Contacts of the helix formed by residues 254 - 265 (chain A) in PDB entry 3N51
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 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A GLY 3.3 2.2 + - - -
253A ALA* 1.3 83.2 + - - +
255A GLU* 1.3 64.9 + - - +
256A TYR* 3.2 9.2 + - - +
257A ASP* 2.8 51.4 + - - +
258A ILE* 3.2 28.2 + - - +
468A GLY* 3.6 20.0 - - - +
469A VAL* 4.6 1.1 - - - +
471A ASP* 5.8 4.9 - - - +
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Residues in contact with GLU 255 (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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208A MET* 4.3 23.6 - - + +
211A LYS* 2.7 42.1 + - - +
214A THR* 5.0 3.2 + - - +
215A ALA* 4.3 13.5 - - + -
254A ASN* 1.3 74.8 - - - +
256A TYR* 1.3 65.3 + - - +
258A ILE* 3.2 9.4 + - - +
259A LEU* 3.0 44.1 + - + +
468A GLY 4.5 3.2 + - - -
469A VAL* 5.7 1.6 + - - +
471A ASP* 6.0 3.5 - - + +
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Residues in contact with TYR 256 (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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254A ASN* 3.2 8.9 + - - +
255A GLU* 1.3 80.4 + - - +
257A ASP* 1.3 65.0 + - - +
259A LEU* 3.3 12.2 + - + -
260A LYS* 2.9 58.9 + - + +
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Residues in contact with ASP 257 (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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252A GLY* 4.0 5.2 - - - -
253A ALA* 3.7 26.2 + - - +
254A ASN* 2.8 41.7 + - - +
256A TYR* 1.3 82.0 - - - +
258A ILE* 1.3 62.0 + - - +
260A LYS* 3.5 9.6 + - - +
261A LYS* 3.3 28.1 + - - +
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Residues in contact with ILE 258 (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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215A ALA* 3.6 37.7 - - + +
216A TYR* 3.5 34.3 - - + +
250A PHE* 3.6 19.9 - - - +
251A ASN 4.5 6.1 - - - -
252A GLY 3.6 27.4 - - - +
254A ASN* 3.2 23.6 + - - +
255A GLU* 3.7 5.2 - - - +
257A ASP* 1.3 76.2 - - - +
259A LEU* 1.3 57.5 - - - +
261A LYS* 3.0 8.2 + - - +
262A VAL* 3.0 26.0 + - + +
469A VAL* 5.9 4.3 - - + -
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Residues in contact with LEU 259 (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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215A ALA* 3.5 31.0 - - + +
218A ILE* 3.9 19.7 - - + -
223A LEU* 3.8 25.5 - - + +
255A GLU* 3.0 39.7 + - + +
256A TYR* 3.8 13.0 - - + +
258A ILE* 1.3 77.2 - - - +
260A LYS* 1.3 56.1 + - - +
262A VAL* 3.7 5.0 - - + +
263A GLU* 2.9 30.9 + - - +
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Residues in contact with LYS 260 (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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256A TYR* 2.9 47.1 + - + +
257A ASP* 3.7 10.8 - - - +
258A ILE 3.2 0.2 - - - -
259A LEU* 1.3 76.5 - - - +
261A LYS* 1.3 58.0 + - + +
263A GLU* 3.6 10.5 + - - +
264A LYS* 3.2 27.7 + - - +
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Residues in contact with LYS 261 (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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249A PRO 5.5 1.6 - - - +
250A PHE* 3.5 23.2 - - + -
251A ASN* 3.2 31.4 + - - +
252A GLY* 5.4 1.5 - - - -
257A ASP* 3.3 12.5 + - - +
258A ILE 3.0 9.7 + - - +
260A LYS* 1.3 77.1 - - + +
262A VAL* 1.3 58.7 + - - +
264A LYS* 3.4 7.0 + - + +
265A GLY 2.9 23.0 + - - -
266A LYS 4.0 8.2 + - - +
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Residues in contact with VAL 262 (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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215A ALA 3.7 21.5 - - - +
216A TYR 4.5 3.4 - - - +
218A ILE* 3.2 26.5 - - + +
220A PRO* 3.7 31.4 - - + +
223A LEU* 4.1 7.2 - - + -
234A TRP* 4.4 5.6 - - + +
250A PHE* 3.5 32.8 - - + -
258A ILE* 3.0 14.7 + - + +
259A LEU* 3.3 9.4 + - - +
261A LYS* 1.3 77.3 - - - +
263A GLU* 1.3 64.3 + - - +
265A GLY* 2.9 16.5 + - - -
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Residues in contact with GLU 263 (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 PRO* 4.3 5.2 - - - -
223A LEU* 4.2 11.2 - - + -
224A HIS* 2.7 43.3 + - + +
259A LEU 2.9 18.3 + - - +
260A LYS* 3.9 9.6 - - - +
262A VAL* 1.3 78.4 - - - +
264A LYS* 1.3 61.0 + - - +
291A TYR* 2.5 27.9 + - - -
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Residues in contact with LYS 264 (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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260A LYS 3.2 18.6 + - - +
261A LYS* 3.9 7.0 - - + +
263A GLU* 1.3 77.6 + - - +
265A GLY* 1.3 62.5 + - - +
266A LYS* 3.2 37.5 + - + +
291A TYR* 4.2 4.7 - - - -
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Residues in contact with GLY 265 (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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234A TRP* 4.5 5.2 - - - -
250A PHE* 3.6 11.4 - - - -
261A LYS 2.9 11.0 + - - -
262A VAL 2.9 14.5 + - - -
264A LYS* 1.3 75.7 - - - +
266A LYS* 1.3 60.4 + - - +
267A TYR* 3.7 15.6 - - - -
289A LEU 5.1 1.9 - - - +
291A TYR* 3.8 20.1 - - - +
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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