Contacts of the helix formed by residues 204 - 217 (chain N) in PDB entry 1PP9
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 GLU 204 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29N GLN* 3.8 26.2 + - - +
203N LEU* 1.3 82.8 - - - +
205N HIS* 1.3 67.1 + - - +
206N ARG* 3.2 30.4 + - + -
207N GLN* 3.0 13.6 + - + +
208N LEU* 3.0 19.9 + - - +
17O VAL* 5.2 4.3 - - - +
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Residues in contact with HIS 205 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15N GLN* 3.3 39.5 + - + -
16N VAL 3.9 2.2 + - - -
17N SER* 2.6 30.9 + - - -
25N VAL* 3.2 36.1 - - + -
26N ALA 4.5 0.2 - - - -
27N SER* 3.0 31.0 + - - +
29N GLN* 4.8 3.6 + - - +
203N LEU 4.2 0.8 + - - -
204N GLU* 1.3 71.7 - - - +
206N ARG* 1.3 58.6 + - - +
208N LEU* 3.1 6.4 + - - +
209N LEU* 2.8 35.7 + - + +
12O GLU 5.7 2.2 - - - +
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Residues in contact with ARG 206 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204N GLU* 3.9 29.0 + - + -
205N HIS* 1.3 82.8 - - - +
207N GLN* 1.3 72.1 + - - +
209N LEU* 3.4 6.5 + - - +
210N ASP* 3.0 30.6 + - - +
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Residues in contact with GLN 207 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103N SER 5.4 1.0 - - - +
106N LEU* 3.4 23.9 - - + +
107N PRO* 3.7 24.2 - - - +
203N LEU* 4.8 6.4 - - - +
204N GLU* 3.0 16.4 + - + +
206N ARG* 1.3 90.2 - - - +
208N LEU* 1.3 66.6 + - - +
210N ASP* 3.3 8.7 + - - +
211N LEU* 3.0 32.1 + - + +
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Residues in contact with LEU 208 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N VAL* 3.6 19.5 - - + -
26N ALA 3.5 13.2 - - - +
27N SER* 3.5 29.8 - - - +
37N VAL* 4.5 2.0 - - + -
106N LEU* 4.6 8.0 - - + +
110N VAL* 4.3 17.5 - - + -
197N LEU* 4.0 21.1 - - + +
199N ALA* 3.7 22.2 - - + +
203N LEU* 4.1 7.0 - - + -
204N GLU 3.0 12.5 + - - +
205N HIS* 3.4 9.4 - - - +
207N GLN* 1.3 76.9 - - - +
209N LEU* 1.3 56.3 + - - +
211N LEU* 3.2 9.6 + - - +
212N ALA* 3.0 24.9 + - - +
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Residues in contact with LEU 209 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17N SER* 3.7 35.0 - - - +
18N GLN 5.0 2.7 - - - +
19N LEU* 3.8 24.2 - - + -
25N VAL* 4.0 17.0 - - + -
205N HIS* 2.8 26.0 + - + +
206N ARG* 3.8 7.2 - - - +
208N LEU* 1.3 71.5 - - - +
210N ASP* 1.3 60.1 + - - +
212N ALA* 3.1 5.5 + - - +
213N GLN* 2.9 42.9 + - - +
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Residues in contact with ASP 210 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206N ARG* 3.0 19.9 + - - +
207N GLN* 3.3 10.5 + - - +
209N LEU* 1.3 76.0 - - - +
211N LEU* 1.3 67.6 + - - +
213N GLN* 3.5 17.3 + - - +
214N LYS* 3.0 31.7 + - - +
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Residues in contact with LEU 211 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106N LEU* 3.7 27.8 - - + -
107N PRO* 3.6 42.8 - - + -
110N VAL* 3.8 21.7 - - + +
207N GLN* 3.0 28.5 + - + +
208N LEU* 3.6 7.0 - - - +
210N ASP* 1.3 81.0 - - - +
212N ALA* 1.3 59.8 + - - +
214N LYS* 4.1 10.1 - - + +
215N HIS* 2.8 50.7 + - + +
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Residues in contact with ALA 212 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N LEU* 3.7 10.4 - - + +
23N LEU* 4.7 1.8 - - + -
25N VAL* 3.7 30.3 - - + -
110N VAL* 4.6 0.4 - - - +
197N LEU* 3.8 17.3 - - + -
208N LEU 3.0 13.4 + - - +
209N LEU 3.3 9.2 - - - +
211N LEU* 1.3 73.8 - - - +
213N GLN* 1.3 60.5 + - - +
216N PHE* 2.7 39.9 + - - +
217N SER 3.6 0.7 + - - -
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Residues in contact with GLN 213 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N LEU* 3.4 22.7 - - + +
209N LEU* 2.9 34.4 + - - +
210N ASP* 3.7 18.2 + - - +
212N ALA* 1.3 75.9 - - - +
214N LYS* 1.3 63.2 + - - +
217N SER* 2.2 36.3 + - - +
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Residues in contact with LYS 214 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210N ASP* 3.0 25.5 + - - +
211N LEU* 3.5 13.8 - - + +
212N ALA 3.1 0.2 - - - -
213N GLN* 1.3 80.5 - - - +
215N HIS* 1.3 85.5 + - + +
217N SER* 5.1 1.4 + - - -
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Residues in contact with HIS 215 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107N PRO* 4.4 2.0 + - - +
110N VAL* 4.2 12.6 - - + +
111N GLU* 3.3 47.0 - - + +
114N ALA* 3.4 19.8 - - + +
118N GLN* 2.9 21.7 + - - +
211N LEU* 2.8 46.4 + - + +
214N LYS* 1.3 105.9 + - + +
216N PHE* 1.3 64.0 + - + +
217N SER 3.6 1.3 - - - -
218N GLY 5.1 0.6 + - - -
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Residues in contact with PHE 216 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N LEU* 4.2 1.8 - - + -
21N ASN* 2.9 20.8 + - - -
23N LEU* 3.5 24.9 - - + -
39N VAL* 4.0 27.4 - - + -
110N VAL* 3.7 22.0 - - + -
113N LEU* 3.9 5.6 - - + -
114N ALA* 3.4 36.1 - - + -
117N VAL* 4.5 10.5 - - + -
118N GLN* 4.1 9.2 - - - +
195N MET* 4.8 0.9 - - + -
197N LEU* 4.2 13.5 - - + -
212N ALA* 2.7 30.5 + - - +
215N HIS* 1.3 77.4 - - + +
217N SER* 1.3 59.4 + - - +
218N GLY 3.2 2.7 - - - -
219N LEU* 3.0 34.1 - - + +
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Residues in contact with SER 217 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N LEU* 4.5 4.8 - - - +
21N ASN* 3.2 20.6 + - - +
212N ALA 3.6 0.8 + - - -
213N GLN* 2.2 36.5 + - - +
214N LYS 5.2 2.0 - - - -
215N HIS 3.6 1.6 - - - -
216N PHE* 1.3 78.0 - - - +
218N GLY* 1.3 58.7 + - - +
219N LEU 3.1 1.4 - - - +
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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