Contacts of the helix formed by residues 213 - 224 (chain B) in PDB entry 3P3B
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 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A GLY* 3.6 13.8 - - - -
180A LEU* 3.5 14.1 - - - +
210A ASN 5.4 1.1 - - - +
211A ALA* 2.9 34.7 + - - +
212A TYR* 4.9 3.6 - - - +
213A ASN* 5.1 0.6 - - - +
216A LEU* 3.5 25.3 - - - +
212B TYR* 1.3 73.0 - - - +
214B LEU* 1.3 64.8 + - - +
215B ASN* 3.4 1.2 + - - -
216B LEU* 3.0 31.3 + - - +
217B THR* 2.8 27.1 + - - -
236B PHE* 3.8 8.5 - - - -
242B LEU* 6.3 0.4 - - - -
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Residues in contact with LEU 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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175A GLY 3.5 9.0 + - - +
176A ARG* 3.7 24.9 - - + -
213B ASN* 1.3 75.8 - - - +
215B ASN* 1.3 58.3 + - - +
217B THR* 3.2 4.0 + - - -
218B LYS* 3.0 47.0 + - - +
236B PHE* 3.8 22.3 - - + -
242B LEU* 3.9 26.8 - - + +
245B ASP* 3.7 32.1 - - + +
246B LEU* 3.8 28.7 - - + -
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Residues in contact with ASN 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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174A GLY 3.0 20.1 + - - +
175A GLY 2.9 10.5 + - - +
176A ARG* 3.4 24.5 + - - +
178A MET 2.7 31.1 + - - -
179A PRO* 4.3 3.7 - - - +
180A LEU* 4.5 12.8 - - + +
213B ASN* 3.3 2.1 + - - +
214B LEU* 1.3 73.7 - - - +
216B LEU* 1.3 60.7 + - - +
218B LYS* 3.3 22.9 + - - +
219B GLU* 3.0 28.8 + - - +
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Residues in contact with LEU 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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180A LEU* 3.3 30.4 - - + +
213A ASN* 3.6 27.6 - - - +
216A LEU* 5.0 0.7 - - + -
180B LEU* 3.7 16.6 - - + -
181B TRP* 4.3 12.1 - - + -
184B THR* 3.9 29.6 - - + +
212B TYR* 4.0 22.9 - - + -
213B ASN* 3.0 23.3 + - - +
215B ASN* 1.3 72.3 - - - +
217B THR* 1.3 65.0 + - - +
219B GLU* 3.2 9.4 + - - +
220B VAL* 3.0 28.6 + - - +
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Residues in contact with THR 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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212B TYR* 3.4 23.7 - - + +
213B ASN 2.8 18.4 + - - -
214B LEU 3.3 10.1 - - - -
216B LEU* 1.3 77.6 - - - +
218B LYS* 1.3 56.3 + - - +
220B VAL* 3.4 1.4 + - - +
221B LEU* 2.9 44.6 + - + +
232B LEU* 3.4 35.9 - - + -
235B ALA* 3.5 13.4 - - + +
236B PHE* 3.6 6.1 - - - -
246B LEU* 4.0 10.8 - - + -
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Residues in contact with LYS 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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176A ARG 5.6 2.6 + - - -
214B LEU* 3.0 33.5 + - - +
215B ASN* 3.7 24.5 + - - +
216B LEU 3.2 0.2 - - - -
217B THR* 1.3 75.6 - - - +
219B GLU* 1.3 58.6 + - - +
222B ALA* 2.9 34.1 + - - +
245B ASP* 2.7 35.8 + - - -
246B LEU* 4.1 7.9 - - + -
249B TRP* 3.5 61.5 - - + +
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Residues in contact with GLU 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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180A LEU* 5.3 4.2 - - - +
181B TRP* 3.6 33.5 - - - -
184B THR* 4.4 16.4 - - + +
188B ILE* 5.3 5.8 - - + +
215B ASN 3.0 14.6 + - - +
216B LEU* 3.5 13.0 - - + +
218B LYS* 1.3 77.0 - - - +
220B VAL* 1.3 62.5 + - - +
222B ALA* 3.4 4.7 + - - +
223B ALA* 3.1 23.4 + - + +
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Residues in contact with VAL 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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171B VAL* 5.6 1.8 - - + -
184B THR* 3.7 25.8 - - + +
187B ASP* 5.3 2.5 - - + -
188B ILE* 4.3 17.3 - - + -
191B VAL* 6.3 0.4 - - + -
206B ILE* 4.4 12.8 - - + -
212B TYR* 3.5 39.0 - - + +
216B LEU 3.0 19.4 + - - +
217B THR 3.8 3.4 - - - +
219B GLU* 1.3 74.6 - - - +
221B LEU* 1.3 64.0 + - + +
223B ALA* 3.3 3.8 + - - +
224B LEU* 3.2 41.1 + - + +
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Residues in contact with LEU 221 (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 ILE* 4.6 12.1 - - + -
217B THR* 2.9 39.8 + - + +
218B LYS 3.8 2.9 - - - +
220B VAL* 1.3 77.0 - - + +
222B ALA* 1.3 57.9 + - - +
224B LEU* 3.0 18.7 + - - +
225B SER 3.3 1.4 + - - -
229B LEU* 4.0 22.2 - - + -
232B LEU* 4.1 15.7 - - + -
246B LEU* 3.9 20.0 - - + -
249B TRP* 3.9 11.7 - - + -
250B LEU* 3.9 16.8 - - + -
255B GLN* 3.0 28.3 + - - +
257B VAL* 4.8 12.8 - - + -
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Residues in contact with ALA 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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218B LYS 2.9 21.9 + - - +
219B GLU* 3.8 5.8 - - - +
221B LEU* 1.3 73.3 - - - +
223B ALA* 1.3 59.6 + - - +
224B LEU 3.1 0.2 - - - -
225B SER* 2.8 20.3 + - - -
249B TRP* 4.0 8.2 - - + -
253B ARG* 3.8 28.1 + - - +
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Residues in contact with ALA 223 (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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188B ILE* 3.7 31.3 - - + +
192B ARG* 2.9 30.1 + - - -
219B GLU* 3.1 17.4 + - + +
220B VAL 3.7 5.6 - - - +
221B LEU 3.2 0.4 - - - -
222B ALA* 1.3 76.4 - - - +
224B LEU* 1.3 60.3 + - - +
225B SER 3.4 1.3 - - - -
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Residues in contact with LEU 224 (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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188B ILE* 3.9 18.4 - - + +
191B VAL* 3.7 36.3 - - + -
192B ARG* 3.9 27.6 - - + +
206B ILE* 4.4 7.0 - - + -
220B VAL* 3.2 34.7 + - + +
221B LEU 3.0 7.7 + - - +
223B ALA* 1.3 81.8 - - - +
225B SER* 1.3 61.9 + - - +
226B ASP 3.1 3.4 - - - -
227B VAL* 3.0 28.7 + - + +
229B LEU* 3.8 25.5 - - + +
255B GLN* 4.0 5.5 + - - -
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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