Contacts of the helix formed by residues 219 - 230 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A VAL* 3.2 38.7 + - - +
71A GLY 5.6 0.2 - - - +
73A GLU* 2.8 21.3 + - - +
116A PHE* 3.7 31.7 - - + -
119A ASN* 4.3 9.7 + - - +
121A TRP* 5.3 2.1 - - - +
217A TYR* 4.9 0.2 - - - +
218A GLN* 1.3 72.6 + - - +
220A HIS* 1.3 63.9 + - - +
221A LYS* 3.0 23.6 + - - +
222A ILE* 3.0 21.2 + - + +
223A THR* 3.5 4.6 + - - -
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Residues in contact with HIS 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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218A GLN 2.9 9.6 + - - +
219A ASN* 1.3 70.7 + - - +
221A LYS* 1.3 67.4 + - - +
223A THR* 3.4 18.0 + - + -
224A GLN* 3.3 37.5 + - + +
15D T 4.4 14.9 + - - -
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Residues in contact with LYS 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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70A VAL* 3.9 28.3 - - + -
119A ASN* 5.8 2.9 - - - -
219A ASN* 3.0 16.3 + - - +
220A HIS* 1.3 81.1 - - - +
222A ILE* 1.3 63.7 + - - +
224A GLN* 3.1 6.7 + - + +
225A LEU* 3.0 22.6 + - + +
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Residues in contact with ILE 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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67A PHE* 3.7 27.1 - - + +
70A VAL* 4.0 26.0 - - + -
71A GLY 3.7 25.4 - - - +
72A THR* 4.3 5.6 - - - -
73A GLU* 4.2 13.9 - - + +
217A TYR* 3.6 30.5 - - + -
219A ASN* 3.0 13.1 + - + +
221A LYS* 1.3 77.5 - - - +
223A THR* 1.3 65.7 + - - +
225A LEU* 2.7 19.9 + - + +
226A LYS* 2.8 21.5 + - - +
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Residues in contact with THR 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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217A TYR* 3.3 31.9 + - + +
219A ASN 3.5 1.0 + - - -
220A HIS* 3.4 30.9 + - + +
221A LYS 3.3 0.6 - - - -
222A ILE* 1.3 80.2 - - - +
224A GLN* 1.3 59.0 + - - +
226A LYS* 3.1 5.6 + - - +
227A ILE* 2.9 34.0 + - + +
14D G 3.5 20.9 - - - +
15D T 3.4 31.1 + - - +
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Residues in contact with GLN 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 HIS* 3.3 28.0 + - - +
221A LYS* 3.1 11.4 + - + +
223A THR* 1.3 79.4 - - - +
225A LEU* 1.3 61.1 + - - +
227A ILE* 4.2 28.9 - - - +
228A GLU* 3.1 36.0 + - + +
236A PHE 4.5 7.7 + - - -
237A ARG* 5.4 2.4 - - - +
15D T 5.7 0.2 + - - -
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Residues in contact with LEU 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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66A LYS* 3.3 44.0 - - + +
67A PHE* 3.7 28.4 - - + -
70A VAL* 4.2 15.5 - - + -
221A LYS* 3.0 13.3 + - + +
222A ILE* 2.7 23.2 + - + +
224A GLN* 1.3 70.1 - - - +
226A LYS* 1.3 62.1 + - - +
228A GLU* 4.3 1.7 - - + -
229A ASN* 3.4 42.8 + - - +
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Residues in contact with LYS 226 (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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67A PHE* 3.6 29.1 - - + -
73A GLU 3.0 26.6 + - - -
74A MET* 3.7 9.5 - - - +
75A ILE 5.2 0.2 - - - +
84A PHE* 2.6 39.5 + - + +
217A TYR* 3.1 35.7 + - + +
222A ILE* 2.8 20.1 + - - +
223A THR* 3.4 6.7 - - - +
225A LEU* 1.3 77.7 - - - +
227A ILE* 1.3 58.3 + - - +
230A ASN* 2.8 40.0 + - + +
233A ALA* 5.0 0.7 - - - -
14D G 3.5 17.3 - - - +
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Residues in contact with ILE 227 (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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223A THR* 2.9 24.4 + - + +
224A GLN* 3.3 25.8 + - - +
225A LEU 3.3 0.2 - - - -
226A LYS* 1.3 78.2 - - - +
228A GLU* 1.3 54.5 + - + +
230A ASN 4.1 0.5 + - - +
233A ALA* 3.8 9.9 - - + +
236A PHE* 3.6 45.8 - - + +
237A ARG* 2.7 43.2 + - + +
14D G 3.5 41.7 - - - +
15D T 4.4 3.8 - - - +
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Residues in contact with GLU 228 (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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224A GLN* 3.1 33.1 + - + +
225A LEU* 4.3 2.0 - - + +
227A ILE* 1.3 73.2 - - - +
229A ASN* 1.3 63.7 + - - +
237A ARG* 2.3 47.1 + - + +
238A GLY 5.7 1.2 + - - -
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Residues in contact with ASN 229 (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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63A LEU* 3.2 34.3 - - + +
66A LYS* 5.1 4.0 - - - +
67A PHE* 5.0 0.7 - - + -
84A PHE* 3.1 25.9 - - + -
225A LEU* 3.4 30.1 + - - +
226A LYS 3.2 2.0 + - - -
228A GLU* 1.3 88.2 - - - +
230A ASN* 1.3 59.7 + - - +
231A PRO* 3.2 9.7 - - - +
237A ARG* 3.6 3.8 - - - +
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Residues in contact with ASN 230 (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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84A PHE* 3.4 40.6 - - + +
226A LYS* 2.8 23.4 + - + +
229A ASN* 1.3 70.9 - - - +
231A PRO* 1.3 64.6 - - - +
232A PHE* 3.3 19.7 + - - -
233A ALA* 2.6 38.5 + - + +
237A ARG* 3.5 8.1 + - - +
13D T 3.5 40.3 + - - -
14D G 5.2 1.2 + - - -
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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