Contacts of the helix formed by residues 207 - 227 (chain B) in PDB entry 1PZN
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 207 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ALA* 3.6 19.5 + - + +
263A LYS* 4.2 1.0 - - - +
266A ALA* 3.3 18.6 - - - +
307A HIS* 5.9 1.1 - - - +
206B PHE* 1.3 76.4 + - - +
208B SER* 1.3 56.2 + - - +
209B ASN* 3.0 9.4 + - - +
210B HIS* 2.7 23.8 + - - +
211B GLN* 2.8 26.2 + - - +
243B HIS* 3.0 20.2 + - - -
247B GLU* 3.0 19.7 - - - +
375B MPD 3.0 32.6 + - - +
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Residues in contact with SER 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ASN* 1.3 70.7 - - - +
209B ASN* 1.3 66.2 + - - +
211B GLN* 3.1 8.5 + - - +
212B MSE 2.9 33.4 + - - +
243B HIS* 3.5 23.3 + - - +
244B PHE* 3.6 29.9 + - - -
247B GLU* 2.7 33.9 + - - -
248B TYR* 4.0 7.6 - - - -
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Residues in contact with ASN 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 4.0 27.7 - - + +
259A GLN* 3.9 18.5 + - - -
207B ASN* 3.0 9.2 + - - +
208B SER* 1.3 81.0 - - - +
210B HIS* 1.3 65.2 + - - +
212B MSE 3.3 10.2 + - - +
213B LEU* 2.9 22.3 + - - +
247B GLU* 4.5 1.2 + - - -
248B TYR* 4.8 0.9 + - - -
260B LYS* 2.9 30.3 + - - +
375B MPD 4.0 13.7 + - + +
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Residues in contact with HIS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLU* 5.1 5.5 - - + +
94A LEU* 2.6 43.6 + - + +
204B ARG 2.9 25.0 + - - -
205B ALA* 4.1 1.6 - - - -
206B PHE* 2.9 38.4 + + + +
207B ASN* 2.7 25.5 + - - +
209B ASN* 1.3 72.3 - - - +
211B GLN* 1.3 64.0 + - - +
213B LEU* 2.9 20.0 + - + +
214B LEU* 2.9 31.4 + - + +
375B MPD 3.7 19.4 - - + +
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Residues in contact with GLN 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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171B ILE* 4.5 8.3 - - + +
173B THR* 3.4 27.7 - - + +
205B ALA* 3.8 15.0 - - + +
207B ASN 2.8 12.1 + - - +
208B SER 3.3 9.0 - - - +
210B HIS* 1.3 79.3 - - - +
212B MSE 1.3 64.2 + - - +
213B LEU 3.1 0.2 + - - -
214B LEU* 3.2 11.6 + - - +
215B VAL* 3.4 10.2 + - - +
237B VAL* 4.0 3.8 - - + +
239B SER 3.9 1.4 - - - +
240B LEU* 2.9 36.0 + - - +
243B HIS* 3.8 19.4 + - - +
244B PHE* 3.7 8.8 - - - -
264B HIS* 3.1 32.3 + - + -
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Residues in contact with MSE 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B SER* 2.9 27.5 + - - +
209B ASN* 3.7 20.2 - - - +
211B GLN* 1.3 72.0 - - - +
213B LEU* 1.3 65.5 + - - +
215B VAL* 3.5 6.4 + - - +
216B GLN* 3.1 25.2 + - - +
244B PHE* 3.8 22.2 - - + -
260B LYS* 3.3 61.5 - - + +
263B LYS* 5.5 5.2 - - - -
264B HIS* 3.7 30.0 - - + -
267B ASP* 5.1 2.6 - - - +
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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
----------------------------------------------------------
60A GLU* 4.9 13.5 - - + +
63A ALA* 4.4 20.2 - - + +
64A VAL* 4.5 14.1 - - + +
89A ARG* 3.6 31.4 - - - +
92A ALA* 5.2 0.9 - - + -
95A GLY* 4.8 5.8 - - - -
209B ASN 2.9 13.8 + - - +
210B HIS* 2.9 25.5 + - + +
212B MSE 1.3 75.3 - - - +
214B LEU* 1.3 64.7 + - - +
216B GLN* 2.8 25.4 + - - +
217B GLN* 2.7 50.5 + - - +
375B MPD 6.4 0.7 - - + -
