Contacts of the helix formed by residues 207 - 224 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262F ALA* 4.1 13.4 + - + +
263F LYS* 4.3 13.3 - - - +
266F ALA* 3.3 23.8 - - - +
206G PHE* 1.3 77.5 - - - +
208G SER* 1.3 56.2 + - - +
209G ASN* 3.0 14.0 + - - +
210G HIS* 2.8 26.2 + - - +
211G GLN* 2.8 25.8 + - - +
243G HIS* 2.9 19.6 + - - -
247G GLU* 2.9 20.6 - - - +
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Residues in contact with SER 208 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207G ASN* 1.3 70.9 - - - +
209G ASN* 1.3 62.9 + - - +
211G GLN* 3.3 6.2 + - - +
212G MSE 3.0 34.2 + - - +
243G HIS* 3.4 25.5 + - - +
244G PHE* 3.4 29.8 + - - -
247G GLU* 2.7 32.7 + - - +
248G TYR* 4.1 6.4 - - - -
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Residues in contact with ASN 209 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259F GLN* 5.1 10.3 - - - +
263F LYS* 6.2 2.4 - - - +
207G ASN* 3.0 12.2 + - - +
208G SER* 1.3 77.7 - - - +
210G HIS* 1.3 58.2 + - - +
212G MSE 3.7 20.8 - - - +
213G LEU* 2.9 32.7 + - + +
247G GLU* 5.2 2.6 + - - -
248G TYR* 4.7 2.5 + - - -
260G LYS* 4.5 12.2 + - - +
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Residues in contact with HIS 210 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204G ARG 2.8 25.1 - - - -
205G ALA* 3.3 2.1 - - - -
206G PHE* 2.8 40.5 + + + +
207G ASN* 2.8 27.1 + - - +
209G ASN* 1.3 74.0 - - - +
211G GLN* 1.3 67.1 + - - +
213G LEU* 3.1 9.2 + - + -
214G LEU* 2.8 43.4 + - + +
217G GLN* 6.0 1.1 - - - -
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Residues in contact with GLN 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171G ILE* 4.5 9.0 - - + +
173G THR* 3.4 28.9 - - + +
205G ALA* 3.7 15.0 - - + +
207G ASN 2.8 11.3 + - - +
208G SER 3.4 8.5 - - - +
210G HIS* 1.3 78.6 - - - +
212G MSE 1.3 63.9 + - + +
214G LEU* 3.0 12.1 + - - +
215G VAL* 3.2 14.4 + - - +
237G VAL* 4.0 2.7 - - + +
239G SER 3.8 3.2 - - - +
240G LEU* 2.9 33.4 + - - +
243G HIS* 3.9 19.1 + - - +
244G PHE* 3.5 10.9 - - - -
264G HIS* 3.1 29.5 - - + +
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Residues in contact with MSE 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208G SER* 3.0 23.5 + - - +
209G ASN* 3.7 23.8 - - - +
211G GLN* 1.3 77.2 - - - +
213G LEU* 1.3 63.0 + - - +
215G VAL* 3.3 12.3 + - - +
216G GLN* 3.4 19.4 + - - +
244G PHE* 3.8 32.8 - - + -
248G TYR* 4.7 0.2 - - - +
260G LYS* 3.9 39.7 - - + +
263G LYS* 5.6 3.8 - - - -
264G HIS* 3.7 28.5 - - + -
267G ASP* 5.2 3.8 - - - +
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Residues in contact with LEU 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209G ASN 2.9 18.3 + - - +
210G HIS* 3.7 8.7 - - + +
212G MSE 1.3 76.9 - - - +
214G LEU* 1.3 62.7 + - - +
216G GLN* 3.4 20.1 + - + +
217G GLN* 3.2 48.0 + - + +
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Residues in contact with LEU 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F THR* 4.1 11.0 - - - +
97F PHE* 3.7 10.6 - - + -
171G ILE* 3.9 17.5 - - + -
203G ALA* 3.6 29.8 - - + -
204G ARG 3.8 7.2 - - - +
205G ALA* 3.6 37.9 - - + +
210G HIS* 2.8 30.3 + - + +
211G GLN 3.0 6.5 + - - +
213G LEU* 1.3 75.1 - - - +
215G VAL* 1.3 55.6 + - - +
217G GLN* 3.0 20.4 + - - +
218G ALA* 2.7 34.7 + - - +
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Residues in contact with VAL 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171G ILE* 4.8 14.1 - - + +
211G GLN* 3.2 5.7 + - + +
212G MSE 3.5 8.5 - - - +
214G LEU* 1.3 78.7 - - - +
216G GLN* 1.3 65.3 + - - +
218G ALA* 3.0 23.9 - - - +
219G GLU 3.7 2.4 + - - -
235G LEU* 5.7 1.1 - - + -
237G VAL* 5.0 2.5 - - + -
264G HIS* 3.0 33.2 - - + +
267G ASP* 3.9 23.6 - - + +
268G LEU* 3.8 29.8 - - + -
