Contacts of the helix formed by residues 219 - 230 (chain E) in PDB entry 4S0H
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 ASN 219 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70E VAL* 3.4 32.5 + - - +
71E GLY 5.5 0.2 + - - -
73E GLU* 3.4 18.1 + - - +
116E PHE* 3.6 25.0 - - + -
119E ASN* 4.8 7.1 + - - -
121E TRP* 5.2 1.8 - - - +
217E TYR* 4.9 0.2 - - - +
218E GLN* 1.3 79.7 + - - +
220E HIS* 1.3 60.2 + - - +
221E LYS* 2.8 35.9 + - - +
222E ILE* 3.3 14.8 + - + +
223E THR* 3.5 9.8 + - - -
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Residues in contact with HIS 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E GLN 3.2 6.9 + - - +
219E ASN* 1.3 74.8 + - - +
221E LYS* 1.3 70.5 + - + +
223E THR* 3.5 15.4 - - + +
224E GLN* 3.3 30.4 + - + +
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Residues in contact with LYS 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E VAL* 3.9 32.2 - - + +
219E ASN* 2.8 19.9 + - - +
220E HIS* 1.3 88.0 - - + +
222E ILE* 1.3 55.2 + - - +
224E GLN* 3.2 5.9 + - - +
225E LEU* 2.8 38.5 + - + +
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Residues in contact with ILE 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E PHE* 3.9 23.6 - - + +
70E VAL* 3.6 23.8 - - + -
71E GLY 3.6 25.6 - - - +
72E THR* 3.8 13.2 - - - -
73E GLU* 3.7 28.3 - - + +
217E TYR* 4.1 8.1 - - + -
219E ASN* 3.3 10.8 + - + +
221E LYS* 1.3 76.2 - - - +
223E THR* 1.3 64.2 + - - +
225E LEU* 3.2 6.2 + - + +
226E LYS* 2.9 52.3 + - + +
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Residues in contact with THR 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E TYR* 3.2 40.5 - - + +
219E ASN 3.5 6.3 + - - -
220E HIS* 3.5 17.1 - - + +
221E LYS 3.2 0.8 - - - -
222E ILE* 1.3 80.4 - - - +
224E GLN* 1.3 60.9 + - + +
226E LYS* 3.1 4.5 + - - +
227E ILE* 3.0 40.4 + - + +
14H G 3.4 27.0 - - - +
15H T 3.5 12.1 - - - +
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Residues in contact with GLN 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E HIS* 3.3 22.5 + - + +
221E LYS* 3.2 6.5 + - - +
223E THR* 1.3 77.1 - - + +
225E LEU* 1.3 59.9 + - - +
226E LYS 3.0 1.8 - - - -
227E ILE* 3.7 26.7 - - + +
228E GLU* 2.9 41.7 + - + +
236E PHE 4.8 7.1 + - - -
237E ARG* 6.1 0.5 - - - +
238E GLY* 5.7 0.7 - - - +
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Residues in contact with LEU 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E LEU* 6.1 0.2 - - + -
66E LYS* 3.8 51.8 - - + +
67E PHE* 3.5 29.9 - - + -
70E VAL* 3.9 21.3 - - + -
221E LYS* 2.8 21.0 + - - +
222E ILE* 3.6 7.6 - - + +
224E GLN* 1.3 73.3 - - - +
226E LYS* 1.3 59.7 + - - +
228E GLU* 4.2 6.0 - - + +
229E ASN* 3.3 31.9 + - - +
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Residues in contact with LYS 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E PHE* 3.4 22.4 - - + -
72E THR* 5.6 0.2 - - - -
73E GLU 2.9 30.1 + - - +
74E MET* 3.5 12.7 - - - +
75E ILE 4.9 1.0 - - - +
84E PHE* 2.7 46.2 + - + +
217E TYR* 3.1 26.1 + - + +
222E ILE* 2.9 24.5 + - - +
223E THR* 3.4 8.7 - - - +
224E GLN 3.0 0.2 - - - -
225E LEU* 1.3 78.3 - - - +
227E ILE* 1.3 58.9 + - - +
228E GLU 3.4 0.2 - - - -
229E ASN 3.9 0.4 - - - +
230E ASN* 3.1 32.1 + - - +
233E ALA* 4.1 2.9 - - - +
14H G 4.3 11.9 - - - +
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Residues in contact with ILE 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223E THR* 3.0 23.1 + - + +
224E GLN* 3.0 32.6 + - - +
226E LYS* 1.3 76.2 - - - +
228E GLU* 1.3 67.7 + - - +
229E ASN 3.3 0.5 + - - -
230E ASN 4.0 2.8 + - - +
233E ALA* 3.7 20.9 - - + +
236E PHE* 3.7 37.7 - - + +
237E ARG* 3.0 28.3 + - + +
14H G 4.1 14.4 - - - -
15H T 3.4 24.5 - - - +
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Residues in contact with GLU 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E GLN* 2.9 24.2 + - - +
225E LEU* 4.2 9.4 - - + +
227E ILE* 1.3 78.2 - - - +
229E ASN* 1.3 68.8 + - - +
237E ARG* 2.9 29.0 + - + +
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Residues in contact with ASN 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E LEU* 3.4 31.4 - - + +
66E LYS* 5.0 7.1 + - - +
67E PHE* 4.7 0.3 - - - -
84E PHE* 3.2 25.4 - - + -
225E LEU* 3.3 28.1 + - - +
227E ILE 3.2 0.6 - - - -
228E GLU* 1.3 91.3 + - - +
230E ASN* 1.3 58.9 + - - +
231E PRO* 3.2 11.3 - - - +
237E ARG* 3.9 2.7 + - - +
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Residues in contact with ASN 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E PHE* 3.3 35.3 - - + +
226E LYS 3.1 19.0 + - - +
227E ILE 4.3 0.2 - - - +
228E GLU 3.8 1.0 - - - -
229E ASN* 1.3 75.7 - - - +
231E PRO* 1.3 62.5 - - - +
232E PHE* 2.8 21.7 + - - -
233E ALA* 2.5 40.1 + - + +
234E LYS 3.6 2.1 + - - -
237E ARG* 3.8 4.1 + - - +
13H T 3.0 40.6 + - - -
14H G 3.9 5.1 + - - +
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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