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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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94A LEU 3.9 4.3 - - - +
95A GLY* 3.9 33.7 - - - +
97A PHE* 3.3 15.7 - - + -
171B ILE* 3.7 17.7 - - + -
203B ALA* 3.7 27.8 - - + -
204B ARG 3.8 23.6 - - - +
205B ALA* 3.8 22.4 - - + -
210B HIS* 2.9 17.3 + - + +
211B GLN 3.2 6.7 + - - +
213B LEU* 1.3 79.1 - - - +
215B VAL* 1.3 57.3 + - - +
217B GLN* 3.2 4.9 + - - +
218B ALA 2.7 23.2 + - - -
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Residues in contact with VAL 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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171B ILE* 4.5 17.0 - - + -
211B GLN 3.4 4.7 + - - +
212B MSE 3.9 7.4 - - - +
213B LEU 2.9 1.4 + - - -
214B LEU* 1.3 77.3 - - - +
216B GLN* 1.3 64.4 + - - +
218B ALA* 3.0 21.5 + - - +
219B GLU* 3.6 2.8 + - - +
235B LEU* 5.2 2.0 - - + -
237B VAL* 4.7 3.4 - - + -
264B HIS* 3.4 28.3 - - + +
267B ASP* 3.9 25.8 - - + +
268B LEU* 3.5 32.3 - - + -
271B LEU* 3.7 16.7 - - + +
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Residues in contact with GLN 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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64A VAL* 6.1 0.9 - - - +
89A ARG* 3.4 35.2 + - - +
212B MSE 3.1 22.9 + - - +
213B LEU* 2.8 10.8 + - - +
215B VAL* 1.3 76.8 - - + +
217B GLN* 1.3 61.2 + - - +
219B GLU* 3.4 24.0 - - - +
220B ASP* 4.4 3.3 + - - +
263B LYS* 5.6 3.2 - - - +
267B ASP* 3.6 31.7 + - - +
271B LEU* 5.8 0.2 - - - -
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Residues in contact with GLN 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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89A ARG* 2.7 46.9 + - + +
92A ALA* 4.2 3.6 - - - +
95A GLY* 3.4 36.5 + - - +
97A PHE* 3.6 9.2 - - + -
213B LEU* 2.7 48.0 + - + +
214B LEU* 3.4 9.7 + - - +
215B VAL 3.1 0.2 - - - -
216B GLN* 1.3 73.6 - - - +
218B ALA* 1.3 64.1 + - - +
219B GLU 3.0 2.8 + - - -
220B ASP* 3.3 25.5 + - + +
221B LYS 3.9 1.7 + - - -
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Residues in contact with ALA 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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97A PHE* 3.4 22.4 - - + -
169B ILE* 4.1 16.1 - - + +
171B ILE* 5.1 0.7 - - + -
214B LEU 2.7 11.4 + - - +
215B VAL* 3.0 19.2 + - - +
217B GLN* 1.3 76.3 - - - +
219B GLU* 1.3 58.7 + - - +
221B LYS* 3.2 5.0 + - - +
222B ILE* 2.9 32.4 + - + +
235B LEU* 4.4 14.6 - - + -
271B LEU* 4.7 0.9 - - + -
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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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215B VAL 3.6 2.2 + - - +
216B GLN* 3.4 17.2 + - - +
217B GLN 3.0 0.2 - - - -
218B ALA* 1.3 76.6 - - - +
220B ASP* 1.3 69.4 + - - +
222B ILE* 3.1 7.8 + - - +
223B LYS* 2.8 41.0 + - + +
270B ARG* 2.5 39.9 + - - -
271B LEU* 3.9 17.3 - - + -
275B TYR* 3.1 28.4 + - + +
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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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90A LYS* 5.1 14.7 - - - +
216B GLN 4.5 6.1 - - - +
217B GLN* 3.3 18.0 + - + +
219B GLU* 1.3 82.2 - - - +
221B LYS* 1.3 60.9 + - - +
223B LYS* 3.1 24.4 - - - +
224B GLU* 3.1 8.9 + - - +
