Contacts of the helix formed by residues 215 - 225 (chain A) in PDB entry 3PEY
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 THR 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A LEU* 4.4 1.1 - - - -
169A ALA 3.6 10.1 - - - +
171A SER 3.6 34.5 - - - +
172A ARG* 3.8 4.7 - - + +
175A ALA* 4.3 0.4 - - + -
196A ILE 3.1 2.6 + - - -
197A VAL* 3.6 24.7 - - + +
198A PRO* 4.0 2.4 - - + +
214A GLY* 1.3 74.6 - - - -
216A PRO* 1.3 71.7 - - - +
217A GLY 3.4 0.7 + - - -
218A THR* 3.5 1.2 + - - -
219A VAL* 3.2 22.4 + - - +
4B U 3.4 20.6 - - - -
5B U 2.7 19.5 + - - +
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Residues in contact with PRO 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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168A LEU* 4.0 18.4 - - + -
169A ALA 3.5 13.7 - - - +
214A GLY 4.6 0.4 - - - +
215A THR* 1.3 88.3 - - + +
217A GLY* 1.3 56.6 + - - +
219A VAL* 3.9 1.4 - - + +
220A LEU* 2.9 33.7 + - - +
244A MET* 3.7 19.1 - - + -
250A LEU* 3.7 20.6 - - + -
253A GLN* 3.6 26.5 - - + +
254A CYS* 3.9 12.1 - - - +
257A VAL* 4.2 1.7 - - + +
4B U 3.7 9.6 - - - +
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Residues in contact with GLY 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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215A THR 3.4 0.6 - - - -
216A PRO* 1.3 75.9 - - - +
218A THR* 1.3 57.5 + - - +
220A LEU* 3.5 4.5 + - - +
221A ASP* 3.0 22.5 + - - +
253A GLN* 3.9 12.1 - - - -
4B U 3.0 16.9 + - - -
5B U 3.1 36.1 - - - +
1009B NO3 4.6 1.1 - - - -
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Residues in contact with THR 218 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A ILE* 3.4 28.5 - - + -
197A VAL* 4.1 4.7 - - - -
198A PRO* 3.4 20.4 - - + +
201A PHE* 3.5 30.1 - - + -
215A THR 4.1 4.0 - - - -
217A GLY* 1.3 73.5 - - - +
219A VAL* 1.3 66.9 + - - +
221A ASP* 3.2 3.5 + - + +
222A LEU* 3.0 22.5 + - + +
5B U 2.6 39.1 + - - +
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Residues in contact with VAL 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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166A ILE* 4.9 5.2 - - + -
168A LEU* 3.8 22.7 - - + -
196A ILE* 3.7 29.6 - - + +
212A ILE* 4.7 7.9 - - + -
214A GLY* 4.3 4.5 - - - -
215A THR 3.2 18.1 + - - +
216A PRO 4.0 2.5 - - - +
218A THR* 1.3 76.6 - - - +
220A LEU* 1.3 63.9 + - - +
222A LEU* 3.2 3.6 + - - +
223A MET* 3.0 48.4 + - + +
228A MET* 4.2 11.8 - - + +
257A VAL* 4.3 11.4 - - + -
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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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216A PRO 2.9 18.5 + - - +
217A GLY* 3.7 5.4 - - - +
219A VAL* 1.3 75.9 - - - +
221A ASP* 1.3 64.9 + - - +
223A MET* 3.1 4.5 + - + +
224A ARG* 2.9 59.4 + - - +
253A GLN* 4.1 24.9 - - + -
256A ARG* 3.9 27.8 - - + -
257A VAL* 3.8 17.5 - - + +
260A PHE* 3.8 27.4 - - + -
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Residues in contact with ASP 221 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A GLY 3.0 15.5 + - - +
218A THR* 3.2 8.7 + - + +
220A LEU* 1.3 77.9 - - - +
222A LEU* 1.3 65.9 + - + +
224A ARG* 3.2 13.1 + - - +
225A ARG* 2.9 66.2 + - - +
5B U 3.4 35.5 + - + +
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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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196A ILE* 3.7 31.2 - - + -
201A PHE* 3.8 35.4 - - + -
205A LYS 5.6 0.7 - - - +
207A ILE* 4.0 22.2 - - + -
218A THR* 3.0 14.2 + - + +
219A VAL 3.8 6.7 - - - +
221A ASP* 1.3 79.3 - - + +
223A MET* 1.3 60.7 + - - +
225A ARG* 3.3 9.0 + - - -
226A LYS 3.1 3.5 + - - -
227A LEU* 3.0 56.0 + - + -
228A MET* 4.0 15.4 + - + -
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Residues in contact with MET 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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166A ILE* 3.6 30.5 - - + -
219A VAL* 3.0 26.1 + - + +
220A LEU 3.5 7.2 - - - +
222A LEU* 1.3 74.1 - - - +
224A ARG* 1.3 64.7 + - - +
226A LYS* 3.0 18.9 + - - +
227A LEU 5.0 0.2 - - - +
228A MET* 4.1 14.6 - - + -
230A LEU* 3.8 23.8 - - + -
257A VAL* 3.7 32.8 - - + -
260A PHE* 3.7 49.5 - - + -
261A LEU* 3.9 6.7 - - + -
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Residues in contact with ARG 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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220A LEU* 2.9 38.9 + - + +
221A ASP* 3.2 15.1 + - - +
223A MET* 1.3 75.7 - - - +
225A ARG* 1.3 61.2 + - + +
226A LYS* 3.2 10.2 + - - +
256A ARG* 3.7 21.6 - - - +
260A PHE* 4.1 15.0 - - + -
1007A NO3 2.7 39.9 + - - +
5B U 5.3 12.1 - - - +
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Residues in contact with ARG 225 (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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204A ASN* 5.4 5.3 + - - -
221A ASP* 2.9 51.2 + - - +
222A LEU* 3.8 8.3 - - - +
223A MET 3.1 0.6 - - - -
224A ARG* 1.3 78.2 - - + +
226A LYS* 1.3 69.7 + - - +
227A LEU* 3.2 25.6 + - + +
1008A GOL 3.2 15.8 - - - -
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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