Contacts of the helix formed by residues 201 - 215 (chain B) in PDB entry 3I58
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 LEU 201 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B TRP* 5.2 16.2 - - + +
137B GLY* 6.2 3.6 - - - -
200B ASP* 1.3 84.9 + - - +
202B GLN* 1.3 68.5 + - + +
203B GLY 3.3 1.7 + - - +
204B PRO* 3.4 8.3 - - + +
205B ALA* 3.0 21.3 + - - +
225B VAL* 4.1 3.6 - - - -
226B GLY 4.0 6.7 - - - +
227B SER* 4.7 4.9 - - - -
401B SAH 3.6 61.7 - - + +
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Residues in contact with GLN 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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201B LEU* 1.3 73.3 - - + +
203B GLY* 1.3 65.1 - - - +
205B ALA* 3.9 0.3 - - - +
206B SER* 3.0 27.4 + - - -
225B VAL* 3.7 28.0 - - + +
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Residues in contact with GLY 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B SER* 4.5 10.1 - - - -
147B ASP* 4.3 6.0 - - - +
201B LEU* 4.7 0.8 - - - +
202B GLN* 1.3 76.9 - - - +
204B PRO* 1.3 70.6 - - - +
206B SER* 2.9 21.0 + - - -
207B ALA* 3.2 8.8 + - - +
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Residues in contact with PRO 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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143B SER* 4.3 10.5 - - - +
146B PHE* 6.4 0.4 - - + -
147B ASP* 3.3 28.5 - - - +
179B GLY* 3.4 29.6 - - - +
180B SER* 3.6 0.2 - - - -
200B ASP* 3.3 24.5 - - - +
201B LEU* 3.4 15.9 - - + +
203B GLY* 1.3 87.8 - - - +
205B ALA* 1.3 50.3 + - - +
207B ALA* 2.8 7.7 + - + +
208B ALA 2.7 31.4 + - - -
401B SAH 3.8 12.8 - - - +
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Residues in contact with ALA 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B GLY 4.5 0.2 - - - -
198B VAL* 5.1 1.8 - - - +
200B ASP* 4.0 17.6 - - + +
201B LEU 3.0 20.5 + - - +
202B GLN 3.9 2.2 - - - +
204B PRO* 1.3 77.0 - - - +
206B SER* 1.3 57.1 + - - +
208B ALA* 3.3 5.4 + - - -
209B HIS* 3.0 22.5 + - - +
223B VAL* 3.1 34.3 - - + +
225B VAL* 3.9 19.1 - - + -
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Residues in contact with SER 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLN 3.0 13.7 + - - -
203B GLY* 2.9 15.6 + - - -
205B ALA* 1.3 74.3 - - - +
207B ALA* 1.3 61.0 + - - +
209B HIS* 3.4 8.9 + - - +
210B ARG* 3.0 44.2 + - - +
223B VAL* 5.2 0.2 - - - -
225B VAL* 5.6 0.6 - - - +
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Residues in contact with ALA 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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147B ASP* 4.3 8.3 - - + +
180B SER* 3.5 22.0 - - - +
203B GLY 3.2 8.9 + - - +
204B PRO* 2.8 11.4 + - + +
206B SER* 1.3 78.4 + - - +
208B ALA* 1.3 65.7 + - - +
210B ARG* 3.4 16.5 + - - +
211B ARG* 3.0 23.2 + - - +
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Residues in contact with ALA 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B GLY 3.7 7.0 - - - +
180B SER 3.1 27.7 + - - -
181B GLY* 3.7 3.6 - - - +
198B VAL* 4.1 7.6 - - + -
204B PRO 2.7 9.5 + - - +
205B ALA 3.4 8.5 - - - +
207B ALA* 1.3 77.6 - - - +
209B HIS* 1.3 62.3 + - - +
211B ARG* 3.0 5.0 + - - +
212B PHE* 2.9 38.1 + - + -
223B VAL* 3.7 11.2 - - + -
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Residues in contact with HIS 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 ALA 3.0 13.3 + - - +
206B SER* 3.4 13.0 - - - +
208B ALA* 1.3 76.0 - - - +
210B ARG* 1.3 64.0 + - - +
212B PHE* 3.2 7.6 + - - +
213B LEU* 3.0 55.1 + - + +
218B SER* 6.1 2.0 - - - -
222B GLN* 6.2 0.2 - - - -
223B VAL* 3.3 23.2 + - + +
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Residues in contact with ARG 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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206B SER* 3.0 40.0 + - - +
207B ALA* 3.7 12.1 - - - +
208B ALA 3.3 0.2 - - - -
209B HIS* 1.3 78.1 - - - +
211B ARG* 1.3 62.5 + - - +
213B LEU* 3.5 10.4 + - - +
214B ASP* 3.2 41.2 + - - +
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Residues in contact with ARG 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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151B SER* 3.3 24.7 + - - -
180B SER* 3.1 36.8 + - - -
181B GLY* 3.8 11.9 - - - -
182B GLY* 3.5 26.3 - - - +
185B SER* 4.0 14.7 + - - +
207B ALA 3.0 14.8 + - - +
208B ALA 3.0 8.2 + - - +
210B ARG* 1.3 73.5 - - - +
212B PHE* 1.3 71.0 + - + +
214B ASP* 3.3 5.2 + - - +
215B THR* 2.9 40.5 + - + +
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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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181B GLY* 4.0 22.4 - - - -
184B LEU* 3.8 7.6 - - + -
185B SER* 4.2 14.6 - - - -
188B LEU* 5.7 0.2 - - + -
198B VAL* 3.6 32.5 - - + -
208B ALA* 2.9 22.6 + - + -
209B HIS* 3.7 7.6 - - - +
211B ARG* 1.3 83.5 - - - +
213B LEU* 1.3 63.1 + - + +
215B THR* 3.3 4.2 + - - -
216B GLY* 3.0 4.5 + - - -
217B LEU* 2.9 36.7 + - + -
218B SER* 3.6 18.7 + - - +
221B ALA* 3.4 40.2 - - + +
222B GLN 4.4 1.1 - - - -
223B VAL* 3.9 17.3 - - + -
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Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B HIS* 3.0 51.7 + - + +
210B ARG* 3.8 7.6 - - - +
211B ARG 3.3 0.2 - - - -
212B PHE* 1.3 76.7 - - - +
214B ASP* 1.3 65.0 + - - +
216B GLY* 3.3 9.9 + - - -
218B SER* 3.9 27.2 + - - +
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Residues in contact with ASP 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ARG* 3.2 30.0 + - - +
211B ARG* 3.8 4.2 - - - +
213B LEU* 1.3 80.5 - - - +
215B THR* 1.3 64.9 + - + +
216B GLY 3.2 1.1 + - - -
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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
----------------------------------------------------------
185B SER* 4.5 6.1 + - - +
211B ARG* 2.9 31.7 + - + +
212B PHE* 3.6 5.2 + - - -
214B ASP* 1.3 80.0 - - + +
216B GLY* 1.3 60.9 + - - +
217B LEU* 3.5 27.3 - - - +
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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