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Residues in contact with LYS 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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97A PHE* 4.6 19.7 + - + +
357A IMD 3.9 11.7 - - - -
169B ILE* 3.4 25.8 - - + -
201B TYR* 3.6 41.5 - - + -
217B GLN 3.9 1.0 + - - +
218B ALA 3.2 9.7 + - - +
219B GLU 3.2 0.6 - - - -
220B ASP* 1.3 75.9 - - - +
222B ILE* 1.3 68.7 + - - +
223B LYS 2.9 1.0 + - - -
224B GLU* 3.0 36.6 + - - +
225B LEU* 3.0 37.1 + - + +
232B VAL* 5.0 0.9 - - + -
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Residues in contact with ILE 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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169B ILE* 4.5 5.2 - - + -
218B ALA 2.9 22.9 + - - +
219B GLU* 3.5 6.5 - - - +
221B LYS* 1.3 71.9 - - - +
223B LYS* 1.3 52.2 + - - +
225B LEU* 3.6 2.1 + - - +
226B LEU* 2.8 34.9 + - + +
232B VAL* 3.7 26.6 + - + +
235B LEU* 4.1 10.5 - - + -
271B LEU* 3.9 35.4 - - + -
275B TYR* 3.6 34.8 - - + -
277B ILE* 3.3 31.2 - - + -
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Residues in contact with LYS 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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219B GLU* 2.8 31.1 + - + +
220B ASP* 3.1 15.3 - - - +
221B LYS 2.9 0.4 + - - -
222B ILE* 1.3 75.0 - - - +
224B GLU* 1.3 59.8 + - - +
226B LEU* 2.5 42.0 + - + +
227B ASN* 4.0 3.3 + - - -
275B TYR* 3.0 34.8 + - + +
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Residues in contact with GLU 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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357A IMD 4.6 8.5 + - - -
220B ASP 3.1 7.0 + - - +
221B LYS* 3.0 33.9 + - - +
223B LYS* 1.3 78.7 - - - +
225B LEU* 1.3 72.1 + - + +
226B LEU 3.0 2.9 + - - -
227B ASN* 3.7 11.6 + - - +
228B THR* 4.4 3.6 + - - -
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Residues in contact with LEU 225 (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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357A IMD 5.4 2.2 - - - +
167B SER* 3.9 18.8 - - - +
199B HIS* 5.8 2.0 - - - +
201B TYR* 3.8 23.8 - - + +
221B LYS* 3.0 45.3 + - + +
222B ILE 3.6 0.4 - - - -
224B GLU* 1.3 84.0 - - + +
226B LEU* 1.3 65.6 + - - +
227B ASN 3.3 0.9 - - - -
228B THR* 3.0 33.7 - - + +
230B ARG 4.0 5.8 - - - +
231B PRO* 3.4 9.7 - - - +
232B VAL* 4.0 24.5 - - + +
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Residues in contact with LEU 226 (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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222B ILE* 2.8 13.8 + - + +
223B LYS* 2.5 29.5 + - + +
225B LEU* 1.3 71.5 - - - +
227B ASN* 1.3 71.5 + - - +
228B THR 3.2 3.8 + - - -
231B PRO* 3.4 23.8 - - + +
232B VAL 5.5 0.2 - - - +
275B TYR* 4.0 41.7 - - + +
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Residues in contact with ASN 227 (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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223B LYS 4.8 2.8 + - - -
224B GLU 3.7 6.6 + - - +
225B LEU 3.3 0.8 - - - -
226B LEU* 1.3 91.5 - - - +
228B THR* 1.3 64.1 + - - +
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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
------------------------------------------------------------
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