Contacts of the helix formed by residues 205 - 218 (chain A) in PDB entry 5AM1
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 ASP 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A VAL* 4.8 0.4 - - - -
204A GLN* 1.4 86.9 + - - +
206A THR* 1.3 62.7 + - - +
207A ASP* 3.7 10.2 - - + +
208A THR* 2.7 46.0 + - - +
209A ALA* 3.3 19.2 + - - +
211A LYS* 4.9 0.5 + - - -
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Residues in contact with THR 206 (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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16A LEU* 4.0 9.4 - - - +
102A ASN* 2.9 41.0 + - - +
104A PRO* 4.2 13.2 - - + -
105A MET* 4.3 10.9 - - + +
203A VAL* 5.0 3.2 - - - +
204A GLN 3.9 1.7 + - - -
205A ASP* 1.3 71.7 - - - +
207A ASP* 1.3 54.4 + - - +
209A ALA* 3.1 8.6 + - - +
210A LEU* 2.7 57.0 + - + +
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Residues in contact with ASP 207 (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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205A ASP* 3.5 9.3 - - + +
206A THR* 1.3 79.3 - - - +
208A THR* 1.4 56.9 + - - +
210A LEU* 3.3 4.0 + - - +
211A LYS* 2.9 46.7 + - - +
222A LEU* 3.6 35.9 - - - +
223A ASN* 5.1 2.1 - - - +
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Residues in contact with THR 208 (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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205A ASP* 2.7 36.7 + - - +
207A ASP* 1.4 69.6 - - - +
209A ALA* 1.3 61.0 + - - +
211A LYS* 3.0 26.2 + - + +
212A GLU* 2.9 45.2 + - + +
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Residues in contact with ALA 209 (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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105A MET* 4.4 6.7 - - + -
183A LEU* 4.7 2.8 - - + +
201A ILE* 3.9 16.4 - - + +
202A LEU 5.1 1.8 + - - -
203A VAL* 3.8 38.6 - - + -
205A ASP 3.3 11.5 + - - +
206A THR* 3.1 10.7 + - - +
208A THR* 1.3 79.1 - - - +
210A LEU* 1.4 56.0 + - - +
212A GLU* 3.4 6.4 + - - +
213A LEU* 2.9 28.2 + - - +
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Residues in contact with LEU 210 (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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104A PRO* 3.8 25.8 - - + +
105A MET* 3.8 21.8 - - - -
108A ALA* 3.5 28.0 - - + -
183A LEU* 5.5 0.2 - - + -
206A THR* 2.7 38.3 + - + +
207A ASP 3.7 4.7 - - - +
209A ALA* 1.4 72.0 - - - +
211A LYS* 1.4 59.1 + - - +
213A LEU* 3.7 13.8 - - + +
214A GLU* 3.0 32.9 + - - +
221A LEU* 4.8 13.2 - - + +
222A LEU* 3.8 27.6 - - + -
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Residues in contact with LYS 211 (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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205A ASP* 4.9 0.4 + - - -
207A ASP* 2.9 37.7 + - - +
208A THR* 3.0 31.5 + - + +
210A LEU* 1.4 73.7 - - - +
212A GLU* 1.4 63.8 + - + +
214A GLU* 3.5 14.4 - - - +
215A LYS* 3.1 33.1 + - - +
222A LEU* 3.7 16.2 - - + -
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Residues in contact with GLU 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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200A THR 4.5 2.8 - - - +
201A ILE* 3.7 35.7 - - + +
202A LEU* 4.5 11.5 + - - +
208A THR* 2.9 28.6 + - + +
209A ALA* 3.4 9.6 - - - +
211A LYS* 1.4 76.9 - - + +
213A LEU* 1.3 61.0 + - - +
215A LYS* 3.3 7.8 + - - +
216A VAL* 3.1 25.8 + - - +
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Residues in contact with LEU 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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6A ALA* 5.2 0.4 - - + -
8A PHE* 4.2 10.3 - - + -
108A ALA* 4.4 3.1 - - + -
112A LEU* 3.8 23.8 - - + -
181A VAL* 3.9 28.3 - - + -
183A LEU* 4.1 20.0 - - + -
201A ILE* 3.7 11.4 - - + +
209A ALA 2.9 17.2 + - - +
210A LEU* 3.8 23.8 - - + +
211A LYS 3.4 0.4 - - - -
212A GLU* 1.3 77.8 - - - +
214A GLU* 1.3 51.4 + - - +
216A VAL* 3.6 1.6 - - - +
217A THR* 2.7 51.1 + - + +
221A LEU* 3.7 17.0 - - + -
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Residues in contact with GLU 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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210A LEU 3.0 17.4 + - - +
211A LYS* 3.5 18.6 - - - +
213A LEU* 1.3 74.6 - - - +
215A LYS* 1.3 60.5 + - - +
217A THR* 3.6 1.8 - - - -
218A GLY* 2.8 29.6 + - - -
219A ILE 3.0 22.2 + - - +
220A GLN* 3.6 12.6 - - - +
221A LEU* 3.1 26.3 + - + +
222A LEU* 3.3 30.6 + - - +
223A ASN* 5.8 0.5 + - - -
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Residues in contact with LYS 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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211A LYS* 3.1 24.1 + - - +
212A GLU* 3.3 8.7 + - - +
214A GLU* 1.3 79.8 - - - +
216A VAL* 1.3 60.6 + - - +
217A THR 3.7 0.2 + - - -
218A GLY* 3.9 5.5 + - - -
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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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3A LEU* 3.4 20.7 - - + +
181A VAL* 4.1 24.5 - - + -
199A VAL* 3.6 31.2 - - + -
201A ILE* 4.3 3.4 - - + -
212A GLU 3.1 19.7 + - - +
213A LEU* 3.6 9.4 - - - +
215A LYS* 1.3 77.9 - - - +
217A THR* 1.4 60.7 + - + +
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Residues in contact with THR 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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3A LEU* 4.0 14.4 - - + -
112A LEU* 3.9 20.5 - - + +
117A PHE* 3.7 33.6 - - + -
181A VAL* 4.2 1.3 - - + -
213A LEU* 2.7 42.3 + - + +
214A GLU* 3.6 4.9 - - - -
216A VAL* 1.4 76.5 - - + +
218A GLY* 1.3 63.3 + - - +
219A ILE* 3.2 20.3 + - - +
221A LEU* 4.0 0.7 - - - +
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Residues in contact with GLY 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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214A GLU 2.8 14.1 + - - -
215A LYS 3.9 5.4 + - - -
216A VAL 3.6 1.8 - - - -
217A THR* 1.3 77.6 - - - +
219A ILE* 1.4 59.1 + - - +
220A GLN 4.4 0.3 + - - -
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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