Contacts of the helix formed by residues 209 - 222 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B ALA* 6.0 0.2 - - - -
206C MET* 3.9 18.0 - - - +
207C LYS 3.7 0.8 - - - -
208C ALA* 1.3 79.2 - - - +
210C GLY* 1.3 64.6 + - - +
211C THR 3.3 2.5 - - - -
212C ILE* 3.4 5.7 + - - +
213C ASN* 3.0 32.6 + - - -
243C VAL* 4.2 12.7 - - - +
606C PCP 3.1 10.7 + - - -
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Residues in contact with GLY 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ALA* 5.1 9.6 - - - +
175C TYR* 3.9 8.7 - - - +
176C VAL* 3.2 24.5 - - - -
208C ALA* 3.5 4.8 + - - +
209C GLY* 1.3 77.2 - - - +
211C THR* 1.3 55.5 + - - +
213C ASN* 3.4 7.3 + - - +
214C GLY* 2.8 26.0 + - - -
606C PCP 3.6 4.4 + - - -
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Residues in contact with THR 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C VAL* 4.0 27.6 - - + -
175C TYR* 3.6 13.3 - - + -
176C VAL 4.0 0.2 + - - -
177C SER* 3.6 10.4 - - - -
186C MET* 3.4 9.4 - - + +
203C ASP* 4.4 3.4 - - - +
209C GLY 3.3 0.2 - - - -
210C GLY* 1.3 69.7 - - - +
212C ILE* 1.3 66.3 + - - +
214C GLY 3.2 1.4 + - - -
215C MET* 3.1 27.1 + - + +
606C PCP 2.5 66.7 + - + +
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Residues in contact with ILE 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C ILE* 4.1 20.2 - - + -
203C ASP* 3.9 19.5 - - + +
206C MET* 3.7 22.4 - - + -
209C GLY 3.4 7.8 + - - +
210C GLY 3.4 0.4 - - - -
211C THR* 1.3 78.0 - - - +
213C ASN* 1.3 59.3 + - - +
215C MET* 3.2 15.2 + - + +
216C ILE* 2.9 37.9 + - + +
229C ILE* 4.2 16.8 - - + -
231C VAL* 3.6 31.0 - - + -
243C VAL* 3.8 25.8 - - + -
606C PCP 5.2 0.4 + - - +
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Residues in contact with ASN 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ALA* 3.4 21.3 + - - +
66B ALA* 4.4 17.2 - - + +
208C ALA 5.6 0.2 + - - -
209C GLY 3.0 24.7 + - - +
210C GLY* 3.6 6.5 - - - +
212C ILE* 1.3 74.7 - - - +
214C GLY* 1.3 60.0 + - - +
216C ILE* 3.3 19.9 + - - +
217C ASN* 2.9 41.5 + - - +
242C LEU* 2.4 33.0 + - - +
243C VAL* 3.8 10.4 - - - +
244C ASP* 4.8 1.6 - - - +
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Residues in contact with GLY 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C ILE* 3.7 16.4 - - - +
174C ASN 5.2 0.4 - - - -
175C TYR* 4.3 7.0 - - - -
186C MET* 3.5 17.3 - - - -
210C GLY 2.8 14.7 + - - -
211C THR 3.2 4.4 + - - -
213C ASN* 1.3 76.1 - - - +
215C MET* 1.3 50.6 + - - +
217C ASN* 3.1 5.6 + - - +
218C LEU* 2.7 35.2 + - - +
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Residues in contact with MET 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C MET* 3.8 25.6 - - - -
136C THR* 3.8 17.7 - - - -
137C VAL* 3.5 37.2 - - + +
159C VAL* 4.7 2.7 - - + -
186C MET* 3.5 7.8 - - - -
201C ILE* 3.6 32.5 - - + -
202C ILE 4.2 11.7 - - - +
203C ASP* 4.8 5.2 - - - +
211C THR* 3.1 22.6 + - + +
212C ILE* 3.2 16.4 + - + +
214C GLY* 1.3 76.1 - - - +
216C ILE* 1.3 62.5 + - - +
218C LEU* 3.2 6.3 + - - +
219C LEU* 2.9 29.2 + - - +
