Contacts of the helix formed by residues 209 - 222 (chain B) in PDB entry 1P4A
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 GLY 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B MET* 3.9 17.5 - - - +
207B LYS 3.7 1.0 - - - -
208B ALA* 1.3 78.2 - - - +
210B GLY* 1.3 58.3 + - - +
211B THR 3.3 3.1 - - - -
212B ILE 3.5 3.0 + - - -
213B ASN* 2.9 31.2 + - - +
238B VAL* 4.3 2.5 - - - -
242B LEU* 4.2 5.6 - - - -
243B VAL* 3.8 16.0 - - - +
605B PCP 3.2 10.3 + - - -
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Residues in contact with GLY 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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175B TYR* 3.8 9.0 - - - +
176B VAL* 3.2 28.9 + - - -
208B ALA* 3.4 5.5 + - - +
209B GLY* 1.3 78.2 - - - +
211B THR* 1.3 56.1 + - - +
213B ASN* 3.7 7.7 + - - +
214B GLY* 2.8 26.2 + - - -
242B LEU* 4.3 6.6 - - - +
605B PCP 3.2 3.8 + - - -
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Residues in contact with THR 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B VAL* 3.6 30.7 - - + -
175B TYR* 3.6 28.8 - - + +
176B VAL 4.0 0.4 + - - -
177B SER* 3.6 4.0 - - - -
186B MET* 3.5 8.4 - - + +
203B ASP* 4.0 3.6 - - - +
210B GLY* 1.3 73.0 - - - +
212B ILE* 1.3 64.4 + - - +
214B GLY* 3.1 3.3 + - - -
215B MET* 3.0 21.9 + - + +
605B PCP 2.6 58.7 + - + +
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Residues in contact with ILE 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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201B ILE* 4.2 9.9 - - + -
203B ASP* 4.3 13.9 - - + +
206B MET* 3.9 22.4 - - + -
209B GLY* 3.5 7.1 + - - +
210B GLY 3.5 0.2 - - - -
211B THR* 1.3 78.9 - - - +
213B ASN* 1.3 58.7 + - - +
215B MET* 3.1 25.1 + - + +
216B ILE* 2.9 37.1 + - + +
229B ILE* 4.2 18.2 - - + -
231B VAL* 3.5 32.5 - - + -
243B VAL* 3.8 26.5 - - + -
605B PCP 5.5 1.3 + - - +
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Residues in contact with ASN 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 2.9 20.1 + - - +
210B GLY* 3.7 7.8 + - - +
212B ILE* 1.3 77.8 - - - +
214B GLY* 1.3 56.4 + - - +
216B ILE* 3.2 9.5 + - - +
217B ASN* 2.9 61.2 + - - +
241B ARG 4.2 3.5 - - - +
242B LEU* 2.8 43.4 + - + +
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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
----------------------------------------------------------
173B ILE* 3.6 18.5 - - - +
174B ASN 5.2 0.2 - - - -
175B TYR* 4.1 7.0 - - - -
186B MET* 3.5 16.2 - - - -
210B GLY 2.8 19.6 + - - -
211B THR 3.1 4.9 + - - -
213B ASN* 1.3 74.1 - - - +
215B MET* 1.3 56.9 + - - +
217B ASN* 3.3 4.5 + - - -
218B LEU* 2.8 29.3 + - - +
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Residues in contact with MET 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B MET* 4.0 18.0 - - - +
136B THR* 3.8 31.2 - - - +
137B VAL* 3.9 22.7 - - + +
159B VAL* 4.6 4.5 - - + -
186B MET* 3.9 17.7 - - + -
201B ILE* 3.7 35.7 - - + -
202B ILE 4.6 0.4 - - - +
203B ASP* 4.2 10.1 - - - +
211B THR* 3.0 12.5 + - + +
212B ILE* 3.1 30.0 + - + +
214B GLY* 1.3 76.2 - - - +
216B ILE* 1.3 57.9 + - - +
218B LEU* 3.3 5.3 + - - +
219B LEU* 3.0 34.0 + - - +
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Residues in contact with ILE 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ILE* 4.1 16.6 - - + -
