Contacts of the helix formed by residues 202 - 216 (chain B) in PDB entry 4U2M
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 ASN 202 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B GLU 3.5 3.4 + - - -
201B ILE* 1.3 78.0 - - - +
203B PRO* 1.3 71.4 - - - +
204B GLU* 2.8 35.8 + - - +
205B GLY* 3.0 10.9 + - - +
206B PHE 3.1 16.6 + - - -
227B ALA* 4.0 27.9 - - + +
231B THR* 4.2 5.2 + - - +
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Residues in contact with PRO 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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161B VAL* 3.8 27.1 - - + +
162B SER* 4.9 7.9 - - - -
163B ARG* 5.7 0.4 - - + +
164B GLU* 4.2 23.1 - - + +
166B PHE* 3.9 6.4 - - + -
201B ILE 3.3 9.9 - - - +
202B ASN* 1.3 88.6 - - - +
204B GLU* 1.3 63.2 + - - +
206B PHE* 3.1 4.1 + - + +
207B CYS* 2.9 24.0 + - - +
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Residues in contact with GLU 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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202B ASN* 2.8 14.2 + - - +
203B PRO* 1.3 82.0 - - - +
205B GLY* 1.3 60.6 + - - +
207B CYS* 3.2 7.7 + - - +
208B ILE* 3.0 35.8 + - + +
224B ASN* 6.1 3.8 - - + -
227B ALA* 6.2 0.2 - - + -
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Residues in contact with GLY 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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202B ASN* 3.0 15.9 + - - -
204B GLU* 1.3 77.1 - - - +
206B PHE* 1.3 63.2 + - - +
208B ILE* 3.5 3.3 + - - +
209B LEU* 3.1 26.2 + - - +
224B ASN* 6.3 0.7 - - - -
227B ALA* 4.3 12.3 - - - +
228B VAL* 4.3 15.4 - - - +
231B THR* 3.9 15.9 - - - -
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Residues in contact with PHE 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE* 3.7 24.0 - - + -
161B VAL* 4.0 14.1 - - + -
166B PHE* 3.6 44.9 - + + -
173B LEU* 5.3 0.4 - - + -
180B PHE* 4.0 15.9 - + - -
197B LEU* 3.9 22.0 - - + -
201B ILE* 4.7 2.2 - - + -
202B ASN 3.1 11.0 + - - +
203B PRO 3.5 6.7 - - - +
205B GLY* 1.3 77.8 - - - +
207B CYS* 1.3 52.7 + - - +
209B LEU* 3.0 3.7 + - - +
210B LEU* 2.7 55.2 + - + +
213B MET* 5.3 2.5 - - + -
231B THR* 3.8 13.9 - - + +
235B LEU* 3.9 26.0 - - + -
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Residues in contact with CYS 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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166B PHE* 3.7 27.1 - - + -
203B PRO 2.9 16.2 + - - +
204B GLU* 3.2 9.8 + - - +
206B PHE* 1.3 76.0 - - - +
208B ILE* 1.3 58.7 + - + +
210B LEU* 3.4 5.5 + - - +
211B ASP* 3.0 49.5 + - - +
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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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204B GLU* 3.0 25.1 + - + +
205B GLY 3.7 4.0 - - - +
207B CYS* 1.3 80.3 - - + +
209B LEU* 1.3 55.8 + - - +
211B ASP* 3.6 7.5 + - - +
212B PHE* 3.0 24.8 + - - +
217B ARG 4.7 1.7 - - - +
218B LEU* 4.2 18.4 - - + -
219B ASN* 4.0 26.0 + - + +
224B ASN* 3.4 37.7 - - + +
228B VAL* 3.9 20.6 - - + -
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Residues in contact with LEU 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 GLY 3.1 10.0 + - - +
206B PHE 3.0 8.1 + - - +
208B ILE* 1.3 75.0 - - - +
210B LEU* 1.3 59.9 - - - +
212B PHE* 3.2 5.7 + - + +
213B MET* 2.9 33.2 + - - +
218B LEU* 4.0 13.7 - - + -
228B VAL* 3.8 11.2 - - + +
231B THR* 3.5 25.1 - - + -
232B ALA* 3.4 33.2 - - + +
235B LEU* 4.0 16.8 - - + -
237B MET* 4.4 15.7 - - + -
240B VAL* 3.7 29.6 - - + -
