Contacts of the helix formed by residues 211 - 224 (chain A) in PDB entry 1PR9
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 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A VAL* 4.0 4.3 - - - -
183A MET* 6.0 2.4 + - - +
208A LYS* 4.6 7.1 - - + +
209A PHE* 3.9 11.7 - - - +
210A ALA* 1.3 77.0 - - - +
212A VAL* 1.3 67.8 + - - +
213A GLU* 4.0 16.4 - - + +
214A HIS* 3.0 39.9 + - + +
215A VAL* 3.4 10.4 + - - +
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Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLY* 4.4 7.2 - - - +
19A ILE* 4.2 16.2 - - + -
22A GLY* 4.1 19.1 - - - -
182A VAL* 3.8 20.6 - - + +
183A MET 6.2 0.2 - - - -
184A THR* 4.3 15.0 - - + -
211A GLU* 1.3 72.0 - - - +
213A GLU* 1.3 64.8 + - - +
215A VAL* 2.9 9.0 + - - +
216A VAL* 2.9 36.9 + - + +
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Residues in contact with GLU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLU* 3.1 14.1 - - + +
212A VAL* 1.3 81.8 - - - +
214A HIS* 1.3 72.8 + - + +
216A VAL* 3.8 7.1 - - - +
217A ASN* 2.9 46.6 + - - +
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Residues in contact with HIS 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A LYS* 4.9 16.1 + - - +
209A PHE 5.0 1.8 + - - -
210A ALA* 3.9 7.8 - - + -
211A GLU* 3.0 53.3 + - + +
213A GLU* 1.3 89.5 - - + +
215A VAL* 1.3 63.8 + - - +
217A ASN* 3.5 8.8 + - - +
218A ALA* 3.4 19.9 + - - +
237A VAL* 3.9 22.8 - - + +
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Residues in contact with VAL 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 3.8 32.8 - - + -
134A VAL* 5.1 1.8 - - + -
177A VAL* 4.5 9.0 - - + -
179A PRO* 4.0 37.2 - - + -
182A VAL* 4.0 14.8 - - + -
210A ALA* 4.8 1.3 - - + -
211A GLU 3.7 12.1 - - - +
212A VAL 2.9 5.9 + - - +
214A HIS* 1.3 74.3 - - - +
216A VAL* 1.3 68.1 + - - +
218A ALA* 3.1 6.5 + - - +
219A ILE* 2.9 31.2 + - + +
237A VAL* 4.5 11.4 - - + -
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Residues in contact with VAL 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 4.2 4.0 - - + +
22A GLY 3.8 6.3 - - - +
23A THR* 3.5 37.7 - - + +
26A ALA* 3.7 28.9 - - + -
212A VAL* 2.9 29.0 + - + +
213A GLU* 3.8 6.5 - - - +
215A VAL* 1.3 78.8 - - - +
217A ASN* 1.3 65.8 + - - +
219A ILE* 3.0 8.2 + - - +
220A LEU* 2.9 34.3 + - + +
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Residues in contact with ASN 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A GLU* 2.9 36.2 + - - +
214A HIS* 3.7 10.2 + - - +
215A VAL 3.2 0.2 - - - -
216A VAL* 1.3 80.0 - - - +
218A ALA* 1.3 57.0 + - - +
220A LEU* 3.5 13.2 + - - +
221A PHE* 3.1 27.4 + - - +
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Residues in contact with ALA 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A VAL* 3.9 14.1 - - + -
214A HIS 3.4 9.7 + - - +
215A VAL 3.1 8.6 + - - +
217A ASN* 1.3 77.4 - - - +
219A ILE* 1.3 66.0 + - - +
221A PHE* 3.3 6.0 + - - +
222A LEU* 3.1 28.8 + - - +