212B ILE* 2.9 29.5 + - + +
213B ASN* 3.5 10.3 - - - +
215B MET* 1.3 75.4 - - - +
217B ASN* 1.3 68.8 + - - +
219B LEU* 3.4 7.0 + - - +
220B ASP* 3.1 26.6 + - - +
226B VAL* 4.3 16.9 - - + +
229B ILE* 4.1 5.6 - - + -
242B LEU 3.8 21.5 - - - +
243B VAL* 4.4 3.1 - - - -
244B ASP* 3.4 24.5 - - - +
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Residues in contact with ASN 217 (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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173B ILE* 4.1 19.6 - - + +
174B ASN 5.4 2.1 - - - +
213B ASN* 2.9 44.7 + - - +
214B GLY* 3.7 6.3 - - - +
216B ILE* 1.3 79.5 - - - +
218B LEU* 1.3 66.2 + - - +
220B ASP* 3.2 20.6 + - - +
221B GLU* 3.3 17.0 + - - +
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Residues in contact with LEU 218 (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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135B MET* 4.8 5.6 - - + -
159B VAL* 3.6 42.0 - - + -
171B VAL* 3.5 45.8 - - + +
173B ILE* 3.6 21.2 - - + +
186B MET* 4.4 8.3 - - + +
188B LEU* 4.0 15.3 - - + +
214B GLY 2.8 21.1 + - - +
215B MET 3.6 5.6 - - - +
216B ILE 3.3 0.2 - - - -
217B ASN* 1.3 73.4 - - - +
219B LEU* 1.3 61.9 + - + +
221B GLU* 3.1 13.1 + - - +
222B PHE* 3.3 26.0 + - + -
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Residues in contact with LEU 219 (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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135B MET* 3.6 30.3 - - + -
193B MET* 3.8 20.9 - - + -
199B VAL* 3.8 34.1 - - + -
201B ILE* 3.9 22.0 - - + -
215B MET 3.0 17.2 + - - +
216B ILE* 3.7 4.9 - - - +
217B ASN 3.3 0.2 - - - -
218B LEU* 1.3 73.6 - - - +
220B ASP* 1.3 66.2 + - - +
222B PHE* 2.9 14.9 + - + +
223B ASN 2.9 9.7 + - - -
224B ALA* 3.0 22.9 + - + +
225B ASN 4.3 4.0 - - - +
226B VAL* 4.0 18.4 - - + -
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Residues in contact with ASP 220 (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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216B ILE* 3.1 19.3 + - - +
217B ASN* 3.3 17.7 + - - +
219B LEU* 1.3 75.1 - - - +
221B GLU* 1.3 68.2 + - - +
223B ASN* 3.2 21.4 + - - +
224B ALA 4.6 2.9 + - - -
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Residues in contact with GLU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B VAL* 3.7 29.7 - - + +
172B SER 5.3 0.7 - - - +
173B ILE* 4.1 16.2 - - + +
217B ASN 3.3 11.6 + - - +
218B LEU 3.1 10.2 + - - +
219B LEU 3.1 0.8 - - - -
220B ASP* 1.3 86.4 - - - +
222B PHE* 1.3 59.4 + - - +
223B ASN* 3.2 2.8 + - - +
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Residues in contact with PHE 222 (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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171B VAL* 3.8 33.7 - - + -
188B LEU* 3.9 28.9 - - + -
189B ALA 3.6 17.3 - - - -
190B LYS* 3.7 28.3 - - + -
193B MET* 3.4 48.0 - - + -
194B LYS 5.3 0.4 - - - +
195B THR* 3.5 22.1 + - - +
218B LEU* 3.3 27.7 + - + -
219B LEU* 2.9 9.6 + - + +
221B GLU* 1.3 77.4 - - - +
223B ASN* 1.3 68.3 + - - +
224B ALA 3.2 1.1 + - - +
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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