Contacts of the helix formed by residues 219 - 226 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A LEU 3.4 2.1 + - - -
218A GLU* 1.3 71.2 - - - +
220A LYS* 1.3 64.3 + - + +
222A ILE* 3.6 10.6 + - - +
223A LYS* 3.4 16.8 + - - +
254A GLU* 2.9 25.9 + - - -
255A THR 2.7 27.4 + - - -
256A LYS* 3.5 18.0 + - - +
257A ASP* 2.8 18.6 + - - +
258A ALA* 3.9 9.2 - - - -
259A LEU* 3.8 19.5 - - + -
491A LEU* 4.3 18.9 - - + +
499A TYR* 3.5 46.8 + - + +
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Residues in contact with LYS 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 GLU* 3.2 2.6 - - + +
219A LYS* 1.3 75.6 - - + +
221A ARG* 1.3 69.0 + - + +
222A ILE 3.0 1.1 - - - -
223A LYS* 2.8 17.9 + - - +
224A LYS* 3.0 14.3 + - - +
257A ASP* 4.6 4.4 + - - +
486A VAL 4.6 11.8 + - - +
487A LYS* 5.5 10.5 - - - +
489A VAL* 4.1 40.6 + - + +
491A LEU* 4.2 26.9 - - + -
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Residues in contact with ARG 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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194A LYS* 4.1 15.8 - - - +
195A GLY 5.3 0.2 + - - -
196A GLY 4.7 10.2 + - - -
197A PHE* 4.0 31.7 - - + +
198A GLY* 4.7 4.4 - - - +
218A GLU* 3.1 38.7 + - - +
220A LYS* 1.3 78.3 - - + +
222A ILE* 1.3 61.3 + - - +
224A LYS* 4.1 8.5 - - + -
225A ARG* 3.3 38.7 + - + +
482A GLN* 4.7 2.2 - - - +
483A PHE* 3.1 58.9 + - - +
484A SER 4.6 4.0 + - - -
485A THR* 4.3 12.9 - - - +
486A VAL 5.9 1.5 - - - +
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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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197A PHE* 4.4 20.0 - - + -
217A LEU* 3.9 30.7 - - + +
218A GLU 3.1 16.2 + - - +
219A LYS* 3.6 10.5 - - - +
220A LYS 3.0 0.8 - - - -
221A ARG* 1.3 74.8 - - - +
223A LYS* 1.3 60.4 + - - +
225A ARG 3.5 0.7 + - - -
226A LYS* 2.8 24.1 + - - -
227A GLY 2.9 36.6 + - - +
228A GLU* 3.8 16.8 - - + +
231A ALA* 4.5 9.2 - - + -
259A LEU* 4.1 21.8 - - + -
498A PHE* 4.9 5.8 - - + -
499A TYR* 5.7 2.0 - - + -
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Residues in contact with LYS 223 (chain A).
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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219A LYS 3.4 8.5 + - - +
220A LYS* 2.8 11.4 + - - +
222A ILE* 1.3 76.3 - - - +
224A LYS* 1.3 65.1 + - - +
226A LYS* 3.0 21.4 + - + +
228A GLU* 3.6 15.0 - - - +
489A VAL* 4.4 16.8 - - + -
490A GLU 3.6 21.3 + - - +
491A LEU* 5.1 4.5 - - + -
492A GLU* 3.7 23.6 + - - +
494A THR* 5.9 1.2 - - - -
495A ASP* 3.0 40.6 + - - +
499A TYR* 5.8 0.9 - - - +
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Residues in contact with LYS 224 (chain A).
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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220A LYS 3.0 13.6 + - - +
221A ARG* 4.0 9.4 - - + +
223A LYS* 1.3 80.6 - - - +
225A ARG* 1.3 63.6 + - + +
226A LYS* 3.3 7.8 + - - +
483A PHE* 5.2 7.3 - - - -
486A VAL* 3.6 41.5 - - + +
489A VAL* 5.3 11.1 - - + +
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Residues in contact with ARG 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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196A GLY* 3.5 29.1 + - - -
197A PHE* 3.9 26.5 - - + -
221A ARG* 3.3 26.5 + - + +
222A ILE 4.3 1.1 - - - +
224A LYS* 1.3 80.8 - - + +
226A LYS* 1.3 69.7 + - - +
227A GLY* 3.2 2.0 + - - -
483A PHE* 5.3 16.6 - - - -
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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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222A ILE 2.8 9.8 + - - -
223A LYS* 3.0 17.8 + - + +
224A LYS 3.1 4.7 - - - +
225A ARG* 1.3 79.8 - - - +
227A GLY* 1.3 55.5 + - - +
228A GLU* 3.1 26.9 + - - +
229A ALA* 4.8 2.9 + - - +
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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