEU* 3.7 20.4 - - + -
164B ILE* 3.3 39.9 - - + +
165B LEU* 3.5 35.9 - - + +
168B LEU* 5.1 1.3 - - + -
178B VAL* 5.2 1.8 - - + -
182B ALA* 4.3 15.7 - - + -
204B ALA 2.9 19.2 + - - +
205B THR* 3.4 12.3 - - - +
207B SER* 1.3 77.3 + - - +
209B GLY* 1.3 61.8 + - - +
211B ALA* 3.8 0.8 - - - +
212B VAL* 3.2 32.2 + - + +
229B LEU* 4.0 15.3 - - + +
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Residues in contact with GLY 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B THR 3.4 2.1 + - - -
206B GLY 3.3 6.8 + - - -
207B SER 3.2 0.4 - - - -
208B ILE* 1.3 80.9 - - - +
210B ALA* 1.3 63.0 + - - +
211B ALA 3.1 1.6 - - - -
212B VAL* 4.2 2.8 - - - +
213B GLN* 3.0 22.5 + - - +
225B LEU* 5.0 3.9 - - - +
229B LEU* 3.6 23.8 - - - -
244B GLN* 3.1 20.9 + - - -
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Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B HIS* 4.8 0.5 + - - -
185B PHE* 4.0 26.7 - - + -
206B GLY 3.1 13.5 + - - +
207B SER* 3.7 10.5 - - - +
209B GLY* 1.3 77.3 - - - +
211B ALA* 1.3 61.2 + - - +
213B GLN* 4.2 2.1 - - - +
214B GLY* 3.3 16.6 + - - -
244B GLN* 3.3 11.5 - - + +
247B ILE* 5.0 1.6 - - + -
248B GLU* 3.7 31.6 - - + +
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Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B VAL* 4.1 8.1 - - + +
181B HIS* 3.7 17.2 - - + -
182B ALA* 3.7 34.1 - - + +
185B PHE* 4.0 1.8 - - + -
207B SER 3.1 17.2 + - - +
208B ILE 3.9 4.3 - - - +
209B GLY 3.1 0.6 - - - -
210B ALA* 1.3 75.8 - - - +
212B VAL* 1.3 65.4 + - - +
214B GLY* 3.0 12.1 + - - -
215B LEU* 3.1 21.1 + - + +
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Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B LEU* 5.1 9.9 - - + -
170B LEU* 4.5 19.5 - - + -
178B VAL* 3.6 26.0 - - + -
208B ILE* 3.2 23.1 + - + +
209B GLY* 4.2 3.1 - - - +
211B ALA* 1.3 79.7 - - - +
213B GLN* 1.3 57.3 + - - +
215B LEU* 3.2 6.6 + - - +
216B GLY 3.0 37.5 + - - +
220B MET* 6.1 0.9 - - + -
225B LEU* 3.7 28.3 - - + -
229B LEU* 6.2 1.8 - - + -
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Residues in contact with GLN 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B GLY 3.0 16.3 + - - +
210B ALA* 4.3 3.1 - - - +
212B VAL* 1.3 77.6 - - - +
214B GLY* 1.3 59.1 + - - +
215B LEU 3.2 1.2 + - - -
216B GLY* 3.8 9.0 + - - +
222B GLY* 4.2 26.8 - - - +
225B LEU* 4.5 13.8 - - + +
226B THR* 5.2 3.3 - - - +
244B GLN* 2.9 23.8 + - - +
248B GLU* 5.3 3.6 - - - +
252D ARG* 5.8 1.0 - - - +
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Residues in contact with GLY 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B HIS* 5.2 5.6 - - - -
210B ALA 3.3 10.4 + - - -
211B ALA 3.0 9.1 + - - -
213B GLN* 1.3 77.6 - - - +
215B LEU* 1.3 63.9 + - - +
216B GLY 3.7 0.4 - - - -
251D LEU* 3.8 15.3 - - - +
252D ARG* 3.6 23.3 + - - +
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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