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Residues in contact with ILE 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C ILE* 4.0 18.4 - - + -
212C ILE* 2.9 26.5 + - + +
213C ASN* 3.5 19.3 - - - +
214C GLY 3.3 0.2 - - - -
215C MET* 1.3 75.0 - - - +
217C ASN* 1.3 69.5 + - - +
219C LEU* 3.3 14.9 + - - +
220C ASP* 3.3 19.0 + - - +
226C VAL* 4.2 15.2 - - + +
229C ILE* 4.0 13.0 - - + -
243C VAL* 4.8 2.2 - - + -
244C ASP* 3.3 38.1 - - - +
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Residues in contact with ASN 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 5.5 1.2 - - - +
63B PRO* 3.6 25.3 - - + +
64B GLY* 3.5 24.1 - - - -
65B ALA 4.4 5.0 + - - +
66B ALA 5.7 0.2 + - - -
173C ILE* 4.1 20.4 - - + +
174C ASN 5.4 0.3 - - - +
213C ASN* 2.9 29.0 + - - +
214C GLY* 3.5 6.1 - - - +
216C ILE* 1.3 80.3 - - - +
218C LEU* 1.3 68.2 + - - +
220C ASP* 3.1 27.1 + - - +
221C GLU* 3.5 9.0 + - - +
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Residues in contact with LEU 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C MET* 4.1 15.5 - - + -
159C VAL* 4.5 8.3 - - + -
171C VAL* 4.0 26.7 - - + +
173C ILE* 3.6 18.0 - - + +
186C MET* 4.2 16.2 - - + +
187C SER* 4.2 15.0 - - - -
188C LEU* 3.8 21.8 - - + -
214C GLY 2.7 18.0 + - - +
215C MET* 3.4 11.2 - - - +
217C ASN* 1.3 73.1 - - - +
219C LEU* 1.3 62.4 + - + +
221C GLU* 3.0 21.1 + - - +
222C PHE* 3.5 29.8 - - + -
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Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C MET* 3.5 29.8 - - + -
193C MET* 4.2 5.4 - - + -
199C VAL* 3.7 34.3 - - + -
201C ILE* 3.9 12.3 - - + -
215C MET 2.9 15.0 + - - +
216C ILE 3.5 7.9 - - - +
217C ASN 3.2 0.2 - - - -
218C LEU* 1.3 78.3 - - + +
220C ASP* 1.3 61.5 + - - +
222C PHE* 3.0 8.7 + - + +
224C ALA* 2.9 53.1 + - + +
225C ASN 4.1 6.1 - - - +
226C VAL* 3.9 25.4 - - + -
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Residues in contact with ASP 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C ILE* 3.3 18.7 + - - +
217C ASN* 3.1 20.2 + - - +
219C LEU* 1.3 78.9 - - - +
221C GLU* 1.3 60.0 + - + +
223C ASN* 3.1 22.0 + - - +
224C ALA 4.9 2.2 - - - -
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Residues in contact with GLU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C VAL* 3.5 35.5 - - + +
172C SER 5.2 1.6 - - - +
173C ILE* 4.1 15.8 - - + +
190C LYS* 6.0 1.9 - - - -
217C ASN 3.9 9.6 - - - +
218C LEU 3.0 11.9 + - - +
220C ASP* 1.3 77.2 - - + +
222C PHE* 1.3 60.9 + - - +
223C ASN 3.2 1.0 + - - -
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Residues in contact with PHE 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C VAL* 3.6 28.3 - - + -
188C LEU* 3.8 14.8 - - + -
189C ALA 3.7 17.3 - - - -
190C LYS* 3.7 24.0 - - + -
193C MET* 3.7 41.7 - - + -
194C LYS 5.0 2.0 - - - -
195C THR* 3.3 29.2 - - + -
218C LEU* 3.5 37.7 - - + -
219C LEU* 3.0 9.8 + - - +
221C GLU* 1.3 79.2 - - - +
223C ASN* 1.3 69.8 + - - +
224C ALA* 3.1 13.1 + - + +
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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