271G LEU* 3.8 16.9 - - + +
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Residues in contact with GLN 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212G MSE 3.4 19.4 + - - +
213G LEU* 3.7 19.4 - - + +
214G LEU 3.2 0.4 - - - -
215G VAL* 1.3 77.3 - - + +
217G GLN* 1.3 62.2 + - + +
219G GLU* 3.3 21.7 + - - +
220G ASP* 4.5 1.4 + - - +
263G LYS* 4.0 17.0 + - - +
267G ASP* 4.4 20.4 - - - +
271G LEU* 6.4 0.2 - - - -
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Residues in contact with GLN 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F THR* 4.4 23.3 - - + +
97F PHE* 4.4 11.8 - - + -
210G HIS* 6.0 0.7 - - - -
213G LEU* 3.2 38.4 + - + +
214G LEU* 3.0 25.2 + - - +
216G GLN* 1.3 72.3 - - + +
218G ALA* 1.3 52.8 + - - +
219G GLU 2.9 6.1 - - - -
220G ASP* 2.7 49.6 + - - +
221G LYS* 4.0 1.2 + - - +
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Residues in contact with ALA 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F PHE* 4.0 19.9 - - + -
169G ILE* 4.2 16.9 - - + +
171G ILE* 5.3 1.1 - - + -
214G LEU 2.7 12.6 + - - +
215G VAL* 3.0 19.9 + - - +
217G GLN* 1.3 77.1 - - - +
219G GLU* 1.3 61.4 + - - +
221G LYS* 3.6 4.4 + - - +
222G ILE* 3.0 30.1 + - + +
235G LEU* 4.4 14.6 - - + -
271G LEU* 4.5 2.2 - - + -
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Residues in contact with GLU 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215G VAL 3.7 2.0 + - - +
216G GLN* 3.3 14.8 + - - +
217G GLN 2.8 1.2 + - - -
218G ALA* 1.3 79.3 - - - +
220G ASP* 1.3 56.2 + - - +
222G ILE* 3.4 5.8 - - - +
223G LYS* 2.6 47.4 + - - +
270G ARG* 2.8 43.4 + - - +
271G LEU* 3.6 20.4 - - + +
275G TYR* 2.8 30.8 + - + +
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Residues in contact with ASP 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F THR* 5.5 5.4 - - + +
216G GLN 5.0 0.9 - - - -
217G GLN* 2.7 41.1 + - - +
219G GLU* 1.3 75.6 - - - +
221G LYS* 1.3 65.6 + - + +
223G LYS* 4.5 1.5 - - - +
224G GLU* 3.1 44.0 + - - +
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Residues in contact with LYS 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F THR* 3.9 11.9 + - - +
97F PHE* 3.9 47.5 + - + +
98F MSE 5.3 0.4 - - - +
169G ILE* 4.0 21.5 - - + -
201G TYR* 3.9 30.1 - - + -
217G GLN 4.0 1.4 + - - +
218G ALA 3.6 4.1 + - - +
220G ASP* 1.3 80.0 - - + +
222G ILE* 1.3 65.8 + - - +
224G GLU* 3.4 11.7 - - - +
225G LEU* 3.3 22.1 - - + +
232G VAL* 4.7 2.5 - - - -
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Residues in contact with ILE 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G ILE* 4.3 6.1 - - + -
218G ALA 3.0 27.6 + - - +
219G GLU* 3.4 4.9 - - - +
221G LYS* 1.3 78.9 - - - +
223G LYS* 1.3 69.3 + - - +
225G LEU* 3.4 10.9 - - - +
226G LEU* 3.5 7.0 + - + +
232G VAL* 3.7 28.5 + - + +
235G LEU* 4.2 10.8 - - + -
271G LEU* 4.1 29.6 - - + -
275G TYR* 3.9 35.7 - - + -
277G ILE* 3.3 27.6 - - + -
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Residues in contact with LYS 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219G GLU* 2.6 32.8 + - - +
220G ASP* 3.4 5.2 - - - +
222G ILE* 1.3 77.5 - - - +
224G GLU* 1.3 69.7 + - + +
225G LEU 2.3 19.2 + - - -
226G LEU* 2.8 30.2 - - + +
275G TYR* 3.1 30.3 + - + -
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Residues in contact with GLU 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220G ASP* 3.1 42.7 + - - +
221G LYS* 3.4 9.1 + - - +
223G LYS* 1.3 95.3 - - + +
225G LEU* 1.3 65.1 + - - +
226G LEU* 5.1 1.1 - - - -
227G ASN* 5.7 2.0 - - - +
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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
------------------------------------------------------------
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