Contacts of the helix formed by residues 216 - 225 (chain G) in PDB entry 6H25
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 216 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215G CYS* 1.3 83.1 - - - +
217G ILE* 1.3 63.8 + - + +
218G ILE 3.4 2.1 + - - -
219G GLN* 3.8 6.2 + - - +
220G GLU* 3.7 19.0 + - - +
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Residues in contact with ILE 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210G LEU* 4.3 19.7 - - + -
215G CYS* 3.7 2.2 - - - -
216G GLU* 1.3 78.5 - - + +
218G ILE* 1.3 61.1 + - - +
220G GLU* 3.4 9.2 + - - +
221G VAL* 3.0 38.1 + - + +
253G ILE* 5.9 7.0 - - + +
254G LEU* 5.5 9.0 - - + -
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Residues in contact with ILE 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210G LEU* 5.0 6.3 - - + +
211G LEU* 5.8 3.1 - - + -
215G CYS* 3.7 30.6 - - + -
217G ILE* 1.3 80.0 - - - +
219G GLN* 1.3 77.2 + - + +
221G VAL* 3.8 7.3 - - + +
222G GLY* 2.9 25.1 + - - -
229G ILE* 4.7 11.2 - - + -
231G PHE* 4.5 19.1 - - + -
254G LEU* 6.4 1.6 - - - -
75K MET* 4.5 22.9 - - + +
76K SER 5.3 6.1 - - - +
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Residues in contact with GLN 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215G CYS 4.9 10.3 - - - +
216G GLU 3.8 6.8 + - - +
217G ILE 3.3 0.4 - - - -
218G ILE* 1.3 94.7 - - + +
220G GLU* 1.3 59.6 + - - +
222G GLY* 3.4 2.1 + - - -
223G LYS* 2.9 29.7 + - - +
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Residues in contact with GLU 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216G GLU 3.7 12.1 + - - +
217G ILE* 3.4 11.0 + - - +
219G GLN* 1.3 78.8 - - - +
221G VAL* 1.3 58.6 - - + +
223G LYS* 3.0 7.8 + - - +
224G LEU* 2.9 49.7 + - + +
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Residues in contact with VAL 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217G ILE* 3.0 24.7 + - + +
218G ILE* 3.8 7.6 - - + +
220G GLU* 1.3 78.8 - - + +
222G GLY* 1.3 63.2 + - - +
223G LYS 3.3 0.3 + - - -
224G LEU* 3.5 12.8 + - - +
225G TYR* 3.5 15.2 + - - +
227G LEU* 3.7 23.8 - - + +
229G ILE* 6.1 2.7 - - + -
250G LEU* 3.7 30.5 - - + -
253G ILE* 4.8 20.4 - - + -
254G LEU* 5.4 7.2 - - + -
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Residues in contact with GLY 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218G ILE 2.9 15.9 + - - -
219G GLN* 3.7 1.8 - - - -
221G VAL* 1.3 77.1 - - - +
223G LYS* 1.3 60.4 + - - +
225G TYR* 4.0 4.7 + - - +
227G LEU* 5.7 0.2 - - - -
77K PHE* 3.6 28.5 - - - +
78K ARG* 3.9 22.0 + - - +
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Residues in contact with LYS 223 (chain G).
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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219G GLN 2.9 17.4 + - - +
220G GLU* 3.0 9.4 + - - +
222G GLY* 1.3 79.6 - - - +
224G LEU* 1.3 68.2 + - + +
225G TYR* 4.8 0.2 - - - -
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Residues in contact with LEU 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220G GLU* 2.9 37.8 + - + +
221G VAL* 3.5 7.1 + - - +
223G LYS* 1.3 84.7 - - + +
225G TYR* 1.3 74.0 + - + +
253G ILE* 6.3 2.9 - - + -
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Residues in contact with TYR 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221G VAL 3.5 12.5 + - - +
222G GLY* 4.0 1.4 - - - +
223G LYS 3.6 1.6 - - - -
224G LEU* 1.3 88.2 - - + +
226G PRO* 1.3 86.0 - - + +
227G LEU* 2.9 30.2 + - + +
241G ALA* 4.7 1.3 - - + -
246G GLN* 2.6 78.1 + - + +
249G ILE* 4.6 8.2 - - + +
250G LEU* 4.1 8.7 + - - +
78K ARG* 3.6 12.4 - - - +
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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