235A LEU* 4.1 13.7 - - + -
237A VAL* 3.9 22.9 - - + -
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Residues in contact with ILE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 4.2 4.5 - - + -
23A THR* 3.8 28.0 - - + +
81A VAL* 3.9 32.3 - - + -
83A ASN* 5.6 0.2 - - - +
132A VAL* 3.9 12.9 - - + +
134A VAL* 4.1 17.5 - - + -
177A VAL* 4.0 22.2 - - + -
215A VAL* 2.9 34.9 + - + +
216A VAL* 3.0 6.5 + - - +
218A ALA* 1.3 77.6 - - - +
220A LEU* 1.3 59.3 + - + +
222A LEU* 3.3 2.9 + - - +
223A LEU* 3.0 36.4 + - + +
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Residues in contact with LEU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 4.5 18.4 - - + +
5A LEU* 3.3 30.1 - - + +
23A THR* 5.7 1.8 - - + -
26A ALA* 4.5 11.2 - - + +
27A LEU* 3.7 22.9 - - + -
30A THR* 5.5 9.0 - - + -
216A VAL* 2.9 36.3 + - + +
217A ASN* 3.7 12.8 - - - +
219A ILE* 1.3 77.1 - - + +
221A PHE* 1.3 65.3 + - - +
223A LEU* 3.3 8.8 + - + +
224A SER* 3.1 24.3 + - - -
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Residues in contact with PHE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.9 16.2 - - + -
3A LEU* 4.9 6.7 - - + +
217A ASN 3.1 16.7 + - - +
218A ALA* 3.8 5.6 - - - +
219A ILE 3.3 0.4 - - - -
220A LEU* 1.3 75.8 - - - +
222A LEU* 1.3 73.9 + - + +
224A SER* 2.8 21.9 + - - -
226A ARG* 4.0 29.8 - - + -
227A SER* 2.9 38.0 + - - -
230A THR* 5.6 3.1 - - + -
235A LEU* 4.6 13.7 - - + -
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Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ALA* 4.3 4.7 - - - +
131A ILE 5.7 0.2 - - - +
132A VAL* 3.9 16.1 - - + +
173A ARG* 3.3 21.8 + - - -
175A ASN* 3.9 38.9 + - + +
176A ALA 4.0 8.7 - - - +
177A VAL* 3.6 31.4 - - + -
218A ALA 3.1 11.3 + - - +
219A ILE 3.6 4.0 - - - +
221A PHE* 1.3 87.8 - - + +
223A LEU* 1.3 61.1 + - - +
224A SER 3.3 0.2 - - - -
227A SER* 3.3 7.2 - - - +
230A THR* 4.2 15.7 - - + -
233A SER* 4.8 2.2 - - - +
235A LEU* 4.3 20.2 - - + -
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Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 4.6 7.4 - - + +
8A ARG* 4.9 3.1 + - - -
10A VAL* 4.5 13.9 - - + -
27A LEU* 4.8 14.6 - - + -
79A LEU* 3.9 30.4 - - + +
80A LEU 4.0 10.3 - - - +
81A VAL* 3.9 20.2 - - + -
130A ALA* 3.8 34.8 - - - +
132A VAL* 3.5 21.5 - - + -
173A ARG* 3.8 5.4 + - - -
219A ILE* 3.0 26.7 + - + +
220A LEU* 3.3 8.7 + - + +
221A PHE 3.2 0.6 - - - -
222A LEU* 1.3 78.5 - - - +
224A SER* 1.3 62.9 + - - +
225A ASP* 4.0 1.2 + - - +
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Residues in contact with SER 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 3.3 41.9 - - - +
5A LEU* 4.5 4.9 - - - -
8A ARG* 5.6 0.7 - - - +
173A ARG* 2.7 23.6 + - - -
220A LEU 3.1 10.1 + - - -
221A PHE* 2.8 17.3 + - - -
223A LEU* 1.3 79.8 - - - +
225A ASP* 1.3 57.0 + - - +
226A ARG* 3.0 23.5 + - - +
227A SER* 2.9 12.8 + - - -
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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