Contacts of the helix formed by residues 219 - 226 (chain B) in PDB entry 3NYN
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 LYS 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B LEU 3.4 2.5 + - - -
218B GLU* 1.3 70.6 - - - +
220B LYS* 1.3 62.0 + - + +
222B ILE* 3.6 10.2 + - - +
223B LYS* 3.3 18.9 + - - +
254B GLU* 3.2 24.2 + - - -
255B THR 2.7 28.9 + - - -
256B LYS* 3.3 22.3 + - - +
257B ASP* 3.3 11.7 + - - +
258B ALA* 3.7 22.9 - - - +
259B LEU* 4.3 6.7 - - + +
491B LEU* 4.5 16.5 - - + +
499B TYR* 3.4 50.3 + - + +
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Residues in contact with LYS 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B GLU* 3.2 2.8 - - + +
219B LYS* 1.3 74.4 - - + +
221B ARG* 1.3 62.4 + - + +
222B ILE 3.1 1.6 - - - -
223B LYS* 2.9 9.2 + - - +
224B LYS* 2.8 29.2 + - - +
257B ASP* 5.1 4.9 + - - +
486B VAL 4.8 13.5 - - - +
487B LYS* 5.3 14.1 - - - +
488B GLY 6.0 0.2 - - - +
489B VAL* 4.0 32.7 + - + +
491B LEU* 4.0 28.3 - - + -
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Residues in contact with ARG 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B LYS* 3.9 26.7 - - - +
196B GLY 4.6 4.5 + - - -
197B PHE* 3.8 34.0 + - + +
198B GLY* 4.5 5.1 - - - +
218B GLU* 3.0 40.3 + - + +
220B LYS* 1.3 79.5 - - + +
222B ILE* 1.3 61.1 + - - +
224B LYS* 3.9 10.0 - - + +
225B ARG* 3.1 39.0 + - + +
482B GLN* 4.7 2.8 - - - +
483B PHE* 3.3 48.2 + - - +
484B SER 4.7 3.4 + - - -
485B THR* 4.7 10.1 - - - +
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Residues in contact with ILE 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B PHE* 4.6 17.5 - - + -
217B LEU* 3.7 32.1 - - + +
218B GLU 3.0 15.2 + - - +
219B LYS* 3.6 11.2 - - - +
221B ARG* 1.3 77.0 - - - +
223B LYS* 1.3 58.8 + - - +
226B LYS* 3.0 22.3 + - - -
227B GLY 3.0 16.6 + - - +
228B GLU* 3.7 34.2 - - + +
231B ALA* 4.0 21.5 - - + -
259B LEU* 4.3 17.5 - - + -
498B PHE* 4.6 7.4 - - + -
499B TYR* 5.8 2.5 - - + +
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Residues in contact with LYS 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B LYS 3.3 9.2 + - - +
220B LYS* 2.9 9.0 + - - +
222B ILE* 1.3 76.6 - - + +
224B LYS* 1.3 68.6 + - - +
226B LYS* 3.3 18.7 + - - +
228B GLU* 3.8 11.4 - - - +
489B VAL* 4.0 22.4 - - + -
490B GLU 2.8 24.4 + - - +
491B LEU* 5.1 5.8 - - + -
492B GLU* 3.7 27.3 + - - +
495B ASP* 3.4 37.2 + - - +
499B TYR* 5.6 0.2 - - - +
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Residues in contact with LYS 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B LYS 2.8 15.4 + - - +
221B ARG* 3.9 11.2 - - + +
223B LYS* 1.3 79.8 - - - +
225B ARG* 1.3 65.2 + - + +
226B LYS* 3.4 3.5 + - - +
483B PHE* 5.2 7.1 - - - -
486B VAL* 3.6 41.0 - - + +
489B VAL* 5.0 18.3 - - + +
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Residues in contact with ARG 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B LYS* 5.6 5.9 - - - +
196B GLY* 3.6 28.6 + - - -
197B PHE* 3.9 28.8 - - + -
221B ARG* 3.1 23.6 + - + +
222B ILE 4.6 0.4 - - - +
224B LYS* 1.3 80.7 - - + +
226B LYS* 1.3 70.5 - - - +
227B GLY* 4.5 0.2 - - - -
483B PHE* 6.0 5.3 - - - -
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Residues in contact with LYS 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B ILE 3.0 7.5 + - - -
223B LYS 3.3 12.0 + - - +
224B LYS 3.2 4.6 - - - +
225B ARG* 1.3 81.9 - - - +
227B GLY* 1.3 57.6 + - - +
228B GLU* 3.2 25.0 + - - +
229B ALA* 6.1 0.7 - - - +
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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