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Residues in contact with LEU 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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149B ARG* 3.5 24.7 - - - +
159B ILE* 6.3 0.2 - - + -
166B PHE* 3.8 38.1 - - + -
167B ARG 4.3 8.1 - - - +
168B ALA* 4.3 5.6 - - + -
173B LEU* 3.6 30.3 - - + -
206B PHE* 2.7 34.6 + - + +
207B CYS* 3.7 5.4 - - - +
209B LEU* 1.3 72.3 - - - +
211B ASP* 1.3 63.7 + - - +
213B MET* 3.1 21.4 + - - +
214B TYR* 3.3 29.8 + - + -
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Residues in contact with ASP 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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149B ARG* 3.1 30.8 + - - +
207B CYS* 3.0 36.3 + - - +
208B ILE* 3.8 7.3 - - - +
210B LEU* 1.3 75.5 - - - +
212B PHE* 1.3 58.7 + - - +
214B TYR 3.3 1.4 + - - -
215B THR* 2.6 41.0 + - + +
217B ARG 4.3 2.7 - - - +
219B ASN* 5.6 6.3 - - - +
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Residues in contact with PHE 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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3B PHE* 3.7 44.0 - + + -
6B HIS* 3.6 30.5 + + - -
208B ILE 3.0 16.3 + - - +
209B LEU* 3.2 8.3 + - + +
211B ASP* 1.3 75.9 - - - +
213B MET* 1.3 65.6 + - - +
215B THR* 3.9 0.2 - - - -
216B SER* 2.8 43.0 + - - -
217B ARG 3.3 19.9 + - - +
218B LEU* 3.9 18.6 - - + -
237B MET* 3.7 32.5 - - + -
240B VAL* 3.7 15.3 - - + -
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Residues in contact with MET 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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6B HIS* 2.8 24.7 + - - -
142B LEU* 3.6 12.0 - - - +
172B VAL* 4.4 4.7 - - + +
173B LEU* 3.6 34.5 - - + -
176B CYS* 3.7 30.8 - - + -
177B SER* 4.2 18.6 - - - -
180B PHE* 4.5 4.7 - - + -
206B PHE* 5.3 2.5 - - + -
209B LEU 2.9 20.7 + - - +
210B LEU* 3.1 15.2 + - + +
212B PHE* 1.3 78.2 - - - +
214B TYR* 1.3 66.8 + - + +
235B LEU* 4.4 12.8 - - + -
237B MET* 3.8 30.1 - - + -
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Residues in contact with TYR 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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142B LEU* 3.3 32.2 - - + +
143B LEU* 5.0 1.0 - - - -
145B LEU* 3.7 15.5 - - + -
146B ASN* 3.3 44.3 - - - +
149B ARG* 3.6 31.6 - - + +
168B ALA* 3.8 3.6 - - + +
169B HIS* 2.7 52.7 + - - +
172B VAL* 3.8 30.6 - - + +
173B LEU* 5.0 0.4 - - + -
210B LEU* 3.3 33.1 + - + +
211B ASP 3.3 2.1 + - - +
212B PHE 3.1 0.4 - - - -
213B MET* 1.3 78.5 - - + +
215B THR* 1.3 57.7 + - - +
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Residues in contact with THR 215 (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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142B LEU* 4.4 3.4 - - - -
146B ASN* 3.6 23.1 - - - +
149B ARG* 5.2 1.1 - - - +
211B ASP* 2.6 30.2 + - + +
214B TYR* 1.3 83.4 - - + +
216B SER* 1.3 70.5 + - - +
217B ARG* 3.0 52.0 + - - +
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Residues in contact with SER 216 (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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1B SER* 6.1 3.7 - - - -
2B ASP* 4.8 2.3 + - - +
3B PHE* 3.9 38.8 + - - +
6B HIS* 3.1 29.6 - - - +
7B SER* 3.9 6.9 + - - -
142B LEU* 3.7 8.0 - - - +
212B PHE* 2.8 26.2 + - - -
215B THR* 1.3 75.3 + - - +
217B ARG* 1.3 61.4 + - - +
218B LEU 4.0 1.6 + - - -
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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